@article {pmid40391192,
year = {2025},
author = {Meng, Z and Li, D and Yang, W and Tang, J},
title = {Metagenomic next-generation sequencing of alveolar lavage fluid improves the detection of pulmonary infection.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20251074},
pmid = {40391192},
issn = {2391-5412},
abstract = {This study evaluated the effectiveness of metagenomic next-generation sequencing (mNGS) in detecting pathogens in patients with pulmonary infections, comparing a low-data-volume, human-depleted quantitative (Q) method and a high-data-volume, non-human-depleted pathogen capture engine (PACE) method. A total of 133 patients were enrolled, comprising 59 in a control group (traditional culture) and 74 in an mNGS group (51 Q and 23 PACE). Bronchoalveolar lavage fluid samples were collected for pathogen detection. Mycobacterium tuberculosis was predominantly detected via general mNGS, whereas Candida albicans and Epstein-Barr virus were more frequently identified by PACE and Q, respectively. Among participants, 22.97% had bacterial mono-infections, and 2.70% had viral mono-infections; the most common co-infection involved bacteria and viruses (25.68%). Patients with fever, abnormal white blood cell, neutrophil percentage, and D-dimer levels exhibited higher detection rates. PACE showed consistently high sensitivity (decreasing from 100 to 92% as thresholds became more stringent) and specificity and accuracy that peaked at 100 and 96%, respectively. The Q method maintained 100% sensitivity at the lowest threshold but showed variable specificity (0.52-0.67) and accuracy (71-75%). These findings highlight the need for caution in clinical applications when using low-data-volume, human-depleted approaches, especially for complex pulmonary infection cases.},
}
@article {pmid40391128,
year = {2025},
author = {Yatera, K and Wang, Z and Shibata, Y and Ishikawa, N and Homma, T and Fukushima, K and Hataji, O and Inoue, Y and Kawabata, H and Miki, K and Sato, K and Tobino, K and Yoshida, M and Ishii, T and Ito, R and Kobayashi, T and Kawamatsu, S and Compton, CH and Jones, PW},
title = {Sputum Microbiome, Potentially Pathogenic Organisms, and Clinical Outcomes in Japanese Patients with COPD and Moderate Airflow Limitation: The Prospective AERIS-J Study.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {20},
number = {},
pages = {1477-1492},
pmid = {40391128},
issn = {1178-2005},
mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Aged ; Female ; Prospective Studies ; Middle Aged ; Japan/epidemiology ; *Microbiota ; Aged, 80 and over ; Adult ; *Lung/microbiology/physiopathology ; Severity of Illness Index ; *Bacteria/pathogenicity/genetics/isolation & purification ; Forced Expiratory Volume ; Disease Progression ; East Asian People ; },
abstract = {BACKGROUND: In Western studies, lung microbiome changes are reported in patients with chronic obstructive pulmonary disease (COPD) and are associated with poorer outcomes, but similar studies in Asian patients or those with less severe COPD are limited.<br><br>METHODS: The Acute Exacerbation and Respiratory InfectionS in COPD Japan (AERIS-J; jRCT1080224632/NCT03957577) was a prospective, non-interventional study to evaluate sputum microbiome diversity at baseline and after 12 months (V2; exploratory analysis), in patients aged 40-80 years with stable COPD (June 2019-June 2022). Baseline sputum potentially pathogenic organisms (PPOs) were identified. Blood cell counts and COPD Assessment Test (CAT) scores were collected at baseline and COPD symptoms measured over 12 months using the Evaluating Respiratory Symptoms in COPD and EXAcerbations of Chronic pulmonary disease Tool, collected by eDiary.<br><br>RESULTS: Patients (N=63) had a mean age of 72.8 years, and percent predicted post-bronchodilator forced expiratory volume in 1 second was 58.3%; 92% were male. Across 62 baseline sputum samples, microbiome composition was similar between 16S rRNA/metagenomic datasets. Patients graded Global Initiative for Chronic Obstructive Lung Disease (GOLD) III versus GOLD I/II had minimal differences in their microbial taxonomic profile and no differences in microbial diversity (Wilcoxon P=0.71). Alpha diversity (Shannon index) positively correlated with blood basophils (rho=0.41; P=0.0019) and negatively correlated with CAT score (rho=0.36; P=0.0069). Alpha diversity and sputum (rho: -0.0637; P=0.7836) or blood (rho: 0.1739; P=0.2043) eosinophils were not correlated. No difference in alpha (P=0.5) or beta (P=0.3) diversity or Operational Taxonomic Unit (Anosim R=-0.024; P=0.892) was observed between PPO-positive or -negative sputum.<br><br>CONCLUSION: A less diverse microbiome correlated with poorer health status and lower blood basophils in patients with COPD and moderate airflow limitation. There was no relationship between PPO presence and microbiome diversity.},
}
@article {pmid40391085,
year = {2025},
author = {Fletcher, SJ and Lawrence, J and Sawyer, A and Manzie, N and Gardiner, DM and Mitter, N and Brosnan, CA},
title = {dsRNAmax: a multi-target chimeric dsRNA designer for safe and effective crop protection.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf064},
pmid = {40391085},
issn = {2631-9268},
mesh = {*RNA, Double-Stranded/genetics ; RNA Interference ; Animals ; *Software ; *Crop Protection/methods ; *Crops, Agricultural/genetics/parasitology ; },
abstract = {Crop protection is undergoing significant evolution, transitioning towards sustainable approaches that minimize impacts on the environment and human health. Exogenous application of double-stranded RNA (dsRNA) that silences pest or pathogen genes via RNA interference (RNAi) has promise as a safe and effective next-generation crop protection platform without the need for genetic modification. However, exogenous dsRNA application at scale presents challenges. Specifically, a single dsRNA sequence needs to balance targeting the standing variation in a target pest or pathogen group against the potential for adverse impacts in a vast array of non-target and beneficial organisms at the application site and broader environment. To address these competing demands, we present dsRNAmax (https://github.com/sfletc/dsRNAmax), a software package that employs k-mer-based assembly of chimeric dsRNA sequences to target multiple related RNA sequences, to broaden the target spectrum. The package ensures that designed dsRNAs have no defined contiguous sequence homology with any off-target sequences, which can range from single transcriptomes through to metagenome sequence data and beyond. The efficacy of this package is demonstrated by a dsRNAmax-designed dsRNA that inhibits multiple root-knot nematode species but not a non-target nematode species, despite its susceptibility to environmental RNAi and high homology of the target gene.},
}
@article {pmid40390443,
year = {2025},
author = {Xu, M and Gao, P and Chen, HQ and Gao, Y and Xiong, SJ and Wang, XH},
title = {[Effects of Typical Microplastics on Methanogenesis and Antibiotic Resistance Genes in Anaerobic Digestion of Sludge].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {5},
pages = {3189-3199},
doi = {10.13227/j.hjkx.202405273},
pmid = {40390443},
issn = {0250-3301},
mesh = {*Sewage/microbiology/chemistry ; *Methane/metabolism/biosynthesis ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; *Microplastics ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Bacteria/genetics ; },
abstract = {Waste sludge is an important carrier of antibiotic resistance genes （ARGs） and an important place for the enrichment of microplastics （MPs）. To explore the impacts of typical MPs on sludge recycling and harmless disposal, the effects of polyamide （PA）, polyethylene （PE）, and polypropylene （PP） MPs on the methanogenesis efficiency of anaerobic digestion were investigated. Meanwhile, based on metagenomic sequencing, the effects of MPs on ARGs, mobile genetic elements （MGEs）, microbial community structure, and host bacteria during anaerobic digestion were analyzed. The results showed that PA-MPs, PE-MPs, and PP-MPs increased the distribution of methane production by 2.2%, 22.3%, and 28.8%, respectively. MPs promoted methanation by improving the dissolution and hydrolysis efficiency of organic matter, and the enrichment of hydrogenotrophic methanogens by PP-MPs further improved the methanogenic efficiency. PA-MPs contributed to the removal of ARGs, while PE-MPs and PP-MPs had adverse effects on the reduction of ARGs. Horizontal gene transfer mediated by integron and insertion sequences was an important factor in the spread of ARGs. Proteobacteria was the key host leading to the diffusion of ARGs. The removal of pathogens from Bacteroidetes by anaerobic digestion contributed to the reduction of ARGs. The selective enrichment or inhibition of Arenimonas, Acinetobacter, Actinobacillus, Nitrospira, and other important host bacteria by MPs was the major cause for the difference in the removal effect of ARGs.},
}
@article {pmid40390350,
year = {2025},
author = {Liu, Y and Wang, J and Pu, Y and Tang, S},
title = {Rapid diagnosis of disseminated Mycobacterium avium complex infection mimicking metastatic malignancy using metagenomic next-generation sequencing.},
journal = {The National medical journal of India},
volume = {38},
number = {1},
pages = {16-17},
doi = {10.25259/NMJI_872_2022},
pmid = {40390350},
issn = {2583-150X},
mesh = {Humans ; Diagnosis, Differential ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Mycobacterium avium Complex/genetics/isolation &amp; purification ; *Mycobacterium avium-intracellulare Infection/diagnosis ; Neoplasm Metastasis/diagnosis ; },
abstract = {Disseminated non-tuberculous mycobacteria (NTM) disease, which is mainly found in immunocompromised individuals, is a rare and severe infection whose diagnosis poses a challenge to clinicians. We present a patient with disseminated NTM infection mistaken for metastatic malignancy in an otherwise healthy patient and the tortuous diagnostic process. Metagenomic next-generation sequencing (mNGS) played a critical role in the diagnosis. Further screening for anti-interferon-γ antibodies revealed that the patient had a potential immunodeficiency.},
}
@article {pmid40390177,
year = {2025},
author = {Ren, Z and Wang, M and Yu, J and Zhang, L and Lin, Z and Li, X and Zhang, Y},
title = {Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70110},
doi = {10.1111/1462-2920.70110},
pmid = {40390177},
issn = {1462-2920},
support = {42301132//National Natural Science Foundation of China/ ; NKL2023-QN02//Key Laboratory of Lake and Watershed Science for Water Security/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation &amp; purification ; *Lakes/microbiology ; Phylogeny ; Biodiversity ; Tibet ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai-Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon index) generally decreased with depth. Euryarchaeota was the most abundant phylum, though its relative abundance declined with depth, while Thaumarchaeota increased. At the order level, Methanosarcinales and Nitrosopumilales showed increased relative abundance with depth, indicating adaptation to deeper anoxic layers, whereas Methanomicrobiales and Methanotrichales decreased. Beta diversity increased with depth, shifting from stochastic to deterministic processes. Network topology revealed reduced species connectivity but heightened modularity at depth, signalling niche specialisation. Functionally, genes associated with the initial steps of methane metabolism (Fwd, Mtd, Mer) increased with depth, while those involved in later steps (Mtr, Mcr) decreased, suggesting reduced energy conservation efficiency and lower overall methanogenesis rates in deeper sediments. These findings highlight the significant impact of vertical stratification on archaeal community structure, interaction networks, and functional capabilities.},
}
@article {pmid40390150,
year = {2025},
author = {Cunningham-Oakes, E and Perez-Sepulveda, BM and Li, Y and Hinton, JCD and Nelson, CA and McIntyre, KM and Wardeh, M and Haldenby, S and Gregory, R and Iturriza-Gómara, M and Hertz-Fowler, C and O'Brien, SJ and Cunliffe, NA and Darby, AC and , },
title = {Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {55},
pmid = {40390150},
issn = {1756-994X},
support = {WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; NIHR203756//NIHR Senior Investigator Award/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Diarrhea/diagnosis/microbiology/virology ; Feces/microbiology/virology ; *Transcriptome ; Metagenome ; Gene Expression Profiling ; Female ; Male ; },
abstract = {BACKGROUND: Current surveillance of diarrhoeal disease is hindered by limitations of traditional diagnostic approaches, which often fail to identify the causative organism, particularly for novel or hard-to-culture bacterial pathogens. Sequencing nucleic acids directly from stool can overcome such constraints, but such approaches need to reliably detect pathogens identifiable by conventional methods.<br><br>METHODS: As part of the INTEGRATE study, we analysed stool microbiomes from 1067 patients with gastroenteritis symptoms using direct sequencing, and compared findings with standard diagnostic techniques (culture, immunoassay, microscopy, and single-target PCR) and molecular assays (Luminex xTAG GPP) for detection of bacterial and viral pathogens in the UK.<br><br>RESULTS: We found strong positive correlations between metatranscriptomic reads and traditional diagnostics for six out of 15 pathogens. The metatranscriptomic data were highly correlated with the Luminex assay for eight out of 14 pathogens. In contrast, metagenomic sequencing only showed a strong positive correlation with traditional diagnostics for three of 15 pathogens, and with Luminex for four of 14 pathogens. Compared with metagenomics, metatranscriptomics had increased sensitivity of detection for four pathogens, while metagenomics was more effective for detecting five pathogens. Metatranscriptomics gave near-complete transcriptome coverage for Human mastadenovirus F and detected Cryptosporidium via identification of Cryptosporidium parvum virus (CSpV1). A comprehensive transcriptomic profile of Salmonella enterica serovar Enteritidis was recovered from the stool of a patient with a laboratory-confirmed Salmonella infection. Furthermore, comparison of RNA/DNA ratios between pathogen-positive and pathogen-negative samples demonstrated that metatranscriptomics can distinguish pathogen-positive/negative samples and provide insights into pathogen biology. Higher RNA/DNA ratios were observed in samples that tested positive via gold-standard diagnostics.<br><br>CONCLUSIONS: This study highlights the power of directly sequencing nucleic acids from human samples to augment gastrointestinal pathogen surveillance and clinical diagnostics. Metatranscriptomics was most effective for identifying a wide range of pathogens and showed superior sensitivity. We propose that metatranscriptomics should be considered for future diagnosis and surveillance of gastrointestinal pathogens. We assembled a rich data resource of paired metagenomic and metatranscriptomic datasets, direct from patient stool samples, and have made these data publicly available to enhance the understanding of pathogens associated with infectious intestinal diseases.},
}
@article {pmid40390128,
year = {2025},
author = {Liao, H and Wen, C and Huang, D and Liu, C and Gao, T and Du, Q and Yang, QE and Jin, L and Ju, F and Yuan, MM and Tang, X and Yu, P and Zhou, S and Alvarez, PJ and Friman, VP},
title = {Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {127},
pmid = {40390128},
issn = {2049-2618},
support = {42277357//National Natural Science Foundation of China/ ; },
mesh = {*Streptomyces/virology/genetics/drug effects ; *Soil Microbiology ; *Bacteriophages/physiology/genetics ; Metagenomics/methods ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; China ; *Drug Resistance, Bacterial/genetics ; Sewage/virology ; },
abstract = {BACKGROUND: Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.<br><br>RESULTS: Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.<br><br>CONCLUSION: Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.},
}
@article {pmid40390074,
year = {2025},
author = {Kazmi, FA and Mander, &#xdc; and Khanongnuch, R and Öpik, M and Ranniku, R and Soosaar, K and Masta, M and Tenhovirta, SAM and Kasak, K and Ah-Peng, C and Espenberg, M},
title = {Distinct microbial communities drive methane cycling in below- and above-ground compartments of tropical cloud forests growing on peat.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {54},
pmid = {40390074},
issn = {2524-6372},
support = {101096403/ERC_/European Research Council/International ; 101079192//HORIZON EUROPE European Research Council/ ; PRG2032//Eesti Teadusagentuur/ ; PRG1789//Eesti Teadusagentuur/ ; PSG714//Eesti Teadusagentuur/ ; TK232//Estonian Ministry of Education and Research/ ; },
abstract = {Cloud forests are unique yet understudied ecosystems regarding CH4 exchange despite their significance in carbon storage. We investigated CH4 fluxes in peat soil and tree stems of two tropical cloud forests on Réunion Island, one featuring Erica reunionensis and the second a mix of E. reunionensis and Alsophila glaucifolia. The study examined microbiomes across below-ground (soil) and above-ground (canopy soil, leaves, and stems) forest compartments. Metagenomics and qPCR analyses targeted key genes in methanogenesis and methanotrophy in soil and above-ground samples, alongside soil physicochemical measurements. CH4 fluxes from peat soil and tree stems were measured using gas chromatography and portable trace gas analyzers. Peat soil in both forests acted as a CH4 sink (- 23.8 ± 4.84 µg C m[- 2] h[- 1]) and CO2 source (55.5 ± 5.51 µg C m[- 2] h[- 1]), with higher CH4 uptake in sites dominated by endemic tree species E. reunionensis. In forest soils, a high abundance of n-DAMO 16 S rRNA gene (3.42 × 10[7] ± 7 × 10[6] copies/g dw) was associated with nitrate levels and higher rates of CH4 uptake and CO2 emissions. NC-10 bacteria (0.1-0.3%) were detected in only the Erica forest soil, verrucomicrobial methanotrophs (0.1-3.1%) only in the mixed forest soil, whereas alphaproteobacterial methanotrophs (0.1-3.3%) were present in all soils. Tree stems in both forests were weak sinks of CH4 (-0.94 ± 0.4 µg C m[- 2] h[- 1]). The canopy soil hosted verrucomicrobial methanotrophs (0.1-0.3%). The leaves in both forests exhibited metabolic potential for CH4 production, e.g., exhibiting high mcrA copy numbers (3.5 × 10[5] ± 2.3 × 10[5] copies/g dw). However, no CH4-cycling functional genes were detected in the stem core samples. Tropical cloud forest peat soils showed high anaerobic methanotrophy via the n-DAMO process, while aerobic methanotrophs were abundant in canopy soils. Leaves hosted methanotrophs but predominantly methanogens. These results highlight the significant differences between canopy and soil microbiomes in the CH4 cycle, emphasizing the importance of above-ground microbiomes in forest CH4 gas budgets.},
}
@article {pmid40390033,
year = {2025},
author = {Teng, T and Huang, F and Xu, M and Li, X and Zhang, L and Yin, B and Cai, Y and Chen, F and Zhang, L and Zhang, J and Geng, A and Chen, C and Yu, X and Sui, J and Zhu, ZJ and Guo, K and Zhang, C and Zhou, X},
title = {Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {128},
pmid = {40390033},
issn = {2049-2618},
support = {82301714//the National Natural Science Foundation of China/ ; 22425404//the National Natural Science Foundation of China/ ; 82271565//the National Natural Science Foundation of China/ ; 2023TQ0398//the China Postdoctoral Science Foundation/ ; CSTB2023NSCQ-BHX0106//Natural Science Foundation of Chongqing, China/ ; 2208013341918508//Postdoctoral Innovation Talents Support Program of Chongqing, China/ ; 2022YFC3400702//National Key R&amp;D Program of China/ ; 2024YFC2707800//National Key R&amp;D Program of China/ ; 2022ZD0212900//STI2030-Major Projects/ ; },
mesh = {Humans ; Adolescent ; Child ; *Gastrointestinal Microbiome/physiology ; Male ; *Depressive Disorder, Major/microbiology/metabolism ; Female ; *Amino Acids/deficiency/blood/metabolism ; Magnetic Resonance Imaging ; Animals ; Rats ; Brain/diagnostic imaging/metabolism ; Feces/microbiology ; Metagenomics/methods ; Metabolomics/methods ; *Depression/microbiology ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.<br><br>RESULTS: We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value&#x2009;<&#x2009;0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value&#x2009;=&#x2009;0.001, M[2]&#x2009;=&#x2009;0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.<br><br>CONCLUSIONS: Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.},
}
@article {pmid40389724,
year = {2025},
author = {Yang, M and Qi, Y and Gao, P and Li, L and Guo, J and Zhao, Y and Liu, J and Chen, Z and Yu, L},
title = {Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {766},
pmid = {40389724},
issn = {2399-3642},
support = {202449CE340009, 202201AU070043, 202101BA070001-174//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 202501AU070008//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 2025J0753//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; 2023J0827//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; },
mesh = {*Endophytes/physiology ; *Plant Diseases/microbiology ; *Amorphophallus/microbiology ; *Microbiota ; *Disease Resistance ; *Adaptation, Physiological ; Stress, Physiological ; *Bacteria ; },
abstract = {Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.},
}
@article {pmid40389632,
year = {2025},
author = {Doyle, B and Reynolds, GZM and Dvorak, M and Maghini, DG and Natarajan, A and Bhatt, AS},
title = {Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40389632},
issn = {1750-2799},
support = {R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32GM007276//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; D43TW010540//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Measurements of prokaryotic absolute abundance can provide important insights into human gut microbiome biology and correct misinterpretations of relative abundance data. Despite the existence of several relatively well-established methods for making these measurements, most microbiome studies do not report absolute abundance. To enable researchers equipped with standard molecular biology capabilities to incorporate absolute quantification into their microbiome studies, we present a detailed, step-by-step protocol for rigorous and reproducible quantification of prokaryotic concentration in stool samples. We include methods for measuring stool sample moisture content, quantifying the concentration of the 16S rRNA prokaryotic marker gene by qPCR or digital droplet PCR (ddPCR) and analyzing the resulting data. We also highlight and provide strategies to overcome common pitfalls of the quantification method, such as 16S rRNA gene contamination. The final output of this approach is 16S rRNA copies per wet or dry gram of stool. In cases where samples have matched metagenomic sequencing information, data can be converted into absolute concentration of prokaryotes and taxon-specific absolute concentrations. To enable researchers to choose the appropriate method for their specific applications, we also compare and contrast our qPCR and ddPCR methods. In 4 days, ~80 samples can be taken from frozen stool to absolute concentration by using qPCR or ddPCR without the need for resequencing. Overall, this protocol provides a sensitive and straightforward way to measure the absolute concentration of prokaryotes in human gut microbiome samples stored with or without preservative.},
}
@article {pmid40389466,
year = {2025},
author = {Salehi, M and Laitinen, V and Bhanushali, S and Bengtsson-Palme, J and Collignon, P and Beggs, JJ and Pärnänen, K and Lahti, L},
title = {Gender differences in global antimicrobial resistance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {79},
pmid = {40389466},
issn = {2055-5008},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 330887//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 348439//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 20220114//Alhopuro Foundation/ ; 20220114//Alhopuro Foundation/ ; 2019-00299//Swedish Research Council/ ; FFL21-0174//Swedish Foundation for Strategic Research/ ; KAW 2020.0239//Data-Driven Life Science/ ; },
mesh = {Humans ; Female ; Male ; Sex Factors ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; Adult ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Global Health ; Middle Aged ; },
abstract = {Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.},
}
@article {pmid40389207,
year = {2025},
author = {Echeveste Medrano, MJ and Lee, S and de Graaf, R and Holohan, BC and Sánchez-Andrea, I and Jetten, MSM and Welte, CU},
title = {Physiological Stress Response to Sulfide Exposure of Freshwater Anaerobic Methanotrophic Archaea.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12489},
pmid = {40389207},
issn = {1520-5851},
abstract = {Freshwater wetlands and coastal sediments are becoming hotspots for the emission of the greenhouse gas methane. Eutrophication-induced deposition of organic matter leads to elevated methanogenesis and sulfate reduction, thereby increasing the concentrations of methane and toxic sulfide, respectively. However, the effects of sulfide stress on the anaerobic methanotrophic biofilter have not been well explored. Here, we show how an enrichment culture dominated by the freshwater anaerobic methane-oxidizing archaeon "Candidatus (Ca.) Methanoperedens" responds to short-term and long-term exposure to sulfide in a bioreactor. The methane-oxidizing activity decreased to 45% and 20% but partially recovered to 70% and 30% within 5 days after short- and long-term sulfide exposure, respectively. Metagenomics indicated that "Ca. Methanoperedens" remained dominant in the enrichment throughout the entire experiment. The first short-term sulfide pulse led to increased expression of genes encoding for sulfide detoxification by low abundant community members, whereas long-term exposure resulted in upregulation of "Ca. Methanoperedens" genes encoding sulfite reductases of group III (Dsr-LP). "Ca. Methanoperedens" consumed polyhydroxyalkanoates during long-term sulfide exposure, possibly to aid in stress adaptation. Together, these results provide a valuable baseline for understanding fundamental ecophysiological adaptations to methane cycling in sulfate- and nitrate-rich aquatic ecosystems.},
}
@article {pmid40389018,
year = {2025},
author = {Leekitcharoenphon, P and Bortolaia, V and Tornblom, VKW and Siriphap, A and Suthienkul, O and Borthong, J and Chonsin, K and Møller, FD and Avot, B and Otani, S and Aarestrup, FM},
title = {Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105765},
doi = {10.1016/j.meegid.2025.105765},
pmid = {40389018},
issn = {1567-7257},
abstract = {Antimicrobial resistance (AMR) is on one of the global priority challenges. This study explored the impact of diet alteration on AMR bacteria through metagenomic analysis during the annual vegetarian festival in Thailand in October 2019. The study investigated the effects of a 10-day shift from a regular to a vegetarian diet by collecting urban sewage from Nakhon Sawan, Surat Thani, and Bangkok before, during, and after the festival. Additionally, faecal samples from individuals in the northern city were analyzed. Using shotgun metagenomic sequencing, the samples were mapped against bacterial, AMR genes, and carbohydrate-active enzymes databases. The results revealed significant changes in AMR gene abundance and increased carbohydrate metabolism genes in sewage samples from all three cities during the festival. There was also a notable shift in the composition and diversity of bacterial species, particularly in the northern city. The total abundance of AMR genes increased during the vegetarian festival across all locations. This study highlights the correlation between a population's vegetarian diet and increased AMR in Thailand. It also demonstrates that metagenomic analysis of sewage can effectively assess the impact of dietary changes on bacterial communities and AMR at a population level, providing valuable insights for public health strategies.},
}
@article {pmid40388929,
year = {2025},
author = {Dong, X and Xie, C and Zhang, Z and Ye, H and Liu, R and Chen, W and Kong, YZ and Yang, X},
title = {Diagnostic challenges in peritoneal dialysis-associated peritonitis with atypical and rare pathogens: A new era of metagenomic next-generation sequencing precision diagnosis.},
journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis},
volume = {},
number = {},
pages = {8968608251333879},
doi = {10.1177/08968608251333879},
pmid = {40388929},
issn = {1718-4304},
abstract = {Peritonitis caused by atypical and rare pathogens is challenging to diagnose. Although the International Society for Peritoneal Dialysis (ISPD) guidelines significantly improve the diagnostic rate by placing peritoneal dialysis fluid into blood culture bottles, peritonitis caused by atypical pathogens, such as tuberculosis and fungi, is difficult to diagnose due to challenges in culturing these organisms using traditional methods, leading to high mortality. Metagenomic next-generation sequencing (mNGS) technology has been widely used as an accurate diagnostic technique for infectious diseases. First used in identifying and quantifying environmental micro-organisms, mNGS technology can identify rare, novel, difficult-to-detect and mixed pathogens directly from clinical samples, and has potential in predicting antibiotic resistance. This paper summarizes the application of mNGS in atypical and rare pathogens peritonitis clinical cases in recent years, and provides reference for the diagnosis of peritonitis in combination with new ISPD guidelines and diagnostic techniques. The development and principles of mNGS technology, diagnostic efficiency in peritonitis, challenges in diagnosis of atypical and rare pathogen-associated peritonitis, and application of mNGS technology are discussed in detail. The development of mNGS technology provides clinicians with powerful tools to more accurately identify and treat peritonitis. Future research needs to focus on reducing costs, improving test accessibility, and developing new bioinformatics tools to better integrate mNGS results into clinical practice.},
}
@article {pmid40388761,
year = {2025},
author = {Liu, Q and Li, Q and Liu, B and Fu, T},
title = {Pulmonary nocardiosis with hilar mass misdiagnosed as lung cancer: A case report.},
journal = {Medicine},
volume = {104},
number = {20},
pages = {e42524},
doi = {10.1097/MD.0000000000042524},
pmid = {40388761},
issn = {1536-5964},
mesh = {Humans ; Female ; *Nocardia Infections/diagnosis/drug therapy/diagnostic imaging ; Middle Aged ; *Diagnostic Errors ; *Lung Neoplasms/diagnosis ; Tomography, X-Ray Computed/methods ; Diagnosis, Differential ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Nocardia/isolation &amp; purification ; Lung/diagnostic imaging/pathology ; *Lung Diseases/diagnosis ; },
abstract = {RATIONALE: Pulmonary nocardiosis (PN) is an opportunistic infectious disease caused by Nocardia of the lungs, which lacks specificity in clinical symptoms and imaging, is rare in individuals with normal immune function, and is highly prone to clinical misdiagnosis and missed diagnosis.<br><br>PATIENT CONCERNS: A 55-year-old woman with normal immune function was admitted to the hospital due to a cough and expectoration for more than 20 days.<br><br>DIAGNOSES: Chest computed tomography revealed a mass in the left hilum and obstructive atelectasis in the lingular segment of the left upper lobe. Initially suspected to be a malignant tumor, bronchoscopy with pathological examination suggested inflammation. Finally, metagenomic next-generation sequencing of pathological tissue confirmed PN.<br><br>INTERVENTIONS: After discharge, the patient regularly took trimethoprim-sulfamethoxazole for anti-infective treatment.<br><br>OUTCOMES: Regular follow-ups with the patient revealed that subsequent chest computed tomography scans showed a gradual reduction in the extent of the lesions, and the patient demonstrated a good clinical response and radiological improvement.<br><br>LESSONS: This case highlights the diagnostic complexity of PN. The radiological manifestations are diverse, commonly including pulmonary consolidation, nodules, and cavities, making it difficult to differentiate from other diseases. Clinicians need to be vigilant and find appropriate testing methods to improve the diagnostic rate of PN.},
}
@article {pmid40388614,
year = {2025},
author = {Peek, J and Bhattacharjee, A and Burian, J and Hsieh, DC and Hernandez, Y and Ternei, M and Panfil, C and Brady, SF},
title = {Environmental resistome-guided development of resistance-tolerant antibiotics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {21},
pages = {e2504781122},
doi = {10.1073/pnas.2504781122},
pmid = {40388614},
issn = {1091-6490},
support = {5R35GM122559//HHS | NIH (NIH)/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Metagenome ; Bacteria/drug effects/genetics ; },
abstract = {Failure to anticipate new forms of antibiotic resistance has led to resistance developing rapidly to virtually all antibiotics that have entered clinical use. Many of the most problematic types of resistance originated in the environment, where ancient arms races between antibiotic-producing microbes and their competitors have created vast arsenals of antibiotics and resistance. Seizing on the knowledge that resistance in nature is frequently a harbinger of future clinical resistance, we propose introducing an additional step into the antibiotic development process that exploits the susceptibility of development candidates to environmental resistance as a metric for prioritizing lead compounds and as a roadmap for their structural optimization. Using the antibiotic albicidin as a model, we show how the environmental resistome can guide the development of more resistance-tolerant leads. We used metagenomic surveys to identify resistance vulnerabilities for albicidin and guide the synthesis of analogs that evade the resistance threats. We found that natural albicidin analogs (congeners) were especially enriched in structural features that escape resistance, which inspired our syntheses and provided compelling evidence for the evolution of families of antibiotics in response to resistance in nature. The coupling of metagenomics-based resistance surveillance with structural optimizations of new antibiotics is a broadly applicable approach that is easily integrated into antibiotic development programs to generate compounds that are more resilient in the face of resistance.},
}
@article {pmid40388589,
year = {2025},
author = {Lei, Z and Wang, H and Zhang, H and Liu, W and He, Z and Wang, Z and Zhang, H and Wang, Y and Tang, Y and Hu, C and Zhao, X},
title = {Sultr1;2-Mediated Recruitment of Selenium-Oxidizing Bacteria Promotes Plant Selenium Uptake.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c01540},
pmid = {40388589},
issn = {1520-5118},
abstract = {Plants can shape their root microbiome to promote growth and selenium uptake. Here, we used metagenomics, 16S high-throughput sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics assays to investigate the role of Sultr1;2, which is the major selenium transporter gene, in recruiting microbial communities to regulate soil selenium bioavailability and plant selenium uptake. Results shows that the overexpression of Sultr1;2 in tomato significantly enriched Methylobacterium genus. The isolated strains of Methylobacterium possess multiple plant-growth-promoting functions and selenium oxidation capability and inoculation with these strains increases soil selenium availability. The upregulated metabolites of Sultr1;2-overexpressing tomato were significantly enriched in the arginine and proline metabolism pathway. The key upregulated metabolites significantly improved the growth rate and selenium-oxidizing ability of Methylobacterium strains, and the combined addition of key upregulated metabolites and synthetic microbial community significantly increased soil selenium bioavailability and plant selenium uptake. This study provides insights into leveraging plant genetic engineering to identify key functional microbial communities for sustainable selenium-rich agricultural development.},
}
@article {pmid40388544,
year = {2025},
author = {Kohnert, E and Kreutz, C},
title = {Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321452},
doi = {10.1371/journal.pone.0321452},
pmid = {40388544},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Benchmarking ; Computer Simulation ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; },
abstract = {Differential abundance (DA) analysis of metagenomic microbiome data is essential for understanding microbial community dynamics across various environments and hosts. Identifying microorganisms that differ significantly in abundance between conditions (e.g., health vs. disease) is crucial for insights into environmental adaptations, disease development, and host health. However, the statistical interpretation of microbiome data is challenged by inherent sparsity and compositional nature, necessitating tailored DA methods. This benchmarking study aims to simulate synthetic 16S microbiome data using metaSPARSim (Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B. MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. Available from: https://doi.org/10.1101/2023.03.23.533996), and sparseDOSSA2 (Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, et al. A statistical model for describing and simulating microbial community profiles. PLOS Comput Biol. 2021;17(9):e1008913. https://doi.org/10.1371/journal.pcbi.1008913 PMID: 34516542) , leveraging 38 real-world experimental templates (S3 Table) previously utilized in a benchmark study comparing DA tools. These datasets, drawn from diverse environments such as human gut, soil, and marine habitats, serve as the foundation for our simulation efforts. We employ the same 14 DA tests that were previously used with the same experimental data in benchmark studies alongside 8 DA tests that were developed subsequently. Initially, we will generate synthetic data closely mirroring the experimental datasets, incorporating a known truth to cover a broad range of real-world data characteristics. This approach allows us to assess the ability of DA methods to recover known true differential abundances. We will further simulate datasets by altering sparsity, effect size, and sample size, thus creating a comprehensive collection for applying the 22 DA tests. The outcomes, focusing on sensitivities and specificities, will provide insights into the performance of DA tests and their dependencies on sparsity, effect size, and sample size. Additionally, we will calculate data characteristics (S1 and S2 Table) for each simulated dataset and use a multiple regression to identify informative data characteristics influencing test performance. Our prior study, where we used simulated data without incorporating a known truth, demonstrated the feasibility of using synthetic data to validate experimental findings. This current study aims to enhance our understanding by systematically evaluating the impact of known truth incorporation on DA test performance, thereby providing further information for the selection and application of DA methods in microbiome research.},
}
@article {pmid40388308,
year = {2025},
author = {Wang, S and Kong, F and Dai, D and Li, C and Hao, Y and Wang, E and Cao, Z and Wang, Y and Wang, W and Li, S},
title = {Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf042},
pmid = {40388308},
issn = {2047-217X},
support = {2022YFD1301400//National Key Research and Development Program/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Female ; *Peripartum Period/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Pregnancy ; },
abstract = {BACKGROUND: Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.<br><br>RESULTS: In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.<br><br>CONCLUSIONS: Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.},
}
@article {pmid40387602,
year = {2025},
author = {Bonacolta, AM and Krause-Massaguer, J and Unuma, T and Del Campo, J},
title = {The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e70013},
doi = {10.1111/jeu.70013},
pmid = {40387602},
issn = {1550-7408},
support = {//University of Miami/ ; PID2020-118836GA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021 SGR 00420//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
mesh = {Animals ; Phylogeny ; *Sea Cucumbers/parasitology ; *Apicomplexa/genetics/classification/isolation &amp; purification ; Host Specificity ; Female ; Host-Parasite Interactions ; Genome, Mitochondrial ; },
abstract = {Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.},
}
@article {pmid40387408,
year = {2025},
author = {Rahimlou, S and Amend, AS and James, TY},
title = {Malassezia in environmental studies is derived from human inputs.},
journal = {mBio},
volume = {},
number = {},
pages = {e0114225},
doi = {10.1128/mbio.01142-25},
pmid = {40387408},
issn = {2150-7511},
abstract = {UNLABELLED: The fungus Malassezia is the most prevalent member of the human skin mycobiota, known for its lipid dependence and inability to synthesize long-chain fatty acids. Malassezia exhibits remarkable niche breadth, inhabiting soils, dust, as well as various marine environments from polar regions to deep-sea vents. The consistent presence of Malassezia in marine habitats, including those associated with marine animals, suggests that the fungus is able to grow and play a fundamental role in marine ecosystems. In this study, we explored metagenomic sequences from the Sequence Read Archive database to investigate the presence, distribution, and origins of Malassezia species within marine ecosystems, with the goal of assembling Malassezia genomes. Using various search methods, we found that up to 10% of the shotgun and amplicon data sets analyzed contained Malassezia sequences. However, the relative abundance of Malassezia in each data set was low, and there was a strong correlation between human and Malassezia sequences in marine environments, consistent with contamination. From the most Malassezia-rich data sets, we attempted to generate metagenome-assembled genomes. However, Malassezia contigs together showed low genome completeness levels, with a maximum of 2.2% in a sample. Phylogenetic analysis identified the contigs as closely related to human-associated Malassezia globosa and Malassezia restricta, along with Malassezia sympodialis and Malassezia pachydermatis, which were the most prevalent species across all studied environments. Our data suggest that many observations of Malassezia in the environment are derived from human sources and that widespread contamination confounds the exploration of Malassezia diversity and ecological role in the marine environment.<br><br>IMPORTANCE: Malassezia is the singular fungus most associated with humans. It colonizes mammalian skin and requires host-derived fatty acids to grow. Widespread sequencing of environmental DNA surprisingly showed that Malassezia is also ubiquitous outside of mammalian hosts. Malassezia is frequently found in marine habitats where it is associated with corals, deep sea vents, diatoms, and more. Given its widespread presence, we reasoned that public metagenomic data could be used to assemble a genome sequence of an uncultured marine Malassezia. However, we found that Malassezia was ubiquitous but never abundant in marine samples and that the few metagenomes we could assemble were consistent with recent human introduction. We also found that the presence of human DNA in sequencing data sets is strongly correlated with the presence of Malassezia DNA, and while not ruling out the growth and survival of Malassezia in marine habitats, they suggest widespread contamination of public data with Malassezia.},
}
@article {pmid40387372,
year = {2025},
author = {Lei, Z and Zhang, H and Liu, W and Sheng, J and Zhang, H and Wang, Y and Tang, Y and Wang, H and Ding, C and Qiao, W and Zhu, Y and Yang, G and Zhang, Y and Liu, Z and Zhou, N and Hu, C and Zhao, X},
title = {Dynamic and Stable Core Microbiota Assist Plants in Enriching Selenium and Reducing Cadmium Absorption.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e00862},
doi = {10.1002/advs.202500862},
pmid = {40387372},
issn = {2198-3844},
support = {2023YFD1900904//National Key Research and Development Program of China/ ; SKLEG2024225//State Key Laboratory of Environmental Geochemical/ ; 23567601H//State Key Laboratory of North China Crop Improvement and Regulation, S&amp;T Program of Hebei/ ; 24XJTRZW13//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; WY22B04//Wuhan Municipal Health Commission/ ; Grants KJ2025-5//2025 Science and Technology Project of Hubei Geological Bureau/ ; Grants 2023AFD215//Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China/ ; D20234501//Science and Technology Research Project of Hubei Province/ ; 23xjz05R//Hubei Polytechnic University/ ; },
abstract = {Rhizosphere microbiome is crucial for regulating rhizosphere complex nutrient dynamics. However, mechanisms by which plants regulate rhizosphere microbes to manage nutrient availability under coexisting beneficial and harmful elements remain unclear. This study focuses on the rhizosphere microbiome of Brassica napus in different naturally selenium (Se)-cadmium (Cd)-rich soils, the functionality of this rhizosphere, and the changes in the availability of rhizosphere nutrients. Microbiome analysis, metagenomics, genomic analysis, strain isolation, and functional validation are performed to investigate these relationships. Results show that a significant negative correlation is observed between the rhizosphere available Se and Cd content across the plant whole growth cycle and identified a group of core microbiota that are highly positively correlated with available Se and negatively correlated with available Cd. Genomics and metagenomics analyses reveal that the core microbiota has a higher substrate preference for amino acids related to the glutathione metabolic pathway. Key glutathione-related-amino acids and synthetic microbial community significantly improve the expression of glutathione anabolism and related amino acid transport genes and enhance Se uptake and reduce Cd absorption in plants grown in various Se-Cd-rich soils. This study provides insights into the mechanisms of root-associated microbes responding to complex soil nutrients during plant growth.},
}
@article {pmid40387216,
year = {2025},
author = {Steriade, C and Thomas, SC and Xu, F and Ahituv, A and Hanin, A and Pleshkevich, M and Hwang, S and Ramirez, A and Foreman, B and Yoo, J and Eka, O and Kellogg, M and Oliger, A and Wainwright, MS and Morales, M and Gaspard, N and Hirsch, LJ and Devinsky, O and Saxena, D},
title = {Patients with status epilepticus and new-onset refractory status epilepticus display drastically altered fecal microbiomes compared to chronic epilepsy patients.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18450},
pmid = {40387216},
issn = {1528-1167},
support = {//NORSE Institute, the Daniel Raymond Wong Memorial Research Fund and CCEMRC/ ; //Parekh Center for Interdiscplinary Neurology/ ; //National Organization for Rare Disorders and American Epilepsy Society/ ; },
abstract = {OBJECTIVE: New-onset refractory status epilepticus (NORSE) occurs in people without pre-existing epilepsy or a rapidly identified structural, toxic, metabolic, or other cause. NORSE is a rare disorder with high morbidity and mortality rates and limited evidence for effective therapies. We aimed to assess whether the gut microbiome of NORSE and status epilepticus (SE) differs from that of chronic epilepsy, whether NORSE differs from SE at different disease time points, and to examine the correlations between specific gut microbiota and cytokines in NORSE and SE.<br><br>METHODS: This longitudinal cohort study observed patients with NORSE (n&#x2009;=&#x2009;15), SE (n&#x2009;=&#x2009;17), and chronic epilepsy who were not in SE (n&#x2009;=&#x2009;12). NORSE patients were recruited through the NORSE Consortium. Patients with NORSE and SE underwent longitudinal serial biospecimen collection. Fecal samples were subjected to whole-community shotgun metagenomics to characterize microbiome features. Cohorts were evaluated for prokaryotic, eukaryotic, and functional diversity. Correlations between blood inflammatory cytokine levels and microbiome features and covariate analysis with critical illness and clinical treatments were examined for NORSE and SE patients during and after SE resolution.<br><br>RESULTS: During SE, NORSE and SE patients had significantly different prokaryotic, eukaryotic, and functional microbiome levels compared to chronic epilepsy patients without SE. Limited microbiome differences were observed within and between NORSE and SE, although these groups displayed differing correlation patterns between microbial species and cytokines. Patients who later died or were tube-fed harbored significantly different microbiomes than those who survived or were orally fed.<br><br>SIGNIFICANCE: NORSE and SE patients present with a more variable and dramatically different fecal microbiome than chronic epilepsy patients, which may indicate gut dysbiosis that may be reciprocally linked to inflammatory responses. Although NORSE and SE patients had similar microbiome structures, fungal and bacterial correlates with inflammatory cytokines differed between NORSE and SE, with confounding factors influencing microbiome structure. Our data suggest a microbiome-specific response to NORSE and SE, with implications for future treatment strategies.},
}
@article {pmid40386988,
year = {2025},
author = {Lin, Y and Shi, X and Mu, J and Ren, H and Jiang, X and Zhu, L and Cai, X and Lian, C and Pei, Z and Zhang, Y and Wang, C and Hou, G and Lin, L and Nie, C and Song, C and Gao, S and Zhao, L and Wang, J and Jiang, X and Wang, J and Guo, Y},
title = {Uncovering stage-specific neural and molecular progression in Alzheimer's disease: Implications for early screening.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {5},
pages = {e70182},
doi = {10.1002/alz.70182},
pmid = {40386988},
issn = {1552-5279},
support = {2022ZD0211600//the Ministry of Science and Technology of China/ ; 2023YFC3603300//National Key R&amp;D Program of China/ ; 82371471//Natural Science Foundation of China/ ; 2024YB59//Research Program of Central Health Commission/ ; JCYJ20240813103817024//Special Foundation for Shenzhen Basic Research Program/ ; },
mesh = {Humans ; *Alzheimer Disease/diagnosis/physiopathology/metabolism/diagnostic imaging ; Disease Progression ; Male ; Female ; *Cognitive Dysfunction/diagnosis/physiopathology ; Aged ; Early Diagnosis ; Magnetic Resonance Imaging ; Electroencephalography ; Metabolomics ; Brain/diagnostic imaging/physiopathology ; Machine Learning ; Biomarkers ; Aged, 80 and over ; },
abstract = {INTRODUCTION: Understanding molecular, neuroanatomical, and neurophysiological changes in cognitive decline is crucial for comprehending Alzheimer's disease (AD) progression and facilitating objective staging and early screening.<br><br>METHODS: We enrolled 277 participants and employed a multimodal approach, integrating genomics, metagenomics, metabolomics, magnetic resonance imaging (MRI), and electroencephalogram (EEG) to investigate the AD continuum, from subjective cognitive decline (SCD) through mild cognitive impairment (MCI) to advanced AD.<br><br>RESULTS: Key markers and mechanisms were identified for each stage: initial neurophysiological deficits in SCD with compensatory metabolomic responses, gut-brain axis dysregulation in MCI, and extensive metabolic disruption and multisystem breakdown in AD. Using random forest models, we identified specific feature combinations that achieved predictive areas under the curve (AUCs) of 0.78 for SCD, 0.84 for MCI, and 0.98 for AD, highlighting EEG as a particularly effective early screening tool.<br><br>DISCUSSION: This study elucidates AD's pathophysiological progression and highlights the potential of machine learning-assisted multimodal strategies for early detection and staging.<br><br>HIGHLIGHTS: Early electroencephalogram (EEG) changes and compensatory metabolomic responses define subjective cognitive decline (SCD) stage. In mild cognitive impairment (MCI), gut-brain axis dysfunction alters microbial diversity and functional pathways. In Alzheimer's disease (AD), systemic breakdown disruption enables near-perfect machine learning (ML) detection. Random forest models yield predictive areas under the curve (AUCs) of 0.78 (SCD), 0.84 (MCI), 0.98 (AD). EEG is a convenient, cost-efficient marker for early screening.},
}
@article {pmid40385501,
year = {2025},
author = {George, UE and De Coninck, L and George, OA and Adeyanju, T and Oragwa, A and Kamani, J and Igbokwe, J and Adamu, A and Faleye, T and Adeleke, R and Adesoji, T and Soh, TK and Sowemimo, O and Eromon, P and Adewumi, OM and Adeniji, JA and Folarin, O and Weaver, SC and Happi, A and Bosse, JB and Cross, RW and Komolafe, I and Matthijnssens, J and Happi, C},
title = {Identification and Genomic Characterization of Known and Novel Highly Divergent Sapoviruses in Frugivorous and Insectivorous Bats in Nigeria.},
journal = {EMI. Animal &amp; environment},
volume = {},
number = {},
pages = {1-37},
pmid = {40385501},
issn = {2998-6990},
abstract = {Sapovirus (SaV) infections have been linked with moderate-to-severe acute gastroenteritis (AGE) in animals and humans and represent a significant risk to public health. SaVs from animals including pigs, chimpanzees, and rodents have been reported to be closely related with human SaVs, indicating the possibility of cross-species transmission. Divergent SaVs have been reported in various bat species across various continents including Asia, Europe, Oceania and Africa. However, little is known about the evolutionary history of SaVs across various bat species and their zoonotic potential. In this report, we describe the findings of a surveillance study across various bat species in Nigeria. Samples were pooled and subjected to metagenomics sequencing and analyses. Nine of 57 sample pools (containing 223 rectal swabs from five bat species) had SaV reads from which we assembled a total of four complete and three near-complete (having complete coding sequences) genomes. The bat SaV (BtSaV) strains from this study formed five distinct lineages of which four represented novel genogroups. BtSaV lineages clustered mainly according to bat families, which might suggest a likely virus-host-specific evolution. The BtSaV VP1 capsid protein structure prediction confirmed three main domains (S, P1, and P2) as reported for Human SaV (HuSaV). We found that the P2 subdomain of the VP1 protein contains a degree of homology to known immunoreactive epitopes suggesting these conserved regions may be valuable for diagnostics or medical countermeasure development. This study expands our understanding of reservoir hosts, provides information on the genetic diversity and continuous evolution of SaVs in bats.},
}
@article {pmid40385308,
year = {2025},
author = {Geonczy, SE and Ter Horst, AM and Emerson, JB},
title = {Soil viral communities shifted significantly after wildfire in chaparral and woodland habitats.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf073},
pmid = {40385308},
issn = {2730-6151},
abstract = {Increased wildfire activity warrants more research into fire-driven biotic changes in soil, including soil viral communities, given the roles of soil microbes in organic matter decomposition, nutrient cycling, and post-fire recovery. Leveraging viral size-fraction metagenomes (viromes), here we studied viral community responses to wildfire in woodland and chaparral soils at five timepoints over 1 year following the California LNU Complex wildfire. We also compared post-fire samples to unburned controls at the final three timepoints and leveraged published viromes from the same sites nine months before the fire as pre-burn controls. Viral community composition differed significantly in burned samples compared to controls from both habitats, as did soil chemistry and prokaryotic communities (16S rRNA gene amplicons). Viromic DNA yields (a proxy for viral particle abundances) indicated initial viral biomass reductions due to the fire, but a return to baseline abundances (indistinguishable from controls) within five months. Fire-associated habitat filtering was further indicated by a comparison to the PIGEON viral "species" (viral operational taxonomic unit (vOTU)) reference database, with vOTUs from a burned conifer forest representing 19%-31% of PIGEON vOTUs detected in the burned habitats but only 0.6%-6% in controls. Together, these results indicate significant changes in soil viral communities due to wildfire, attributable at least in part to concomitant changes in their prokaryotic host communities and soil physicochemistry.},
}
@article {pmid40384975,
year = {2025},
author = {Que, T and Li, W and Zhang, Z and He, Y and He, K and Qiu, H and Huang, J and Lu, Z and Jiang, C and Huang, Y and Huang, H and Wu, Q and Chen, P and Hu, Y and Liu, W},
title = {HPD-Kit: a comprehensive toolkit for pathogen detection and analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1580165},
pmid = {40384975},
issn = {2235-2988},
mesh = {Humans ; *Computational Biology/methods ; *Metagenomics/methods ; *Software ; Animals ; *Communicable Diseases/diagnosis/microbiology ; },
abstract = {INTRODUCTION: Unbiased metagenomic sequencing (mNGS) is crucial for infectious disease diagnosis and epidemiological surveillance. However, its analysis requires specialized bioinformatics skills, creating barriers for clinicians. We developed HPD-Kit (Henbio Pathogen Detection Toolkit) with an integrated pathogen database to simplify pathogen detection and analysis for both human and animal pathogens.<br><br>METHODS: HPD-Kit includes a specifically curated pathogen database and optimized bioinformatics pipeline. We evaluated its performance using simulated datasets at varying pathogen abundances and clinical samples. The toolkit provides both open-source software and a web interface for streamlined one-click analysis.<br><br>RESULTS: Validation with simulated data showed HPD-Kit maintains high detection accuracy even at low pathogen abundance. Clinical dataset analysis demonstrated superior pathogen identification compared to conventional methods. The web interface retained this performance while significantly improving usability.<br><br>DISCUSSION: HPD-Kit effectively addresses the bioinformatics barrier in mNGS analysis while maintaining high accuracy. Its dual open-source and web-based implementation facilitates clinical and public health applications, promoting wider adoption of mNGS technology in diagnostic settings.},
}
@article {pmid40384881,
year = {2025},
author = {Oehler, JB and Burns, K and Warner, J and Schmitz, U},
title = {Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks.},
journal = {Current clinical microbiology reports},
volume = {12},
number = {1},
pages = {10},
pmid = {40384881},
issn = {2196-5471},
abstract = {PURPOSE OF REVIEW: Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public health decision-making while addressing limitations and prospects for integrating LRS into global outbreak surveillance.<br><br>RECENT FINDINGS: Unlike short-read sequencing, LRS-pioneered by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio)-resolves complex genomic structures, antimicrobial resistance determinants, and transmission dynamics with unprecedented accuracy. The portability of some LRS devices has facilitated rapid pathogen identification in field settings, notably during the Ebola and COVID-19 pandemics. Despite advancements in basecalling algorithms and target enrichment, challenges including sequencing errors, computational bottlenecks, and cost barriers remain.<br><br>SUMMARY: By critically evaluating recent findings and discussing future directions, this review highlights the importance of leveraging LRS for outbreak preparedness and response, equipping researchers and public health professionals with the knowledge necessary to navigate the complexities of modern infectious disease challenges.},
}
@article {pmid40384801,
year = {2025},
author = {Deng, C and Hong, L and Sun, D and Miao, H and Tang, F and Li, Z and Liu, X},
title = {Diagnosis of Mycoplasma Hominis Peritonitis in a CAPD Patient with Metagenomic Next-Generation Sequencing: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2469-2473},
pmid = {40384801},
issn = {1178-6973},
abstract = {BACKGROUND: Mycoplasma hominis (Mh) is a conditional pathogenic microorganism in humans, typically colonizing the genitourinary tract of adults and causing infections in this system. However, Mh is rarely reported as a causative agent of peritoneal dialysis (PD)-associated peritonitis.<br><br>CASE PRESENTATION: A 46-year-old woman undergoing maintenance PD presented with abdominal pain and cloudy PD effluent. Her PD modality is continuous ambulatory peritoneal dialysis (CAPD). Cultures of the PD effluent and blood were negative, and empirical antibiotic therapy was ineffective, leading to a diagnosis of refractory peritonitis. Metagenomic next-generation sequencing (mNGS) detected Mh in the PD effluent. Treatment was adjusted to intraperitoneal (IP) clindamycin combined with intravenous drip(ivdrip) moxifloxacin, resulting in complete recovery.<br><br>CONCLUSION: Patients with culture-negative PD-associated peritonitis or refractory peritonitis should be evaluated for potential Mh infection. mNGS enables rapid detection of pathogens that traditional methods may fail to identify. A combination of moxifloxacin and clindamycin is effective for treating PD-associated peritonitis caused by Mh.},
}
@article {pmid40384785,
year = {2025},
author = {Rivera, I and Harlow, K and Cole, RN and O'Meally, R and Garrett, W and Xiong, W and Oliver, W and Wells, JE and Summers, KL and Chhetri, N and Postnikova, O and Rempel, L and Crouse, M and Neville, B and Davies, CP},
title = {A metaproteomic analysis of the piglet fecal microbiome across the weaning transition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1504433},
pmid = {40384785},
issn = {1664-302X},
abstract = {Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and 4 weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.},
}
@article {pmid40383397,
year = {2025},
author = {Merrick, B and Prossomariti, D and Allen, E and Bisnauthsing, K and Kertanegara, M and Sergaki, C and Le Guennec, AD and Delord, M and Bell, JT and Conte, MR and Moyes, DL and Shankar-Hari, M and Douiri, A and Goodman, AL and Shawcross, DL and Goldenberg, SD},
title = {Faecal microbiota transplant to ERadicate gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO): a feasibility randomised controlled trial.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106504},
doi = {10.1016/j.jinf.2025.106504},
pmid = {40383397},
issn = {1532-2742},
abstract = {OBJECTIVES: The gastrointestinal tract (GIT) is a reservoir of multidrug-resistant organisms (MDRO). Colonisation with MDRO precedes invasive infections which can be challenging to treat with excess morbidity and mortality compared to antimicrobial susceptible infections. Currently, there are no effective GIT decolonisation strategies. Whilst Faecal Microbiota Transplant (FMT) has emerged as a potential therapeutic, there remains uncertainty about its feasibility, safety and efficacy.<br><br>METHODS: Population: Patients with invasive infection with Extended-spectrum Beta-Lactamase (ESBL-) or Carbapenem-resistant Enterobacterales (CRE) and persistent GIT carriage.<br><br>INTERVENTION: Three doses of encapsulated lyophilised FMT.<br><br>COMPARATOR: Matched placebo capsules.<br><br>OUTCOMES: Primary outcome was participant consent rate as a proportion of those approached to be screened for GIT carriage of ESBL-E/CRE. Secondary outcomes were additional feasibility, safety and tolerability, and efficacy metrics. Exploratory outcomes included stool metagenomic analysis.<br><br>RESULTS: Of 460 approached individuals, 124 (27%) consented. 53/124 participants (43%) fulfilled all eligibility criteria. 44/53 (83%) of those eligible were randomised and 41/44 (93%) received investigational medicinal product (IMP): 20 FMT and 21 placebo. 39/41 (95%) completed IMP dosing. Abdominal bloating and skin and subcutaneous tissue disorders were more common following FMT but there were no unanticipated harms. MDRO carriage decreased over time across arms but was lower at all time points in the FMT arm. FMT increased microbiome diversity and microbiome-based health measures. FMT recipients' samples clustered into two groups with those with more dissimilar community composition to donors more likely to decolonise post-FMT (3/5 vs. 0/12, p=0.01). Patients that decolonised exhibited a trend towards increased proportional representation of donor-derived strains in their post-FMT samples (p=0.05) and change in strain dominance within MDRO at species-level.<br><br>CONCLUSIONS: Progression to a substantive trial is feasible with modifications to the existing FERARO protocol. FMT was safe, well tolerated, and acceptable to patients colonised with MDRO. Microbiome analysis infers that greater donor-recipient microbiome dissimilarity at baseline and higher rates of donor-derived strain engraftment favour MDRO decolonisation, which in turn maybe facilitated by conspecific strain replacement.},
}
@article {pmid40383308,
year = {2025},
author = {Zhang, G and Hu, M and Wang, X and Liu, C and Ya, T and Wang, X},
title = {Self-regulatory mechanisms of anammox system in response to CuO nanoparticles revealed by microbial ecological networks and metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132682},
doi = {10.1016/j.biortech.2025.132682},
pmid = {40383308},
issn = {1873-2976},
abstract = {Anaerobic ammonia oxidation (Anammox) has attracted widespread attention as an advanced biological nitrogen removal technology. CuO nanoparticles (CuO NPs) is one of the most common nanomaterials widely used in industrial production. In this study, microbial network construction, metagenomics and binning analysis were integrated to elucidate the impact of CuO NPs on anammox system. Nitrogen removal efficiency initially fluctuated but eventually stabilized after the addition of 1 mg/L CuO NPs. Network analysis revealed a significant increase in cooperative associations between anammox bacteria (AnAOB: Candidatus_Kuenenia, Candidatus_Jettenia, and Candidatus_Brocadia) and Chloroflexi from 0 % to 75 %. Metagenomic and binning analysis elucidated the intricate metabolic interactions between AnAOB and Chloroflexi, particularly in the biosynthesis of polysaccharide, protein, and cofactors.The collaboration between AnAOB and Chloroflexi was crucial for maintaining the ecological balance of the community structure under CuO NPs stress in anammox system.},
}
@article {pmid40382874,
year = {2025},
author = {Miao, S and Zhang, Y and Wu, L and Wang, Y and Zuo, J},
title = {Resistance induction potency assessment of antibiotic production wastewater and associated resistome shaping mechanisms.},
journal = {Water research},
volume = {283},
number = {},
pages = {123811},
doi = {10.1016/j.watres.2025.123811},
pmid = {40382874},
issn = {1879-2448},
abstract = {Antibiotic production wastewater (APW) contains multiple substances known to select for and facilitate horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs); however, whether these substances can induce the evolution of antibiotic resistance in real wastewater environments and the fate of such resistance induction potency during the treatment process are poorly understood, nor are its relationship with wastewater quality parameters and function in shaping the antibiotic resistome. In this study, the impacts of filter-sterilized APW and municipal wastewater on the resistance selection of Escherichia coli and the transfer dynamics of conjugative RP4 plasmid-borne ARGs across indigenous sludge communities were evaluated. The resistance development and transfer processes were accelerated in APW owing to enhanced growth inhibition, oxidative stress, and membrane permeability, with antibiotic concentrations much lower than their minimum inhibition concentrations. The effects were reduced simultaneously with the removal of COD and NH3N, but APW effluents still exhibited significant resistance induction potency with wastewater quality parameters meeting discharge standards. In contrast, municipal wastewater did not result in any detectable changes. Based on the metagenomic assembly and binning, stronger resistance induction potency in the antibiotic production wastewater treatment plant endowed indigenous sludge and effluent with greater accumulation, genetic mobility, and pathogenic accessibility of ARGs than in the municipal wastewater treatment plant. Antibiotic resistome assembly was determined primarily by deterministic processes, driven jointly by resistance induction potency, mobilome variance, and microbiome shifts. These results provide novel insights into the application of bioassays to comprehensively evaluate the antibiotic resistance induction effects of APW and their relationships with the resistome to manage risks during the treatment process.},
}
@article {pmid40382544,
year = {2025},
author = {Zhang, S and Fu, Y and Fang, L and Xu, Q and Gu, S and Zhou, H and Zhou, J},
title = {Psittacosis pneumonia with the reversed halo sign: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {717},
pmid = {40382544},
issn = {1471-2334},
support = {2021YFC2301805//National Key Research and Development Program of China/ ; WKJ-ZJ-2109//Medical and Health Technology Program of Zhejiang Province/ ; },
mesh = {Humans ; Male ; Adult ; *Psittacosis/diagnostic imaging/drug therapy/diagnosis/microbiology ; *Chlamydophila psittaci/isolation &amp; purification/genetics ; Tomography, X-Ray Computed ; Animals ; Lung/diagnostic imaging/microbiology ; Columbidae/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Lung Diseases/diagnosis ; },
abstract = {BACKGROUND: Chlamydia psittaci is a rare pathogen that causes community-acquired pneumonia. The reversed halo sign (RHS) is a computed tomography (CT) finding that is commonly observed in diseases such as cryptogenic organizing pneumonia, invasive fungal infections, tuberculosis, sarcoidosis, and pulmonary thromboembolism, but has seldom been described in association with psittacosis pneumonia.<br><br>CASE PRESENTATION: We report a case in which a 26-year-old man with a history of close contact with pigeons and chicken manure presented with fever and cough for 6 days. A CT examination revealed the RHS in the right lower lobe of the lung. Psittacosis pneumonia was diagnosed by metagenomic next-generation sequencing of the patient's bronchoalveolar lavage fluid. Treatment with omadacycline abolished his symptoms. We also discuss six other cases of psittacosis pneumonia with the RHS identified by literature search.<br><br>CONCLUSIONS: When clinicians encounter patients with atypical pneumonia with the RHS and a history of contact with poultry, psittacosis should be considered.},
}
@article {pmid40382475,
year = {2025},
author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG},
title = {The Microbial Ecology of Antarctic Sponges.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {44},
pmid = {40382475},
issn = {1432-184X},
mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; },
abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.},
}
@article {pmid40382365,
year = {2025},
author = {Schilling, M and Jagdev, M and Thomas, H and Johnson, N},
title = {Metagenomic analysis of mosquitoes from Kangerlussuaq, Greenland reveals a unique virome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17141},
pmid = {40382365},
issn = {2045-2322},
mesh = {Animals ; Greenland ; *Virome/genetics ; *Metagenomics/methods ; *Aedes/virology/genetics ; *Mosquito Vectors/virology ; Metagenome ; Phylogeny ; *Culicidae/virology ; Climate Change ; },
abstract = {Climate change is dramatically affecting vector ecology in extreme environments such as the Arctic. However, little is known about the current status of viruses of arthropod vectors located in such northerly locations. As part of a field survey on the role of wildlife in international movement of zoonotic pathogens, we sampled mammalophilic mosquitoes near the settlement of Kangerlussuaq, Greenland in July 2022 and July 2023 to investigate their virome. The majority of mosquitoes were identified as either Aedes impiger or Aedes nigripes. Metagenomic analysis of RNA extracted from species pools detected a number of novel RNA viruses belonging to a range of different virus families, including Flaviviridae, Orthomyxoviridae, Bunyavirales, Totiviridae and Rhabdoviridae. However, the sequence identities when compared to previously published, were as low as 34% at the amino acid level. Furthermore, a comparison of virome diversity between Aedes species emphasises the uniqueness of both Aedes impiger and Aedes nigripes from this secluded ecosystem. It also highlights the need to better understand the viromes of potential pathogen vectors as the impacts of climate change are experienced in such northerly ecosystems.},
}
@article {pmid40382068,
year = {2025},
author = {Zhang, Z and Ran, X and Guo, Z and Hou, Q and Qu, D and Wang, C and Xu, Y and Wang, Y},
title = {Microbial diversity, functional properties, and flavor characteristics of high-temperature Daqu with different colors.},
journal = {Food research international (Ottawa, Ont.)},
volume = {212},
number = {},
pages = {116406},
doi = {10.1016/j.foodres.2025.116406},
pmid = {40382068},
issn = {1873-7145},
mesh = {Color ; *Taste ; *Food Microbiology ; *Hot Temperature ; Odorants/analysis ; Humans ; *Bacteria/classification/genetics ; *Microbiota ; China ; },
abstract = {High-temperature Daqu (HTD) plays a crucial role in the quality of sauce-flavor baijiu. Daqu of different colors serves distinct functions in the baijiu brewing process. However, indicators for distinguishing among different-colored Daqu remain insufficient. This study investigated the microbial community structures, physicochemical properties, and E-sensory characteristics of different-colored HTD from Shandong Province. The results revealed significant differences in microbial communities among the three HTD types (P < 0.05). Kroppenstedtia eburnea, three Bacillus species, and Weizmannia coagulans were significantly enriched in white Daqu; an unclassified Staphylococcus species dominated in black Daqu; and Aspergillus oryzae, Aspergillus fumigatus, and Proteus mirabilis were highly abundant in yellow Daqu. Compared to HTD from Guizhou and Hubei, Shandong HTD was characterized by microbial species such as Proteus mirabilis and Bacillus velezensis. Using metagenomic analysis, we, for the first time, identified Thermomyces lanuginosus, Lentibacillus daqui, and an unclassified Thermoascus species as potential major contributors to pyrazine synthesis in HTD. The primary differences among the three colored Shandong Daqu types lay in their aroma profiles rather than taste. Electronic nose and electronic tongue analyses demonstrated that the W6S and W3S sensors effectively distinguished black and white Daqu, respectively, marking a novel application of these technologies in Daqu analysis. Acidity was identified as a key factor influencing microbial community structure, flavor characteristics, and enzyme activities, with a nonlinear relationship observed between acidity and enzyme activities. This study highlights the microbial and sensory distinctions among different-colored HTD and provides effective indicators for distinguishing these three types of Daqu.},
}
@article {pmid40381442,
year = {2025},
author = {Zhang, X and Li, M and Xiao, Y and Yang, X and Zhou, H and Qu, Y and Zhan, J},
title = {Metagenomics reveals combined effects of microplastics and antibiotics on microbial community structure and function in coastal sediments.},
journal = {Marine pollution bulletin},
volume = {218},
number = {},
pages = {118153},
doi = {10.1016/j.marpolbul.2025.118153},
pmid = {40381442},
issn = {1879-3363},
abstract = {Microplastics and antibiotics are emerging pollutants in marine environments, yet their combined effects on coastal sediments remain poorly understood. This study examined the impacts of microplastics and antibiotics on sediment properties and microbial communities through a 60-day laboratory simulation. Results showed that microplastics significantly reduced carbon, nitrogen, and phosphorus levels in sediments, while both antibiotics and combined pollution decreased phosphorus content. Combined pollution also increased NH4[+]-N concentration. Enzyme activity analysis revealed that microplastics elevated alkaline phosphatase activity, antibiotics increased fluorescein diacetate (FDA) hydrolase activity but decreased urease activity, and their combination further enhanced FDA hydrolase activity. Metagenomics analysis demonstrated that the presence of microplastics and antibiotics altered microbial community structure and metabolic functions. The dominant phylum Pseudomonadota (42.62 %-56.24 %) showed reduced abundance under combined pollution. Antibiotics significantly increased resistance gene abundance, while combined pollution led to selective enrichment of these genes. Both pollutants inhibited ammonia assimilation, and antibiotics also suppressed dissimilatory nitrate reduction. Conversely, combined pollution promoted nitrification and nitrogen fixation. While microplastics and antibiotics inhibited methane synthesis, combined pollution increased methane production via elevated mttB and hdrA genes. Antibiotics also reduced methane-oxidizing bacteria and genes, suppressing methane oxidation. These findings provide crucial insights into the ecological impacts of microplastics and antibiotics on coastal sediments, offering a theoretical basis for future marine pollution management strategies.},
}
@article {pmid40381353,
year = {2025},
author = {Xin, Y and Zhang, J and Tang, Q and Wei, M and Zhu, L and Zhao, Y and Cui, Y and Sun, T and Wei, Y and Richnow, HH},
title = {Virus-host interactions driving the transfer of antibiotic resistance genes in a river-reservoir system under heavy rainfall.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138605},
doi = {10.1016/j.jhazmat.2025.138605},
pmid = {40381353},
issn = {1873-3336},
abstract = {Global river systems are grappling with severe pollution from antibiotic resistance genes (ARGs), with river-reservoir (R-R) systems being a common feature in urban waterways. The intensified extreme rainfall events triggered by global climate change exacerbate the spread of ARGs posed by non-point source pollution and combined sewage overflows. This study employs a metagenomics approach to decipher the profile of ARGs and virus-host interactions driving their transfer under heavy rainfall in North Canal, Beijing, with extensive R-R systems. Results indicated that R-R systems contributed to ARGs reduction despite continuous discharge of treated wastewater into the North Canal. The ARGs assembly is predominantly governed by stochastic process, and heavy rainfall enhances the dispersal capability. Nonetheless, the deterministic process determined the assembly of both microbial and viral community. Heavy rainfall not only significantly increased the abundance and diversity of ARGs within the rivers with minimal change in the reservoir, but also promotes the horizontal gene transfer of ARGs with higher conjugative mobility. Although the species accumulation curves approached saturation, no viruses carrying ARGs were detected among the 23,835 non-redundant viral operational taxonomic units (vOTUs), and lytic phage-ARB interactions drove the ARGs reduction with higher VHRs, highlighting its contribution to the reduction of ARGs in R-R system after heavy rainfall.},
}
@article {pmid40381349,
year = {2025},
author = {Feng, W and Ye, Y and Xiang, Y and Peng, S and He, S and Peng, H and Zhang, Z and Yang, Z and Xiong, W},
title = {Unraveling the dual role in enhancing methane production and mitigating antibiotic resistance gene spread in anaerobic co-digestion of microalgae and waste activated sludge.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138606},
doi = {10.1016/j.jhazmat.2025.138606},
pmid = {40381349},
issn = {1873-3336},
abstract = {Waste activated sludge (WAS) is a double-edged sword - a recognized repository for antibiotic resistance genes (ARGs) but also a renewable substrate for methane production. Developing effective WAS treatment strategies is therefore of both ecological and practical importance. In this study, we proposed an anaerobic co-digestion approach of WAS and microalgae Chlorella sp. at a 1:2 ratio (MAcoD-1:2). Results showed that MAcoD-1:2 notably increased cumulative methane production by 52.7 %. Co-digestion also demonstrated a significant increase in the abundance of hydrolyzing acidifying bacteria Candidatus_Promineofilum (12.25 %) and methanogenic archaea Methanothrix (61.2 %). This microbial shift suggested that cosubstrates availability fostered a stable bacterial community structure and synergistic metabolic interactions, thus enhancing methane production. Metagenomic analysis revealed a significant reduction in both ARGs and mobile genetic elements in MAcoD-1:2. Notably, substrate level regulation was found to drive restructuring of microbial communities and metabolic patterns. Investigation showed that the Embden-Meyerhof-Parnas pathways were significantly inhibited while the pentose phosphate pathway was promoted, which constrained the cellular energy budget available for ARG horizontal transfer. Partial least squares path modelling (PLS-PM) further substantiated these findings, revealing methane metabolism negatively affected ARGs (-4.52), whereas confirming its positive correlation with methane production (0.22). Our findings provided distinctive perspectives on WAS resource utilization and novel technologies to inhibit the spread of ARGs.},
}
@article {pmid40380820,
year = {2025},
author = {Lakamp, AD and Neujahr, AC and Fernando, SC and Snelling, WM and Spangler, ML},
title = {Short Communication: Imputation accuracy of host genomic data from metagenomic sequence information.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf175},
pmid = {40380820},
issn = {1525-3163},
abstract = {Metagenomic sequencing is the process of extracting all the genomic information from a given sample. Most metagenomic studies remove any host reads as a matter of course. However, host reads can be used as the basis for genotype imputation to obtain whole genomic sequences. The accuracy of these imputed genotypic calls from a bovine ocular sample was determined by comparing results to those from a commercial array. Overall, imputed genotype calls proved to have a high concordance with array genotype calls (average concordance of 83% and correlation of 0.81 with no filtering). Accuracy increased as filters for host read depth and imputed call confidence were implemented. With filters in place the average percent concordance was 98% (88 - 99%) while the mean correlation was 0.98 (0.89-0.99). Further, identity verification of the metagenomic samples can be carried out if the host is genotyped on another platform.},
}
@article {pmid40380332,
year = {2025},
author = {Kapandji, N and Salmona, M and Lemoine, A and Ulmann, G and Calderaro, J and Roche, B and Kapel, N and Biard, L and Lengline, E and Goff, JL and Rodriguez, C and Thomas, M and Zafrani, L},
title = {Unravelling neutropenic enterocolitis: insights from gut microbiota, and intestinal barrier analyses.},
journal = {Experimental hematology &amp; oncology},
volume = {14},
number = {1},
pages = {74},
pmid = {40380332},
issn = {2162-3619},
abstract = {BACKGROUND: Neutropenic enterocolitis (NE) is a severe digestive complication of chemotherapy, primarily affecting patients with acute myeloid leukemia (AML). We hypothesized that NE is linked to intestinal barrier dysfunction and gut dysbiosis.<br><br>METHODS: Sixty-five AML patients undergoing induction chemotherapy were included in this prospective monocentric cohort. Among them, 26 patients (40%) were diagnosed with NE. Stool samples were subjected to bacterial load quantification (all bacteria quantitative PCR), 16s rRNA metagenomic analysis, and short-chain-fatty-acids quantification. Additionally, fecal calprotectin and human &#x1d6c3;-defensin 2 along with plasmatic inflammatory cytokines, and citrulline levels were measured. Human transcriptomic analysis was conducted on samples obtained from anatomical specimens of colectomies of NE patients.<br><br>RESULTS: Gut microbiota underwent significant alterations after chemotherapy, transitioning from a diverse and balanced enterotype to enterotypes exhibiting a reduced &#x3b1;-diversity, an increased abundance of Enterococcus faecalis, and a decreased abundance of butyrate-producing genera, which correlated with a decreased fecal concentration of butyrate. Simultaneously, post-chemotherapy, plasma citrulline concentrations decreased indicating enterocyte damages. Finally, human transcriptomic analysis found a significant upregulation of the JAK-STAT signaling KEGG pathway in the colons of NE patients encompassing cytokines (IL-6, OSM-OSMR) that play a pivotal role in sustaining local inflammation within the digestive tract.<br><br>CONCLUSIONS: This work reaffirms the significant influence of chemotherapy on the gut microbiota and the integrity of the enterocyte barrier. Severe NE is marked by the development of a local inflammatory response that may be induced by the reduction in butyrate levels.<br><br>TRIAL REGISTRATION: The study was registered on Clinicaltrials.gov (identifier: NCT04438278).},
}
@article {pmid40380289,
year = {2025},
author = {Amutuhaire, H and Faigenboim-Doron, A and Kraut-Cohen, J and Friedman, J and Cytryn, E},
title = {Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {52},
pmid = {40380289},
issn = {2524-6372},
abstract = {BACKGROUND: Soilborne fungal phytopathogens pose a significant threat to global food security. While chemical control remains an effective method for managing these pathogens, increasing regulations due to health and environmental concerns, along with rising fungicide resistance, have restricted their use, underscoring the urgent need for sustainable alternatives. The use of compost to enhance soil fertility and suppress plant diseases is well documented. Several studies have underlined the role of microorganisms in disease suppression, but the mechanisms facilitating this disease suppression remain unclear. We evaluated the impact of compost amendment on the composition and functional capacity of the rhizosphere microbiome in cucumber plants (Cucumis sativus) inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) under controlled greenhouse conditions using amplicon sequencing, shotgun metagenomic and culture-based techniques.<br><br>RESULTS: Compost amendment significantly reduced FORC-induced disease in cucumber relative to non-amended treatments. While FORC inoculation resulted in significant shifts in microbial (bacterial and fungal) community composition in the rhizosphere of non-amended plants, this phenomenon was substantially less pronounced in the rhizosphere of compost-amended plants. Specifically, compost amendment sustained the presence of Actinomycetota (Streptomyces, Actinomadura, Saccharomonospora, Pseudonocardia, Glycomyces, Thermobifida) and Bacillota (Planifilum, Novibacillus) in FORC inoculated plants, that diminished significantly in inoculated plants without compost. These taxa contained a myriad of non-ribosomal peptides and polyketides synthetases biosynthetic gene clusters (BGCs) with putative antimicrobial and iron-chelating functions. We successfully isolated two Streptomyces strains from FORC-suppressing compost amended rhizospheres that were almost identical to the Streptomyces bin2 (99% ortho ANI) metagenome assembled genome identified in the shotgun metagenome analysis. These strains produced extracellular metabolites that inhibited growth of FORC in-vitro and contained BGCs that encode for compounds with potential antimicrobial capacity.<br><br>CONCLUSIONS: Based on results presented in this study, we demonstrate that compost alleviates FORC-induced dysbiosis of the rhizosphere microbiome, maintaining abundance of specific bacterial taxa. These bacterial groups may contribute to disease suppression through a myriad of mechanisms including iron chelation and production of fungal antagonizing secondary metabolites.},
}
@article {pmid40380272,
year = {2025},
author = {Zhang, S and Zheng, N and Zhao, S and Wang, J},
title = {Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {124},
pmid = {40380272},
issn = {2049-2618},
support = {2023M743835//Project Funded by China Postdoctoral Science Foundation/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 2022YFD1301000//National Key Research and Development Program of China/ ; 2004DA125184G2406//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/chemistry ; *Urease/antagonists &amp; inhibitors/metabolism/chemistry ; *Rumen/microbiology ; *Urea/metabolism ; Disulfides/pharmacology ; *Nitrogen/metabolism ; Cattle ; Molecular Docking Simulation ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/drug effects/classification/genetics ; Enzyme Inhibitors/pharmacology ; },
abstract = {BACKGROUND: Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and [15]N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.<br><br>RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77&#x2009;&#xb1;&#x2009;1.21&#xa0;&#x3bc;M. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A [15]N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.<br><br>CONCLUSION: Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.},
}
@article {pmid40379383,
year = {2025},
author = {Haas, G and Lee, B},
title = {De novo rescue of new henipaviruses under BSL-4 conditions - From sequence to pathogen.},
journal = {Advances in virus research},
volume = {121},
number = {},
pages = {61-99},
doi = {10.1016/bs.aivir.2025.03.004},
pmid = {40379383},
issn = {1557-8399},
mesh = {Animals ; Humans ; *Reverse Genetics/methods ; *Henipavirus/genetics/pathogenicity/isolation &amp; purification ; Genome, Viral ; *Henipavirus Infections/virology/transmission ; *Containment of Biohazards/methods ; Zoonoses/virology ; },
abstract = {Zoonotic paramyxoviruses, including the highly pathogenic henipaviruses (HNVs), pose significant risks to global health due to their high mortality rates, potential for human-to-human transmission, and lack of approved countermeasures. Recent metagenomic surveys have uncovered an extensive diversity of HNVs and related paramyxoviruses circulating in wildlife, the majority of which remain uncharacterized due to the dearth of viral isolates. In lieu of viral isolates, reverse genetics systems offer an approach to derive infectious clones de novo in the laboratory, facilitating research into the biology, zoonotic potential, and pathogenicity of novel HNVs. This chapter explores the methodologies and applications of reverse genetics systems for novel HNVs, including considerations for virus sequence validation, full-length virus recovery, and the development of platforms such as minigenomes, replicons, and virus replicon particles. Such biologically-contained life cycle modeling systems enable research to be conducted at lower biocontainment, and provide accessible tools through which to investigate HNV biology. This work demonstrates the versatility of reverse genetics systems in advancing our understanding of high-consequence pathogens, enabling the proactive development of vaccines, antivirals, and diagnostic tools. By integrating these methodologies within a framework of biosafety and biosecurity, researchers can better prepare for and respond to future zoonotic threats.},
}
@article {pmid40379020,
year = {2025},
author = {Goto, M and Yamamoto, K and Horiba, K and Hashino, M and Kubono, Y and Ohmagari, N},
title = {Detection of Prevotella species in anaerobic culture-negative multiple abscesses using next-generation sequencing.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102733},
doi = {10.1016/j.jiac.2025.102733},
pmid = {40379020},
issn = {1437-7780},
abstract = {Next-generation metagenomic sequencing (mNGS) provides a comprehensive analysis of DNA and RNA in samples. In this case report, pus specimens were collected from an 86-year-old male with multiple muscle, periarticular, and bone abscesses, and osteomyelitis, without prior antimicrobial therapy. Results of bacterial culture tests, including anaerobic and intensified cultures, were negative. Despite this, mNGS using shotgun sequencing revealed a significant number of DNA and RNA nucleic acid reads from Prevotella spp. Although the subspecies could not be identified, mNGS allowed the selection of an appropriate antimicrobial agent and suggested significant oral contamination as the portal of entry. In summary, mNGS helped identify the causative organism in a case without prior antimicrobial therapy wherein culture test results were negative.},
}
@article {pmid40378832,
year = {2025},
author = {Sarhan, MS and Antonello, G and Weissensteiner, H and Mengoni, C and Mascalzoni, D and Waldron, L and Segata, N and Fuchsberger, C},
title = {Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?.},
journal = {Cell},
volume = {188},
number = {10},
pages = {2561-2566},
doi = {10.1016/j.cell.2025.03.023},
pmid = {40378832},
issn = {1097-4172},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Metagenome ; *Metagenomics/ethics ; Privacy ; Microbiota ; *Genetic Privacy/ethics ; },
abstract = {Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.},
}
@article {pmid40378756,
year = {2025},
author = {Zhan, Y and Chen, N and Feng, C and Dai, T and Gao, H and Yuan, Y and Hu, W and Dong, H},
title = {Electron flow dynamics in sulfur-based autotrophic bioreduction of Cr(VI) mediated by inorganic carbon species: Insights for environmental remediation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138585},
doi = {10.1016/j.jhazmat.2025.138585},
pmid = {40378756},
issn = {1873-3336},
abstract = {The deployment of sulfur-based autotrophic bioremediation for in situ groundwater remediation faces hurdles due to electron competition among electron acceptors, impacting contaminant removal efficiency and causing pH instability. Notably, the sulfur-based bioreduction of Cr(VI) [Cr(VI)-SAR] exemplifies gaps in our comprehension of electron competition dynamics with inorganic carbon (IC), and its subsequent influence on pH. Herein, we established a Cr(VI)-SAR system interfaced with diverse IC species, providing definitive insights into electron transfer mechanisms through rigorous multi-biocycle analysis and thermodynamically consistent half-reaction calculations. Through quantification of electron transfer pathways, we derived reaction equations for Cr(VI) reduction in conjunction with various IC species. Furthermore, metagenomics were used to quantify functional enzymes and identify diverse electron transport patterns alongside IC fixation pathways. Notably, the enrichment of genes associated with electron shuttles and conductive pili expands the paradigm of extracellular electron transfer, while the Wood-Ljungdahl pathway streamlines microbial metabolic proliferation with reduced energy expenditure. Quantitative analysis of these functional genes offers a plausible mechanism underlying the observed shifts in electron competition between IC and Cr(VI). This research marks an advancement in the Cr(VI)-SAR foundational theory, with a particular focus on the dynamics of electron competition, contributing to a deeper understanding of this environmentally significant process.},
}
@article {pmid40378749,
year = {2025},
author = {Yu, YL and Lin, WH and Surampalli, RY and Chen, SC and Kao, CM},
title = {Adaptive fluoride removal across concentration scales: Potential roles of microbial and acicular gypsum interactions in nitrogen and phosphate cycling.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138628},
doi = {10.1016/j.jhazmat.2025.138628},
pmid = {40378749},
issn = {1873-3336},
abstract = {Fluoride contamination in groundwater is a critical environmental and public health concern. Traditional remediation methods, including chemical precipitation and adsorption, are hindered by low nucleation efficiency at low fluoride concentrations and severe microbial inhibition under high fluoride stress. This study introduces an adaptive two-stage remediation system that synergistically integrates abiotic and biotic mechanisms to achieve effective fluoride removal across concentration scales. In Stage I, under elevated fluoride stress (100 mg/L), acicular gypsum (AG) facilitated abiotic calcium precipitation, effectively reducing fluoride toxicity and creating favorable conditions for microbial activity. Residual calcium released from AG further supported microbial-induced calcium precipitation (MICP) in Stage II under lower fluoride stress (10 mg/L). The system achieved a fluoride removal efficiency of 98.85 % under high fluoride conditions and demonstrated consistent performance across a broad concentration range. This integrated approach, combining abiotic and biotic mechanisms, offers a promising strategy for addressing diverse fluoride contamination scenarios. Here, phosphate (P)-mediated mineralization and microbial denitrification drive pH modulation, stabilizing fluoride as fluorapatite [Ca5(PO4)3F]. Microbial community and network analysis revealed key taxa, including Cupriavidus and Ralstonia, which facilitated P cycling and fluorapatite formation. Additionally, Bradyrhizobium enhanced nitrogen (N) cycling and supported early microbial adaptation, emphasizing the interplay of microbial interactions in driving system functionality. Functional predictions using PICRUSt2 identified genes associated with N and P cycling, highlighting the capacity of the system for nutrient adaptation under complex environmental conditions.},
}
@article {pmid40378468,
year = {2025},
author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW},
title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.},
journal = {Water research},
volume = {283},
number = {},
pages = {123683},
doi = {10.1016/j.watres.2025.123683},
pmid = {40378468},
issn = {1879-2448},
abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.},
}
@article {pmid40378175,
year = {2025},
author = {Wan, J and Liu, T and Li, F and Xu, S},
title = {Diagnosis, clinical features, and mortality risk factors in a Chinese cohort with pulmonary mucormycosis.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323624},
pmid = {40378175},
issn = {1932-6203},
mesh = {Humans ; *Mucormycosis/mortality/diagnosis ; Male ; Middle Aged ; Female ; Risk Factors ; Retrospective Studies ; Adult ; *Lung Diseases, Fungal/mortality/diagnosis ; Aged ; China/epidemiology ; Tomography, X-Ray Computed ; East Asian People ; },
abstract = {BACKGROUND: Pulmonary mucormycosis is a rare and often fatal fungal infection. Identifying high-risk factors for pulmonary mucormycosis holds the potential to improve patient outcomes. This study aimed to identify the clinical characteristics and risk factors associated with pulmonary mucormycosis outcomes in a Chinese cohort.<br><br>MATERIALS AND METHODS: A retrospective analysis was conducted on 37 patients diagnosed with pulmonary mucormycosis, focusing on clinical records, laboratory findings, and computed tomography (CT) imaging. Diagnosis was primarily based on histopathology or next-generation sequencing.<br><br>RESULTS: The median age of the patients was 55 years, and the most common underlying conditions were hematological malignancies, diabetes, and organ transplantation. Imaging frequently revealed bilateral lung involvement with ground-glass opacities and nodular lesions. The overall mortality rate was 29.7%, with significant risk factors for 90-day mortality including hypertension (Hazard Ratio [HR] = 3.36, 95% Confidence Interval [CI] = 1.01-11.12, P&#x2009;=&#x2009;0.048), organ transplantation (HR&#x2009;=&#x2009;4.93, 95% CI&#x2009;=&#x2009;1.48-16.4, P&#x2009;=&#x2009;0.009), and immunosuppression (HR&#x2009;=&#x2009;8.83, 95% CI&#x2009;=&#x2009;1.13-69.14, P&#x2009;=&#x2009;0.038).<br><br>CONCLUSIONS: Early suspicion and timely diagnostic measures, such as biopsy or metagenomic sequencing, are crucial for improving patient outcomes. These findings underscore the importance of recognizing and managing pulmonary mucormycosis in high-risk populations.},
}
@article {pmid40377870,
year = {2025},
author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM},
title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40377870},
issn = {1867-1314},
abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.},
}
@article {pmid40377844,
year = {2025},
author = {Paul, B and Pan, P and Bhattacharyya, N},
title = {Investigating the impact of fly ash contamination on soil microbial diversity: a metagenomic study near Kolaghat Thermal Power Plant, India.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40377844},
issn = {1614-7499},
abstract = {Soil metagenomics using whole genome shotgun sequencing (WGS) uncovers microbial diversity and functionality in soils. This study aimed to explore microbial diversity and functional adaptation in soils exposed to fly ash near the Kolaghat Thermal Power Plant, West Bengal, India, using whole genome shotgun sequencing. Understanding how microbial communities respond to such contamination is essential for developing effective bioremediation strategies. Soil samples were collected from the area, designated as BP1 sample selected for detailed metagenomics analysis. The study extracted DNA with a concentration of 46.2 ng/µl, followed by quality checks and profiling to identify microbial communities. Analysis showed that bacterial communities were dominated by Actinobacteria (48.28%) and Proteobacteria (40.80%), while fungi were primarily represented by Ascomycota (89.50%). Among viruses, Negarnaviricota were most prevalent, with the class Insthoviricetes accounting for 94.60%. Diversity analysis indicated that bacterial populations remained stable, fungal diversity fluctuated, and viral diversity increased, reflecting complex ecological interactions. The presence of key genes involved in lipid and carbohydrate metabolism suggests that microbes adapted to contamination by heavy metals and organic pollutants. The dominance of stress-tolerant Proteobacteria and Actinobacteria highlights their potential role in bioremediation. Future research should explore the potential of these microbes, particularly the role of ABC transporters, in improving pollutant degradation.},
}
@article {pmid40377330,
year = {2025},
author = {Thajudeen, J and Venkatachalam, S and Vipindas, PV},
title = {Antibiotic resistome in the glacier forelands of polar regions.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0076225},
doi = {10.1128/aem.00762-25},
pmid = {40377330},
issn = {1098-5336},
abstract = {UNLABELLED: Antibiotic resistance genes (ARGs) pose a significant threat, exacerbated by climate change impacts on polar regions, particularly melting glaciers and permafrost. While ancient antibiotic resistance exists in the environments, the release and dissemination of ARGs remain poorly understood. This study investigated ARG composition and distribution in 43 metagenomes from Arctic and Antarctic glacier forelands. We identified 154 ARGs, predominantly bacitracin resistance, followed by rifamycin, fosfomycin, vancomycin, tetracycline, and beta-lactam resistance genes. Significant correlations were observed between ARGs and mobile genetic elements (MGEs), with 20 ARGs associated with tnpA MGEs. Actinomycetota and Pseudomonadota were the primary ARG-carrying phyla. Metagenome-assembled genomes revealed Mycobacterium sp., Pseudomonas sp., and Tatlockia sp. as major ARG-harboring pathogens in the glacier forelands. Evolutionarily adapted, distinct ancient ARGs were abundant in the polar environments, varying between different geographic regions. The environmental parameters such as pH and total organic carbon significantly influenced the ARG distribution in the Arctic and Antarctic glacier forelands. This study provides crucial baseline data on antimicrobial resistance, highlighting potential risks associated with rapid environmental change in the regions.<br><br>IMPORTANCE: Antibiotic resistance poses a significant global health threat, exacerbated by the release of antibiotic resistance genes from melting glaciers and permafrost due to climate change. This study provides crucial baseline data on the composition and distribution of antibiotic resistance genes in these vulnerable polar environments, which is essential for understanding and mitigating the risks associated with their release. The findings have far-reaching implications for global health security and emphasize the need for further research to address this emerging threat.},
}
@article {pmid40377187,
year = {2025},
author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM},
title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {40377187},
issn = {2050-084X},
support = {1746045//National Science Foundation Graduate Research Fellowship Program/ ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; },
abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.},
}
@article {pmid40376801,
year = {2025},
author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW},
title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.},
journal = {Circulation. Heart failure},
volume = {},
number = {},
pages = {e012524},
doi = {10.1161/CIRCHEARTFAILURE.124.012524},
pmid = {40376801},
issn = {1941-3297},
abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.<br><br>METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4&#xd7;10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.<br><br>RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.<br><br>CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.},
}
@article {pmid40376464,
year = {2025},
author = {Shao, X and Yang, C and Chen, Y and Liu, C and Liu, C and Shi, X and Zhou, Y},
title = {Sorghum-peanut intercropping under salt stress mediates rhizosphere microbial community shaping in sorghum by affecting soil sugar metabolism pathways.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589415},
pmid = {40376464},
issn = {1664-302X},
abstract = {Soil salinization is a substantial impediment to agricultural production, and investigating sustainable mitigation measures is essential for addressing food security. We conducted a two-year pot experiment to investigate the shaping mechanism of sorghum rhizosphere microbial community in sorghum-peanut intercropping system under salt stress. The experiment comprised four treatments: sole-cropped sorghum under normal soil conditions (NSS), intercropped sorghum under normal soil conditions (NIS), sole-cropped sorghum under salt-stress conditions (SSS), and intercropped sorghum under salt-stress conditions (SIS). The sorghum rhizosphere soil metabolites were examined using GC-MS, and the rhizosphere microbial community was characterized through metabolome sequencing. We identified 123 metabolites across treatments, with significant differences between normal and salt-stress soil conditions. The major metabolite classes included carbohydrates, alcohols, and acids. Key carbohydrates, including fructose and sucrose, were significantly reduced in the SIS than in SSS, NSS, and NIS treatments. Metabolic pathway analyses revealed that these differences were primarily associated with "Fructose and mannose metabolism," "Starch and sucrose metabolism" and "ABC transporter." Metabolome analyses revealed significant differences in microbial community structure across diverse soil conditions and cropping patterns. At phylum level, Proteobacteria, Gemmatimonadetes, and Verrucomicrobia predominated, with their relative abundance experiencing substantial changes under salt stress. SIS facilitated the enrichment of specific genera (Rhodanobacter), which were associated with soil health and stress tolerance. Additionally, the responses of rare microbial taxa to salt stress and intercropping varied, with specific rare microbial taxa (Rhizopus) exhibiting relative abundance under salt stress. Correlation analysis of metabolites and microbial taxa revealed that certain carbohydrates were significantly positively correlated with specific microbial phyla (Cyanobacteria and Nitrospirae) while demonstrating a significant negative correlation with Planctomycetota and Bacteroidota. These correlations indicate that sorghum intercropped with peanuts can promote the enrichment of microbial taxa under salt stress, thereby enhancing soil metabolic functions and stress tolerance by optimizing the rhizosphere microbial community. This study reveals the mechanism through which sorghum-peanut intercropping under salt stress influences the composition of sorghum's rhizosphere microbial community by modulating soil sugar metabolism pathways. This finding provides a new perspective on sustainable agricultural practices in saline soils and emphasizes the pivotal role of plant-metabolite-microbe interactions in abiotic stress mitigation.},
}
@article {pmid40376462,
year = {2025},
author = {Han, Y and Cao, B and Tang, J and Wang, J},
title = {A comprehensive multi-omics analysis uncovers the associations between gut microbiota and pancreatic cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592549},
pmid = {40376462},
issn = {1664-302X},
abstract = {Pancreatic cancer is one of the most lethal malignant neoplasms. Pancreatic cancer is related to gut microbiota, but the associations between its treatment and microbial abundance as well as genetic variations remain unclear. In this study, we collected fecal samples from 58 pancreatic cancer patients including 43 pancreatic ductal adenocarcinoma (PDAC) and 15 non-PDAC, and 40 healthy controls, and shotgun metagenomic sequencing and untargeted metabolome analysis were conducted. PDAC patients were divided into five groups according to treatment and tumor location, including treatment-naive (UT), chemotherapy (CT), surgery combined with chemotherapy (SCT), Head, and body/tail (Tail) groups. Multivariate association analysis revealed that both CT and SCT were associated with increased abundance of Lactobacillus gasseri and Streptococcus equinus. The microbial single nucleotide polymorphisms (SNPs) densities of Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus were positively associated with CT, while Lachnospiraceae bacterium 2_1_58FAA was positively associated with Head group. Compared with Tail group, the Head group showed positive associations with opportunistic pathogens, such as Escherichia coli, Shigella sonnei and Shigella flexneri. We assembled 424 medium-quality non-redundant metagenome-assembled genomes (nrMAGs) and 276 high-quality nrMAGs. In CT group, indole-3-acetic acid, capsaicin, sinigrin, chenodeoxycholic acid, and glycerol-3-phosphate were increased, and the accuracy of the model based on fecal metabolites reached 0.77 in distinguishing healthy controls and patients. This study identifies the associations between pancreatic cancer treatment and gut microbiota as well as its metabolites, reveals bacterial SNPs are related to tumor location, and extends our knowledge of gut microbiota and pancreatic cancer.},
}
@article {pmid40376454,
year = {2025},
author = {Yu, T and Cheng, L and Zhang, Q and Yang, J and Zang, H and Zeng, Z and Yang, Y},
title = {Characterization of antibiotic resistance genes and virulence factors in organic managed tea plantation soils in southwestern China by metagenomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1580450},
pmid = {40376454},
issn = {1664-302X},
abstract = {Sustainable organic management practices have gained significant attentions for its potential health and environmental benefits. However, the spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils, plants, and agricultural products has severely limited the development of organic managements on agriculture. At present, the distribution and assembly of ARGs and VFs in organic managed tea plantation systems remains largely unknown. Here, we used metagenomic analysis to explore soil microbial taxa, ARGs and VFs in 20 years of conventional managed (CM) and organic managed (OM) tea plantation soils. Results showed that total abundance of ARGs in OM was 16.9% (p < 0.001) higher than that in CM, and the increased ARGs were rpoB2, evgS, MuxB, TaeA, and efrA. As for VFs, OM significantly increased the abundance of adherence, stress protein and actin-based motility compared to CM. Moreover, OM increased the relative abundance of soil microbial taxa harboring ARGs and VFs, which were Streptomyces, Pseudomonas, and Terrabacter, compared to CM. Network analysis suggested that OM increased the positive interactions of microbial taxa-ARGs, microbial taxa-VFs and ARGs-VFs compared to CM. Impact of stochastic process on the assembly of soil microbial taxa, ARGs and VFs in OM was stronger than that in CM. Overall, these findings provide a basis for integrating ARGs, VFs and pathogen hosts to assess the ecological and health risks in long-term organic managed soils, and increased efforts need to be done in reducing ARGs, VFs and bacterial pathogens in fertilizers for organic managements on agriculture.},
}
@article {pmid40375904,
year = {2025},
author = {Santarelli, G and Bianco, DM and Capriati, M and Sanguinetti, M and Rendeli, C and De Maio, F},
title = {Bladder Microbiota Snapshots Help to Monitor Urinary Tract Infections in Vulnerable Patients.},
journal = {Mediterranean journal of hematology and infectious diseases},
volume = {17},
number = {1},
pages = {e2025028},
pmid = {40375904},
issn = {2035-3006},
}
@article {pmid40375895,
year = {2025},
author = {Chen, S and Ouyang, T and Wang, K and Hou, X and Zhang, R and Li, M and Zhang, H and He, Q and Li, X and Liu, Z and Wang, X and Huang, B},
title = {Application of metagenomic next-generation sequencing in pathogen detection of lung infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1513603},
pmid = {40375895},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/genetics/isolation &amp; purification/classification ; Adult ; Viruses/genetics/isolation &amp; purification/classification ; Fungi/genetics/isolation &amp; purification/classification ; Sensitivity and Specificity ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; *Lung Diseases/microbiology/diagnosis ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely reported to provide crucial information for the diagnosis and treatment of infectious diseases. In this study, we aimed to evaluate mNGS in pathogens diagnosis of lung infections.<br><br>METHODS: A total of 188 patients who were suspected of pulmonary infection and received medical treatment at the Second Affiliated Hospital of Nanchang University from August 2022 to December 2023 were enrolled in this study. Conventional microbiological tests (CMTs) and mNGS were employed for pathogens diagnosis.<br><br>RESULTS: Statistical results indicated that mNGS were significantly better than CMTs in sensitivity, negative predictive value, and negative likelihood ratio. Remarkably, the positive detection rate of mNGS was significantly higher than that of CMTs (86.17% vs 67.55%, P < 0.01). Through mNGS, we identified 96 pathogens, comprising 59 bacteria, 18 fungi, 15 viruses, and 4 special pathogens. In contrast, CMTs detected 28 species, including 25 bacteria and 3 fungi. The effectiveness rate of antibiotic treatment decisions based on mNGS results was 40.60%. Out of 54 cases with positive treatment impacts, mNGS results contributed to the treatment and improved prognosis of 16 infections caused by atypical pathogens.<br><br>CONCLUSION: Our results proved the essential role of mNGS in lung infection diagnosis, enabling early detection and the prompt development of targeted anti-infection therapies. We recommended that the clinical application of mNGS can enhance treatment effectiveness and improve patient prognosis.},
}
@article {pmid40375193,
year = {2025},
author = {Chen, P and Wei, X and Que, T and Yan, T and Li, S and Zhong, Y and Li, Y and He, M and Liu, W and Hu, Y},
title = {Molecular detection of novel Jingmen tick virus in hard ticks from diverse hosts in Guangxi, southwestern China.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {143},
pmid = {40375193},
issn = {1743-422X},
support = {2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; 2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; 2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; No. Guike AB22035027//Guangxi Key Research and Development Program/ ; 2023YFC2605400//National Natural Science Foundation of China/ ; },
mesh = {Animals ; China ; Phylogeny ; *Ixodidae/virology/classification ; Genome, Viral ; Genetic Variation ; Metagenomics ; Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Ticks are the second most important vectors of arboviruses after mosquitoes, and they also serve as reservoir hosts for some zoonotic diseases. It is essential to understand the prevalence of tick-borne viruses in ticks from different sampling sites and vectors, as this information can facilitate the surveillance and prevention of arboviral infectious diseases.<br><br>METHODS: We systematically collected ticks from a variety of animals, including wildlife and domestic livestock, across 18 distinct regions in Guangxi Zhuang Autonomous Region(Guangxi). We then identified the ticks using traditional morphological classification and molecular biology methods to investigate the diversity of ticks in the regionWe also systematically examined the diversity of viruses carried by ticks using comprehensive virological methods based on viral metagenomics. We performed phylogenetic and recombination analyses for the assembled viral sequences.<br><br>RESULTS: We collected 1286 Ixodidae from 18 sampling sites in 17 districts of Guangxi. We identified 4 genera and 6 species of Ixodidae. We annotated 2 unclassified viruses and 13 known viral families. We assembled 208 nucleotide sequences and obtained six near full-length sequences of Jingmen tick virus (JMTV). Among these sequences, GXTV-PC4.2 and GXTV-43 were new mutant strains of JMTV. We detected genetic recombination of JMTV in segments 2, 3, and 4 of JMTV.<br><br>CONCLUSIONS: Our study uncovers a diverse tick fauna in Guangxi, including 4 genera and 6 species, and a broad virome with 13 viral families and 2 novel viruses. The JMTV, in particular, shows significant genetic diversity and potential for cross-species transmission, marked by new strains and recombination events. These findings underscore the need for vigilant tick-borne disease surveillance in Guangxi.},
}
@article {pmid40375084,
year = {2025},
author = {Rahman Hera, M and Koslicki, D},
title = {Estimating similarity and distance using FracMinHash.},
journal = {Algorithms for molecular biology : AMB},
volume = {20},
number = {1},
pages = {8},
pmid = {40375084},
issn = {1748-7188},
support = {R01GM146462//National Institutes of Health, United States/ ; R01GM146462//National Institutes of Health, United States/ ; },
abstract = {MOTIVATION: The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing k -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the containment and Jaccard indices. However, theoretical investigations for other metrics are still lacking.<br><br>THEORETICAL CONTRIBUTIONS: In this paper, we present a theoretical framework for estimating similarity/distance metrics by using FracMinHash sketches, when the metric is expressible in a certain form. We establish conditions under which such an estimation is sound and recommend a minimum scale factor s for accurate results. Experimental evidence supports our theoretical findings.<br><br>PRACTICAL CONTRIBUTIONS: We also present frac-kmc, a fast and efficient FracMinHash sketch generator program. frac-kmc is the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. frac-kmc is also the first parallel tool for this task, allowing for speeding up sketch generation using multiple CPU cores - an option lacking in existing serialized tools. We show that by computing FracMinHash sketches using frac-kmc, we can estimate pairwise similarity speedily and accurately on real data. frac-kmc is freely available here: https://github.com/KoslickiLab/frac-kmc/.},
}
@article {pmid40374064,
year = {2025},
author = {Wang, J and Zhou, Y and Zhang, T and Zhang, Y and Lian, Q},
title = {Pre-treatment of excess sludge with sulfide-containing wastewater for composite electron donor formation to enhance denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132673},
doi = {10.1016/j.biortech.2025.132673},
pmid = {40374064},
issn = {1873-2976},
abstract = {Utilizing the fermentation liquor of excess sludge (ES) for the denitrification process represents an effective strategy for the valorization of ES and achieving environmentally friendly denitrification. However, ES fermentation technologies require significant energy or chemical product inputs. The present study proposes a novel method utilizing sulfide-containing wastewater to pretreat ES for generating dissolved organic matter (DOM), with sulfides and DOM collectively forming a composite electron donor (S-ES-DOM). The introduction of S-ES-DOM enables the establishment of integrated autotrophic and heterotrophic denitrification (IAHD) process, achieving 100 % denitrification efficiency. Molecular analysis identified an increase in biodegradable components within S-ES-DOM, which were effectively utilized during the IAHD process. The functional genes associated with nitrate-sulfide-organic carbon metabolism and electron transfer exhibited upregulation. The mixotrophic microbial community enables flexible adoption of multiple metabolic pathways. This strategy simultaneously achieves low-cost ES valorization and low-carbon nitrate/sulfide removal through integrated nitrogen-sulfur-carbon metabolism.},
}
@article {pmid40373994,
year = {2025},
author = {Pereira, S and Rubina, M and Roga, A and Selga, T and Skinderskis, E and Gudrā, D and Kalniņa, I and Vonda, K and Fridmanis, D and Muter, O},
title = {Evaluation of functional capacity and plastic-degrading potential of Bacillus spp. and other bacteria derived from the Getliņi landfill (Latvia).},
journal = {Environmental research},
volume = {},
number = {},
pages = {121849},
doi = {10.1016/j.envres.2025.121849},
pmid = {40373994},
issn = {1096-0953},
abstract = {The mechanisms of plastic biodegradation by microorganisms remain poorly understood because of high variability in environmental conditions. This study aimed to isolate, identify, and characterise bacteria with plastic-degrading potential derived from the Getliņi EKO landfill (Riga, Latvia). Among the bacteria selected, Bacillus was the predominant genus identified, whereas Pseudomonas dominated the metagenome. Comparative testing revealed the highest non-specific esterase activity in cultures of B. licheniformis and B. altitudinis. Following a 6-week batch experiment, a newly developed bacterial consortium biologically reduced the weight of untreated low-density polyethylene (LDPE), polyethylene terephthalate (PET), and high-density polyethylene (HDPE) by 19.44%, 5.99%, and 2.58%, respectively. Thermally pre-treated PET and acid pre-treated HDPE resulted in greater weight losses than their respective untreated forms. Scanning electron microscopy primarily showed single cells and microcolonies attached to the granule surfaces. Microbial respiration and fluorescein diacetate hydrolysis tests suggested that the granules had a stimulating effect on the metabolic activity of planktonic cells. Cultures with untreated LDPE and PET exhibited the highest ecotoxicity for Thamnocephalus platyurus, reducing ingestion activity by 60.39% and 71.25% of the control, respectively. In conclusion, the Getliņi EKO landfill appears to be a promising sampling source for bacteria capable of biodegrading fossil-based polymers. Further refinement of methods for the isolation and evaluation of plastic degraders will provide new insights into the potential of microbial resources for plastic degradation.},
}
@article {pmid40373900,
year = {2025},
author = {Yin, CY and Sadiq, H and Liao, WH and Wang, HN and Fu, Z and Yu, WG and Han, F},
title = {Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144153},
doi = {10.1016/j.ijbiomac.2025.144153},
pmid = {40373900},
issn = {1879-0003},
abstract = {Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.},
}
@article {pmid40373514,
year = {2025},
author = {Tong, X and Zhang, X and Fu, J and He, R},
title = {Mechanisms on nitrogen amendment stimulating methane oxidation in landfill cover soils.},
journal = {Waste management (New York, N.Y.)},
volume = {203},
number = {},
pages = {114893},
doi = {10.1016/j.wasman.2025.114893},
pmid = {40373514},
issn = {1879-2456},
abstract = {Landfill cover soil plays a pivotal role in mitigating CH4 input to the atmosphere. However, the community and activity of methane-oxidizing bacteria (MOB), and their responses to nutrient amendment remain insufficiently understood in landfill cover soils. In this study, the influencing mechanisms of nitrogen amendment on MOB activity, and their functional microorganisms and genes were investigated in landfill cover soils. An exogenous ammonium and nitrate addition could enhance CH4 oxidation activity of 13.9-34.1 times in the landfill cover soil. The NH4[+]-N addition of 800 mg kg[-1] could cause a maximum nitrite accumulation of 41.2 mg kg[-1] in the landfill cover soils and inhibit CH4 oxidation. Nitrogen was mainly deposited in the landfill cover soil in the form of organic nitrogen, with a slight loss of 1.47-3.21 % in the treatments amended with ammonium and nitrate at each stage. A high CH4 oxidation could increase the secretion of CH4-derived carbon and improve the organic matter of soil. Compared with ammonium, the nitrate addition had a greater stimulating effect on microbial and MOB growth. Type I MOB predominated in the soils amended with ammonium and nitrate, whereas type II MOB dominated in the nitrogen-deficient soils. Metagenomic analysis showed that the genes related to nitrogen fixation (nifDKH) were more abundant in the nitrogen-deficient soil than the others. These findings suggest that an appropriate ammonium and nitrate addition could induce carbon and nitrogen accumulation, and stimulate microbial metabolism such as CH4 oxidation and element cycles in the landfill cover soils to mitigate CH4 emission.},
}
@article {pmid40373448,
year = {2025},
author = {Liu, H and Fan, Y and Su, E and Liu, S and Ming, Y and Huang, Z and Yu, H and Liu, F and Wang, C and Yu, X and Niu, M and Wu, K and Yang, Y and He, Z and Zhang, T and Yan, Q},
title = {Mariculture increases microbially-driven carbon metabolism and sequestration in coastal ecosystems.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125756},
doi = {10.1016/j.jenvman.2025.125756},
pmid = {40373448},
issn = {1095-8630},
abstract = {Mariculture has expanded significantly in recent decades due to rising seafood demand and its contribution to ocean carbon sequestration. While the mechanisms of carbon sequestration in mariculture are well-established, the roles of microorganisms in sedimentary carbon sequestration have rarely been explored. How microorganisms mediate organic carbon metabolism and their effects on coastal carbon pools remain unclear. Here we tested the carbon fraction and contents, as well as extracellular hydrolase activities in macroalgae culture area, fish or abalone culture area, and control area without mariculture. We profiled microbial community composition and carbon metabolism characteristics in sediments through 16S rRNA gene amplicon sequencing and metagenomics. Our findings revealed that macroalgae culture areas exhibited a significantly greater potential for carbon sequestration than the control area, the concentration of TOC in seawater and the contents of SOC, DOC, and ROC in sediments were significantly (p < 0.05) increased by 18.93 %, 6.98 %, 33.98 %, and 18.30 % respectively. These results can be attributed to decreased activities of extracellular hydrolase and a lower abundance of carbon-degrading genes. Moreover, metabolic profiling identified taxa from families such as Alteromonadaceae, Pseudomonadaceae, Rhodobacteraceae, Enterobacteriaceae, and Flavobacteriaceae, which are highly metabolically flexible in utilizing a wide range of organic and inorganic energy sources, playing crucial roles in carbon formation. Their respiratory metabolism, such as sulfate reduction, thiosulfate oxidation, and denitrification as well as secondary metabolism products could also affect the formation and persistence of sedimentary carbon pools. Specifically, increased total nitrogen (TN) and nitrate-nitrogen (NO3[-]) could potentially enhance microbial degradation of organic carbon, decreasing carbon stock within coastal sediments. This study enhanced our understanding of microbial regulation of the organic carbon pool in the mariculture ecosystem.},
}
@article {pmid40373419,
year = {2025},
author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS},
title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.},
journal = {Meat science},
volume = {226},
number = {},
pages = {109848},
doi = {10.1016/j.meatsci.2025.109848},
pmid = {40373419},
issn = {1873-4138},
abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.},
}
@article {pmid40373403,
year = {2025},
author = {Zhao, F and Wu, S and Shen, X and Huang, Y and Zhang, B and Luo, Z and Wu, D and Shen, L and Cao, S and Wang, Y and Zhang, J and Yu, S},
title = {Metagenomic analysis reveals the diversity, transmission and potential ecological risks of yak nasal bacteria-carried antibiotic resistance genes in the Sichuan region of Qinghai-Tibet plateau.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138476},
doi = {10.1016/j.jhazmat.2025.138476},
pmid = {40373403},
issn = {1873-3336},
abstract = {The Qinghai-Tibet Plateau (QTP) and yaks play respectively vital roles in global and plateau ecosystems. Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants. However, few studies have investigated the abundance and diversity of ARGs and mobile genetic elements (MGEs) in the yak upper respiratory tract and their surrounding pastures. Moreover, the possible pathways for ARG transmission within these ecosystems have not yet been elucidated. Therefore, we investigated the ARG profiles, MGE profiles, and ARG-carrying host bacteria in yaks and their pasture collected from Ganzi and Aba region in Sichuan Province. Metagenomic analyses showed that 22 ARG types and 5 MGEs types were identified in 18 samples. Multidrug resistance gene (mexT) and bacitracin resistance gene (bacA) was identiffed as hotspots, which may compromise medical treatment options. Co-occurrence network analysis revealed that 12 bacterial genera may be potential hosts at the genus level. The enrich of ARGs and MGEs diversity were observed in QTP (Sichuan province) pasture ecosystems which demands evidence-based interventions to mitigate ARGs transmission risks.},
}
@article {pmid40373385,
year = {2025},
author = {Xu, Z and Pei, Y and Wang, H and Li, X},
title = {Comparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {55},
number = {},
pages = {101530},
doi = {10.1016/j.cbd.2025.101530},
pmid = {40373385},
issn = {1878-0407},
abstract = {Bile acids (BAs) are cholesterol derivatives synthesized by the liver, exhibit variation between different species. Researchers have long appreciated that microbiota play the roles in the biotransformation of BAs. However, relatively few studies have been reported on microbial-mediated production and transformation of BAs in amphibians. Our focus here is principally on difference of intestinal microbial diversity and BAs profiles between two common amphibians, Bufo gargarizans (B. gargarizans) and Rana chensinensis (R. chensinensis) tadpoles, through intestinal targeted BAs metabolomics and fecal metagenomic sequencing. The results demonstrated that B. gargarizans possessed higher levels of total BAs and higher ratio of unconjugated / conjugated BAs. In addition, the relative abundance of microbiota with bile salt hydrolase (BSH) activity in B. gargarizans was significantly higher than that of R. chensinensis, which may facilitate the conversion of conjugated to unconjugated BAs. Meanwhile the higher prevalence of bile-acid-induced (BAI) gene encoding microbiota in R. chensinensis may promote the synthesis of deoxycholic acid (DCA). Furthermore, discrepancies in virulence factors (VFs) and energy metabolism were observed between the two species, which may be linked to differences in the microbiota. This study revealed substantial differences in intestinal microbes and BAs across amphibian species, emphasizing the significant impact of intestinal microbes on BAs metabolism.},
}
@article {pmid40373374,
year = {2025},
author = {Li, Y and Bhatt, P and Xagoraraki, I},
title = {In-depth comparison of untargeted and targeted sequencing for detecting virus diversity in wastewater.},
journal = {Water research},
volume = {283},
number = {},
pages = {123803},
doi = {10.1016/j.watres.2025.123803},
pmid = {40373374},
issn = {1879-2448},
abstract = {Sequencing approaches may enable monitoring of a broad range of viruses in wastewater, including potential emerging and non-reportable human viruses. Considering the fact that metagenomic sequencing may be non-specific for low-abundance human viruses, integration of viral amplification and enrichment strategies are proposed to enhance the accurate detection of a broad range of human viruses in municipal wastewater. In this study, we focused on the in-depth comparison analysis of three untargeted amplification methods (Multiple Displace Amplification [MDA], Reverse Transcription - MDA [RT-MDA], and a PCR-based random amplification [PCR-based]) and one targeted method (Twist Comprehensive Viral Research Panel [TWIST]) for detecting virus diversity in wastewater. In addition, we included the comparisons of two extraction kits (Qiagen QIAamp VIRAL RNA Mini Kit and ZymoBIOMICSTM DNA/RNA Minipre Kit) and four virus identification tools (Diamond blast, Kraken2, VirSorter2 and geNomad) for a systematic study. Performances of Qiagen and Zymo extraction kits in recovering viruses and human viruses in wastewater were comparable. By the three untargeted methods we detected 12,808 contigs with lengths longer than 10,000 bp. No contig longer than 10,000 bp was detected by the targeted method. Presence of human viruses were analyzed further by comparing the viral contigs against a custom Swiss-Prot human virus database. There were 45 viruses that are potentially associated with human health found in wastewater, 8 of them were unique to the targeted method and 7 of them were unique to the three untargeted methods. Four enteric viruses Mamastrovirus, Norovirus, Rotavirus and Sapovirus were detected with high abundance in samples prepared with the targeted method. Dimensional scaling analysis demonstrated the divergent virus and human virus communities from the untargeted and targeted methods. Patterns of virus and human virus populations identified by Kraken2 and geNomad were similar. Presence of selected viruses (SARS-CoV-2 [N1&amp;N2], SC2, RSV, Norovirus GI and GII) were confirmed with ddPCR. This work indicates integration of untargeted and targeted sequencing methods, and complementary ddPCR can ensure the accurate detection of known and novel viruses using wastewater surveillance.},
}
@article {pmid40372916,
year = {2025},
author = {Ramar, M and Wiscovitch-Russo, R and Yano, N and Singh, H and Lamere, E and Short, M and Gonzalez-Juarbe, N and Fedulov, AV},
title = {Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115684},
doi = {10.1016/j.celrep.2025.115684},
pmid = {40372916},
issn = {2211-1247},
abstract = {Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.},
}
@article {pmid40372723,
year = {2025},
author = {Al-Najim, A and Hauns, S and Tran, VD and Backofen, R and Alkhnbashi, OS},
title = {HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40372723},
issn = {2047-217X},
support = {2168/23//Deutsche Forschungsgemeinschaft/ ; 2168/25-1//Deutsche Forschungsgemeinschaft/ ; //University of Freiburg/ ; },
mesh = {*Deep Learning ; *Metagenomics/methods ; *Bacteriophages/genetics ; Genome, Viral ; *DNA, Viral/genetics ; Metagenome ; *Computational Biology/methods ; *Sequence Analysis, DNA/methods ; Humans ; *Software ; },
abstract = {BACKGROUND: Bacteriophages are among the most abundant organisms on Earth, significantly impacting ecosystems and human society. The identification of viral sequences, especially novel ones, from mixed metagenomes is a critical first step in analyzing the viral components of host samples. This plays a key role in many downstream tasks. However, this is a challenging task due to their rapid evolution rate. The identification process typically involves two steps: distinguishing viral sequences from the host and identifying if they come from novel viral genomes. Traditional metagenomic techniques that rely on sequence similarity with known entities often fall short, especially when dealing with short or novel genomes. Meanwhile, deep learning has demonstrated its efficacy across various domains, including the bioinformatics field.<br><br>RESULTS: We have developed HVSeeker-a host/virus seeker method-based on deep learning to distinguish between bacterial and phage sequences. HVSeeker consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. In addition to the robust architecture of HVSeeker, three distinct preprocessing methods were introduced to enhance the learning process: padding, contigs assembly, and sliding window. This method has shown promising results on sequences with various lengths, ranging from 200 to 1,500 base pairs. Tested on both NCBI and IMGVR databases, HVSeeker outperformed several methods from the literature such as Seeker, Rnn-VirSeeker, DeepVirFinder, and PPR-Meta. Moreover, when compared with other methods on benchmark datasets, HVSeeker has shown better performance, establishing its effectiveness in identifying unknown phage genomes.<br><br>CONCLUSIONS: These results demonstrate the exceptional structure of HVSeeker, which encompasses both the preprocessing methods and the model design. The advancements provided by HVSeeker are significant for identifying viral genomes and developing new therapeutic approaches, such as phage therapy. Therefore, HVSeeker serves as an essential tool in prokaryotic and phage taxonomy, offering a crucial first step toward analyzing the host-viral component of samples by identifying the host and viral sequences in mixed metagenomes.},
}
@article {pmid40372371,
year = {2025},
author = {Li, X and He, N and Wang, H and Wu, Z and Wang, M and Liang, H and Xiao, L and Yang, Z and Li, C and Xu, P and Dai, T and Li, S and Zou, Y},
title = {Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf119},
pmid = {40372371},
issn = {1365-2672},
abstract = {AIMS: This study explores the impact of Faecalibacterium longum CM04-06 on inflammatory bowel disease (IBD) by regulating gut microbiota in mice.<br><br>METHODS AND RESULTS: We reanalyzed the distribution of the CM04-06 genome in the metagenome of the IBD cohort and observed a significantly higher abundance of CM04-06 in healthy individuals compared to patients with UC or CD. The prophylactic administration of CM04-06 was evaluated for its effects on intestinal microbial diversity and community composition after a two-week trial in mice. The intestinal microbiota was characterized using metagenomic sequencing of fecal samples on the DNBSEQ platform. CM04-06 treatment resulted in a significant reduction in the Disease Activity Index (DAI) and histological scores, as well as a decrease in the levels of pro-inflammatory cytokines, including IL-1&#x3b2;, IL-6, and TNF-&#x3b1;, in both the colon and serum of DSS-induced mice. Furthermore, supplementation with CM04-06 significantly reduced the levels of pro-inflammatory cytokines in both the colon and serum. Additionally, CM04-06 enhanced the integrity of the intestinal epithelial barrier by increasing the expression of tight junction proteins and mucin. Moreover, we observed greater abundances of Faecalibaculum rodentium, Alistipes onderdonkii, Alistipes shahii, and Bifidobacterium animalis after CM04-06 treatment.<br><br>CONCLUSIONS: CM04-06 prevents and alleviates intestinal inflammation by modulating the composition of the microbiota community, increasing the abundance of beneficial probiotics, and suppressing pro-inflammatory cytokine levels.},
}
@article {pmid40372056,
year = {2025},
author = {Kok, CR and Thissen, JB and Cerroni, M and Tribble, DR and Cancio, A and Tran, S and Schofield, C and Colombo, RE and Troth, T and Joya, C and Lalani, T and Be, NA},
title = {Field expedient stool collection methods for gut microbiome analysis in deployed military environments.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081824},
doi = {10.1128/msphere.00818-24},
pmid = {40372056},
issn = {2379-5042},
abstract = {Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.},
}
@article {pmid40371968,
year = {2025},
author = {Jansen, D and Deleu, S and Caenepeel, C and Marcelis, T and Simsek, C and Falony, G and Machiels, K and Sabino, J and Raes, J and Vermeire, S and Matthijnssens, J},
title = {Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2499575},
doi = {10.1080/19490976.2025.2499575},
pmid = {40371968},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/virology/microbiology ; *Virome ; Male ; Female ; Feces/virology ; Adult ; Gastrointestinal Microbiome ; Middle Aged ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Young Adult ; },
abstract = {Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.},
}
@article {pmid40371337,
year = {2025},
author = {Lehner, MD and Ulsemer, P and Christochowitz, S},
title = {Menthacarin, a proprietary combination of peppermint and caraway oil, alters cultured human fecal microbiota composition, resulting in increased SCFA production.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1569052},
pmid = {40371337},
issn = {1663-9812},
abstract = {BACKGROUND: Disruptions in the gut microbiota metabolism may contribute to the pathophysiology of gut-brain interaction disorders, and correction of intestinal dysbiosis is considered a promising therapeutic approach. Menthacarin, a proprietary fixed combination of Mentha x piperita L. and Carum carvi L. essential oils, is used clinically for the treatment of functional dyspepsia and irritable bowel syndrome. Rodent model data indicate that treatment effects of Menthacarin on visceral hypersensitivity could be mediated via the normalization of gut dysbiosis. However, the impact of Menthacarin on human bacterial gut microbiota has not yet been studied.<br><br>AIM: The aim of the present study was to assess whether Menthacarin affects the composition and metabolic activity of human fecal microbiota.<br><br>METHODS: Fecal slurry samples from 10 healthy volunteers were cultivated for 36&#xa0;h under anoxic conditions with and without Menthacarin. Relative bacterial abundance at the phylum and genus levels was evaluated using 16S rRNA metagenomic analysis. Short-chain fatty acids (SCFAs) in the supernatants were measured using the LC-MS technology.<br><br>RESULTS: Menthacarin induced robust changes in microbial composition at both the phylum and genus levels among the 10 donor microbiomes. The relative abundance of Firmicutes (+13.6 &#xb1; 8.6%) and Actinobacteria (+54.9 &#xb1; 47.6%) significantly increased, whereas that of Bacteroidetes (-27.7% &#xb1; 21.9%) and Proteobacteria (-25.7% &#xb1; 12.3%) significantly decreased in the presence of Menthacarin. At the genus level, the most notable changes were significant increases in Bifidobacterium (+105.1 &#xb1; 78.4%) and several SCFA-producing genera accompanied by a significant decrease in genera containing members involved in pro-inflammatory processes. In addition, Menthacarin significantly increased the levels of several SCFAs, namely, propionate, butyrate, isobutyrate, valerate, and isovalerate.<br><br>CONCLUSION: Menthacarin alters the microbiota composition and enhances SCFA production in human microbiota samples under in vitro conditions. These effects may contribute to the clinical benefits observed with Menthacarin treatment.},
}
@article {pmid40371178,
year = {2025},
author = {Lanclos, VC and Feng, X and Cheng, C and Yang, M and Hider, CJ and Coelho, JT and Kojima, CY and Barnes, SJ and Cleveland, CS and Xie, M and Zhao, Y and Luo, H and Thrash, JC},
title = {New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf068},
pmid = {40371178},
issn = {2730-6151},
abstract = {The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007[T] (= ATCC TSD-433[T] = NCMA B160[T]).},
}
@article {pmid40370734,
year = {2025},
author = {Yu, F and Guo, Y and Li, Y and Gai, W and Zhang, Q and Li, P and Xu, R and Zhang, L and Zheng, Y and Zhang, X},
title = {Liver abscess and septic shock due to Clostridium perfringens infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1575454},
pmid = {40370734},
issn = {2296-858X},
abstract = {Clostridium perfringens causes liver abscesses with a low incidence, rapid progression, and high mortality. Within a few days or even within 24 h, patients may progress from a liver abscess to sepsis, multi-organ failure, and potentially death. Diagnosing Clostridium perfringens infection by routine microbiological testing (CMT) is often challenging. Here, we present a patient with negative blood cultures who was ultimately diagnosed with a liver abscess due to Clostridium perfringens infection, confirmed by metagenomic next-generation sequencing (mNGS). The patient initially presented with fever only, and his blood cultures were negative. Subsequently, the patient's condition progressed rapidly, and he developed signs of septic shock. Immediately after admission to the ICU, he received combined anti-infective therapy with meropenem and tigecycline, as well as urgent ultrasound-guided puncture and drainage. Blood mNGS identified Clostridium perfringens and a variety of anaerobic bacteria, confirming that the pathogen had been covered by empirical antibiotics. Continued anti-infective therapy and drainage improved the patient's symptoms, and he was eventually discharged from the hospital. Clinicians should be highly suspicious of liver abscesses with negative blood cultures. The use of mNGS to identify the pathogen, appropriate antibiotics, and abscess aspiration and drainage are key to patient survival.},
}
@article {pmid40370716,
year = {2025},
author = {Yang, Z and Zhou, S and Yang, Z and Liu, P and Chen, S and Zhu, W},
title = {Metagenomic next-generation sequencing enabled diagnosis of Aspergillus spondylitis in an immunocompetent patient: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1575363},
pmid = {40370716},
issn = {2296-858X},
abstract = {BACKGROUND: Aspergillus fumigatus spondylitis is a rare fungal spondylitis that often occurs in immunocompromised patients. This article reports a case of Aspergillus spondylitis with specific image signs, which is rarely reported in an immunocompetent patient.<br><br>CASE PRESENTATION: This is a case of L3-4 segmental Aspergillus spondylitis diagnosed. The diagnosis was confirmed by intraoperative metagenomic next-generation sequencing (mNGS) testing of the diseased tissue. The patient was treated with voriconazole and underwent surgical debridement and internal fixation with pedicle screws.<br><br>CONCLUSION: The diagnosis of Aspergillus spondylitis is often delayed or missed. Doctors should consider Aspergillus spondylitis in the differential diagnosis of unexplained low back pain so that appropriate treatment can be administered to prevent spinal cord injury and disability. Aspergillus spondylitis usually results in endplate inflammatory response line on fluid or enhancement sequences and a diffuse low signal in the diseased vertebral body on T2-weighted imaging (T2WI). It also results in large paraspinal abscesses, which requires further research to better differentiate between Aspergillus spondylitis and tuberculous spondylitis. Prompt diagnosis and treatment can improve the patient's prognosis.},
}
@article {pmid40370098,
year = {2025},
author = {Wang, N and Wu, M and Gu, W and Dai, C and Shao, Z and Subbalakshmi, KP},
title = {MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
pmid = {40370098},
issn = {1477-4054},
support = {JUSRP123035//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Computational Biology/methods ; Algorithms ; },
abstract = {More and more recent studies highlight the crucial role of the human microbiome in maintaining health, while modern advancements in metagenomic sequencing technologies have been accumulating data that are associated with human diseases. Although metagenomic data offer rich, multifaceted information, including taxonomic and functional abundance profiles, their full potential remains underutilized, as most approaches rely only on one type of information to discover and understand their related correlations with respect to disease occurrences. To address this limitation, we propose a multistage fusion tabular transformer architecture (MSFT-Transformer), aiming to effectively integrate various types of high-dimensional tabular information extracted from metagenomic data. Its multistage fusion strategy consists of three modules: a fusion-aware feature extraction module in the early stage to improve the extracted information from inputs, an alignment-enhanced fusion module in the mid stage to enforce the retainment of desired information in cross-modal learning, and an integrated feature decision layer in the late stage to incorporate desired cross-modal information. We conduct extensive experiments to evaluate the performance of MSFT-Transformer over state-of-the-art models on five standard datasets. Our results indicate that MSFT-Transformer provides stable performance gains with reduced computational costs. An ablation study illustrates the contributions of all three models compared with a reference multistage fusion transformer without these novel strategies. The result analysis implies the significant potential of the proposed model in future disease prediction with metagenomic data.},
}
@article {pmid40369676,
year = {2025},
author = {Zhang, Y and Liu, H and Jing, H},
title = {Community differences and potential function along the particle size spectrum of microbes in the twilight zone.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {121},
pmid = {40369676},
issn = {2049-2618},
support = {424QN341//the Hainan Provincial Natural Science Foundation of China/ ; JRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; 2023YFC2812804//the National Key R&amp;D Program of China/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; },
mesh = {Particle Size ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Seawater/microbiology/chemistry ; *Microbiota/genetics ; Metagenomics/methods ; Carbon/metabolism ; Metagenome ; },
abstract = {BACKGROUND: The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.<br><br>RESULTS: Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.<br><br>CONCLUSION: Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.},
}
@article {pmid40369669,
year = {2025},
author = {Purse, C and Parker, A and James, SA and Baker, DJ and Moss, CJ and Evans, R and Durham, J and Funnell, SGP and Carding, SR},
title = {Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {47},
pmid = {40369669},
issn = {2524-4671},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//BBSRC/ ; },
abstract = {BACKGROUND: Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.<br><br>RESULTS: Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20&#xa0;years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.<br><br>CONCLUSIONS: We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.},
}
@article {pmid40368959,
year = {2025},
author = {Song, XL and Wang, ZJ and Yin, XW and Sun, YL and Jang, DJ and Hong, SK},
title = {The impact of nitrogen deposition on nitrogen metabolism in ryegrass lawn with different soil nutrient levels.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16755},
pmid = {40368959},
issn = {2045-2322},
mesh = {*Nitrogen/metabolism ; *Lolium/metabolism ; *Soil/chemistry ; Soil Microbiology ; Nitrogen Fixation ; Nitrification ; *Nutrients/metabolism ; Denitrification ; Nitrogen Cycle ; Microbiota ; Nitrates/metabolism ; },
abstract = {Nitrogen deposition is a crucial factor in global change, which is widespread across various regions globally. It has drawn extensive attention due to its direct modification of soil nitrogen retention and nitrogen species distribution, thereby influencing nitrogen metabolism across entire ecosystems. Previous studies on its influence on nitrogen metabolism have not reached a consensus. In an urban ryegrass lawn mesocosm experiment, we set two levels of nitrogen deposition and soil nutrients respectively, aiming to study the impacts of these factors on the N-cycling process through metagenomic analysis. The results demonstrated nitrogen deposition increased nitrification, nitrogen fixation, denitrification, and dissimilatory nitrate reduction, but decreased assimilatory nitrate reduction in the nitrogen metabolism process by changing soil nitrogen availability and the abundance of N-cycling functional genes in the soil microbial community. The soil nutrient levels exhibited effects opposite to those of nitrogen deposition, negatively impacting nitrification, denitrification, and nitrogen fixation in the nitrogen metabolism process. This work further elucidates the impacts of nitrogen deposition on the ecological functions of the ryegrass lawn with different soil nutrient levels, and predicts the potential impacts of intensified nitrogen deposition on these ecological functions. It provides valuable theoretical support for understanding and evaluating complex ecological interactions.},
}
@article {pmid40368955,
year = {2025},
author = {Krishnavajhala, A and Gingras, MC and Urquieta, E and Chao, H and Bandaranaike, D and Chen, Y and Bhamidipati, S and Korchina, V and Griffin, SM and Masternak, MM and Moreno, H and Mohammed, J and Murugan, M and Posey, JE and Wu, JH and Muzny, D and Gibbs, RA and Doddapaneni, H},
title = {The GENESTAR manual for biospecimen collection biobanking and omics data generation from commercial space missions.},
journal = {NPJ microgravity},
volume = {11},
number = {1},
pages = {16},
pmid = {40368955},
issn = {2373-8065},
abstract = {The surge in commercial and civilian spaceflight enables the systematic and longitudinal, large-scale biospecimen collection to understand the prospective effects of space travel on human health. The Genomics and Space Medicine (Space Omics) project at BCM-HGSC involves a comprehensive biospecimen collection plan from commercial/private space flight participants. The manuscript addresses the critical gaps in the biospecimen collection process including details of the informed consent process, a provision for subjects to obtain custom CLIA-WGS reports, a data dictionary and a LIMS enabled biobank. The manuscript also discusses the biospecimens collection, processing methodologies and nucleic acid suitability for Omics data generation. Results from Axiom-2 mission where, 339 biospecimens were collected using 'Genomic Evaluation of Space Travel and Research (GENESTAR)' manual, at two different sites, showed that 98% of the blood samples and 91.6% of the non-blood samples passed the QC requirements for Omics assays, underscoring the reliability and effectiveness of the GENESTAR manual.},
}
@article {pmid40368948,
year = {2025},
author = {Serivichyaswat, PT and Scholte, T and Wilms, T and Stranddorf, L and van der Valk, T},
title = {Metagenomic biodiversity assessment within an offshore wind farm.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16786},
pmid = {40368948},
issn = {2045-2322},
mesh = {*Biodiversity ; *Metagenomics/methods ; North Sea ; Animals ; *Wind ; Seawater ; *DNA, Environmental/genetics/analysis ; Ecosystem ; *Metagenome ; Denmark ; },
abstract = {Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.},
}
@article {pmid40368316,
year = {2025},
author = {Wang, P and He, D and Zhao, J and Xiao, Z and Tan, J and Ma, J and Zheng, M},
title = {Transition from Anammox to Feammox metabolic modes: Regulation strategies for nitrite in Anammox enrichment cultures.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132674},
doi = {10.1016/j.biortech.2025.132674},
pmid = {40368316},
issn = {1873-2976},
abstract = {This studyachievedthe metabolic transition from anaerobic ammonium oxidation (Anammox) to Fe(III)-mediated ammonium oxidation (Feammox)usingiron-carbon micro-electrolytic spheres as a slow-release iron sourcethrougha stepwise reductionin influent NO2[-]-N concentration. The results demonstrated that sustained Feammox activitywas governed bynitrate-dependent ferrous oxidation (NDFO) metabolismcombined withoxygen-regulated Fe(III) regeneration,resulting ina peak total nitrogen removal efficiency of 91.6 %at40 mg/L NO2[-]-N.Whileexclusive NH4[+]-N feeding inhibited Feammox activity,this suppression was reversible upon NO2[-]-N supplementation. Intriguingly, Anammox activityremained robustdespite decreasing NO2[-]-N levelsand showedsignificant positive correlation with Feammox activity,suggesting shared metabolic modules. Metagenomic profilingfurther identifiedCa. Brocadia as the core functional genus driving NH4[+]-N oxidation,highlighting its niche adaptationin iron-mediated systems.These mechanistic insights establish a framework fordesigning energy-efficient nitrogen removal processesleveraging iron-redox cycling.},
}
@article {pmid40368259,
year = {2025},
author = {Wu, S and Zhang, N and Wan, Q},
title = {Disulfide bonds enhance thermal stability and thumb region drives activity of the glycoside hydrolase 11 xylanase rMxyl[cd].},
journal = {Journal of structural biology},
volume = {},
number = {},
pages = {108209},
doi = {10.1016/j.jsb.2025.108209},
pmid = {40368259},
issn = {1095-8657},
abstract = {Thermostable enzymes have significant advantages in industries, yet uncovering novel candidates with superior properties remains a scientific pursuit. This study identified rMxyl[cd], a glycoside hydrolase 11 family thermophilic xylanase from compost-soil metagenome, which exhibited a high specific activity of 5954 U·mg[-1] at pH 5.5 and 80°C. rMxyl[cd] was crystallized and diffracted to 1.5 Å resolution. Compared to the mesophilic xylanase Xyn II, rMxyl[cd] exhibits a more compact architecture. Notably, B-factor analysis reveals a uniquely flexible thumb region, hinting at its critical role in the enzyme's catalytic mechanism. rMxyl[cd] contains two disulfide bonds in the thumb and the N-terminal regions. Breaking these disulfide bonds by mutagenesis has dramatically decreased activities and thermostability. Conversely, introducing an extra disulfide bond at the N-terminal region of its α-helix extended its half-life for more than five folds at 80°C. Our studies firmly establish that the disulfide bonds are essential for its high thermal stability and the flexibility of the thumb region is crucial for its activity. Comparing the rMxyl[cd] crystal structure with the AlphaFold2-predicted model shows overall similarity, but the crystal structure offers higher local accuracy, especially in key functional regions. These findings not only deepen our understanding of the structure-function relationship of thermophilic xylanases but also inform a rational design of industrial enzymes.},
}
@article {pmid40368038,
year = {2025},
author = {Silvester, R and Perry, WB and Webster, G and Rushton, L and Baldwin, A and Pass, DA and Byrnes, NA and Farkas, K and Heginbothom, M and Craine, N and Cross, G and Kille, P and Kasprzyk-Hordern, B and Weightman, AJ and Jones, DL},
title = {Metagenomic profiling of hospital wastewater: A comprehensive national scale analysis of antimicrobial resistance genes and opportunistic pathogens.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106503},
doi = {10.1016/j.jinf.2025.106503},
pmid = {40368038},
issn = {1532-2742},
abstract = {BACKGROUND: Healthcare settings are recognised as potential hotspots for the emergence and spread of antimicrobial resistance (AMR).<br><br>METHOD: Metagenomic sequencing was conducted on a national scale using wastewater from hospitals across Wales to screen for antimicrobial resistance genes (ARGs) and opportunistic pathogens.<br><br>RESULTS: The total abundance and diversity of ARGs varied significantly across the hospitals. Genes conferring resistance to aminoglycosides, beta-lactams, and Macrolide-Lincosamide-Streptogramin-class antibiotics were predominant, with distinct resistome patterns emerging spatially. OXA-type beta-lactamases were the dominant ARG types. Spatial variability was observed in the distribution of the "big five" carbapenemases (KPC, IMP, VIM, NDM, OXA-48-like) and mcr genes, as well as WHO-listed fungal priority pathogens and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli (ESKAPEE) pathogens. Furthermore, antibiotic concentrations in the effluents often exceeded risk quotients, posing a substantial risk for AMR emergence.<br><br>CONCLUSIONS: Overall, the study highlights the effectiveness of combining wastewater-based epidemiology with metagenomics to gain critical insights into the distinct resistome and microbiome profiles in hospital settings. Tailored strategies are essential to mitigate the spread of antibiotics, clinically relevant ARGs and pathogens in these settings. This study underscores the necessity of implementing pre-treatment processes for hospital effluents before release into community sewers and environmental waters to curb the spread of these micro-pollutants.<br><br>AVAILABILITY OF DATA: The data will be made available upon request.},
}
@article {pmid40367945,
year = {2025},
author = {Antonaru, LA and Rad-Menéndez, C and Mbedi, S and Sparmann, S and Pope, M and Oliver, T and Wu, S and Green, DH and Gugger, M and Nürnberg, DJ},
title = {Evolution of far-red light photoacclimation in cyanobacteria.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.04.038},
pmid = {40367945},
issn = {1879-0445},
abstract = {Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.},
}
@article {pmid40367908,
year = {2025},
author = {Yuan, L and Chen, Y and Xie, M and Wang, J and Zheng, J and Zhou, J and Li, B and Zhang, D and Han, D},
title = {Utility of clinical metagenomics in complex infections: Cryptococcal meningitis complicated by Nocardia brain abscess.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {1},
pages = {116895},
doi = {10.1016/j.diagmicrobio.2025.116895},
pmid = {40367908},
issn = {1879-0070},
abstract = {Nocardia farcinica brain abscess (BA) is a rare yet life-threatening infection of the central nervous system (CNS) that predominantly affects immunocompromised patients. Its nonspecific symptoms often lead to delayed diagnosis and poor outcomes. Early diagnosis and precise treatment are essential to improve the prognosis of patients. We report the rare case of a 75-year-old man with IgG4-related disease undergoing long-term methylprednisolone therapy who presented with a N. farcinica brain abscess. The patient initially presented with cryptococcal meningitis but exhibited persistent symptoms despite standard antifungal treatment. Follow-up neuroimaging revealed new intracranial abscess formations. Metagenomic next-generation sequencing (mNGS) of brain tissue and cerebrospinal fluid (CSF) identified abundant N. farcinica-specific sequences, confirming a concurrent Nocardia brain abscess complicating the cryptococcal infection. The patient's condition gradually improved with timely antibiotic treatment and is currently in recovery. This case underscores the heightened risk of sequential opportunistic infections in immunocompromised individuals and exemplifies the clinical value of mNGS in detecting rare infectious diseases. We further conducted a systematic review of patients with Nocardia central nervous system infections confirmed by mNGS, analyzing their clinical presentations, laboratory parameters, therapeutic regimens, and prognostic outcomes. In summary, our study demonstrates that mNGS offers significant diagnostic advantages compared to conventional microbiological methods for uncommon infections. These findings provide clinically actionable, evidence-based guidance for the diagnosis and management of Nocardia brain abscesses.},
}
@article {pmid40367885,
year = {2025},
author = {Mo, S and Wu, X and Kashif, M and Zeng, S and Sang, Y and Meng, C and He, S and Jiang, C},
title = {Effects of Spartina alterniflora invasion on carbon fixation and sulfate reduction in a subtropical marine mangrove ecosystem.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118128},
doi = {10.1016/j.marpolbul.2025.118128},
pmid = {40367885},
issn = {1879-3363},
abstract = {Mangrove sediments host diverse microbial communities that are crucial for carbon fixation, but their functions and pathways in subtropical ecosystems-particularly under Spartina alterniflora invasion and across varying sediment depths-remain unclear. This study employed metagenomic and qPCR analyses to explore microbial carbon fixation in Rhizophora stylosa, S. alterniflora, and bare beach habitats. Environmental factors like Cd, sulfide, pH, and salinity significantly influenced carbon fixation and sulfate reduction. Specifically, the invasion increased the abundance of key carbon fixation genes, including aclA/B, cbbL, and korA, which are involved in the Calvin-Benson-Bassham (CBB) and Arnon-Buchanan (rTCA) cycles, respectively. This shift in gene abundance was accompanied by elevated Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity (0.47-21.82 nmol CO2 g[-1] soil min[-1]), suggesting a potential increase in microbial CO2 fixation rates in S. alterniflora-invaded sediments. Sediment depth also affected the distribution of carbon fixation genes and carbon-metabolizing microbes. Desulfobacterota were identified as major contributors to carbon fixation via both the rTCA and CBB cycles. Moreover, a strong correlation was observed between carbon fixation and sulfate reduction. These findings reveal how S. alterniflora invasion impacts carbon fixation and enhance our understanding of the mangrove ecosystems' role in climate change regulation.},
}
@article {pmid40367854,
year = {2025},
author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL},
title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179554},
doi = {10.1016/j.scitotenv.2025.179554},
pmid = {40367854},
issn = {1879-1026},
abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.},
}
@article {pmid40367785,
year = {2025},
author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J},
title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138594},
doi = {10.1016/j.jhazmat.2025.138594},
pmid = {40367785},
issn = {1873-3336},
abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.},
}
@article {pmid40367670,
year = {2025},
author = {Yu, S and Cao, T and Xu, Z and Zhou, H and Li, Q},
title = {Metagenomic next-generation sequencing (mNGS) identified Clostridium perfringens infection presenting as acute hemolysis after surgery.},
journal = {Journal of infection and public health},
volume = {18},
number = {8},
pages = {102798},
doi = {10.1016/j.jiph.2025.102798},
pmid = {40367670},
issn = {1876-035X},
abstract = {Clostridium perfringens (C. perfringens) septicaemia is a rare, but rapidly fatal infection, characterized by massive hemolysis. In numerous documented instances, the patient was not diagnosed in time due to the absence of typical clinical features. In order to enhance diagnostic accuracy, metagenomic next-generation sequencing (mNGS) has been adopted as a novel approach to pathogen identification. CASE PRESENTATION: A 67-year-old male who had undergone transcatheter arterial chemoembolization (TACE) surgery four days earlier presented with severe anemia, and laboratory investigations disclosed intravascular hemolysis. Swift and accurate identification was imperative, resulting in the confirmation of mNGS analysis, his medical history, clinical symptoms, physical signs, additional tests, and C. perfringens as the causative pathogen of hemolysis. After successful treatment with effective antibiotics, the patient recovered and was discharged from the hospital after 19 days. CONCLUSIONS: mNGS achieves expedited diagnostic turnaround time through rapid pathogen identification, significantly surpassing conventional culture methods. This may enable the diagnosis of atypical cases of C. perfringens infection, which can cause rapid systemic shock, renal failure, intravascular hemolysis, and even death.},
}
@article {pmid40367615,
year = {2025},
author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Shi, F and Wang, H and Chen, L and Pu, H and Liu, B and Zhou, Y},
title = {Water regime alters microbial mechanisms of N2O emission in metal-contaminated paddy soils.},
journal = {Ecotoxicology and environmental safety},
volume = {298},
number = {},
pages = {118304},
doi = {10.1016/j.ecoenv.2025.118304},
pmid = {40367615},
issn = {1090-2414},
abstract = {Microorganisms are essential for soil nitrous oxide (N2O) emissions through participating in key nitrogen (N)-related processes. However, the effect of water regimes on the interactions between N2O emissions and microbial processes in metal-contaminated soils is unclear. Here, we conducted a soil microcosm experiment with two water management strategies (non-flooding and flooding) and six metal addition treatments including low (2 and 200 mg kg[-1]) and high (10 and 1000 mg kg[-1]) levels of individual and combined Cd and Cu. The effects of high levels of individual Cd and Cu contamination on soil N2O emissions varied depending on water regimes, showing antagonistic effects under non-flooding conditions and synergistic effects under flooding conditions. High levels of co-contamination significantly inhibited nitrification under both water regimes, primarily due to reduced abundance of Nitrosospira. In contrast, this co-contamination decreased the abundance of Ramlibacter, thereby inhibiting denitrification and dissimilatory nitrate reduction to ammonium (DNRA) under flooding conditions. The inhibition of these key microorganisms and their mediated N-cycle processes reduced soil N2O emissions under both water regimes. This reduction was greater under flooding conditions because more N-related processes were inhibited. Metagenomic binning further indicated that Nitrosospira carried nitrifying genes, while Ramlibacter contained genes involved in denitrification, assimilatory nitrate reduction to ammonium (ANRA), and DNRA. These findings implied that both microorganisms had potential to produce N2O. Overall, water management strategies and metal contamination altered the microbial processes of N2O emissions, highlighting the importance of appropriate water management in mitigating greenhouse gas emissions from metal-contaminated paddy soils in southern China.},
}
@article {pmid40367351,
year = {2025},
author = {Heo, H and Nguyen-Dinh, T and Jung, MY and Greening, C and Yoon, S},
title = {Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf092},
pmid = {40367351},
issn = {1751-7370},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is a key process used by diverse microorganisms in the global nitrogen cycle. For long, DNRA has been considered primarily as an organotrophic reaction, despite evidence that oxidation of inorganic electron donors also supports DNRA. Evidence of DNRA coupling with molecular hydrogen (H2) oxidation has been reported for several microbial isolates; however, the underlying physiology of the microbial process remains understudied. In this study, we report the isolation of two Campylobacterotastrains, Aliarcobacter butzlerihDNRA1 and Sulfurospirillumsp. hDNRA2, which grow using H2as the sole electron donor for DNRA, and physiological insights gained from a close examination of hydrogenotrophic DNRA in these isolates. In both batch and continuous cultures, DNRA sensu stricto(i.e. NO3-reduction that includes stoichiometric NO2--to-NH4+reduction) was strictly dependent on the presence of H2and exhibited stoichiometric coupling with H2oxidation, indicating that electrons required for NO2-reduction were unequivocally derived from H2. Successful chemostat incubation further demonstrated that hydrogenotrophic DNRA is viable under NO3-limiting, H2-excess conditions. Genomic and transcriptomic analyses identified group 1b [NiFe]-hydrogenase and cytochrome c552nitrite reductase as the key enzymes catalyzing hydrogenotrophic DNRA. Additionally, metagenomic surveys revealed that bacteria capable of hydrogenotrophic DNRA are taxonomically diverse and abundant in various ecosystems, particularly in the vicinity of deep-sea hydrothermal vents. These findings, integrating physiological, genomic, and transcriptomic analyses, clarify that H2can solely serve as a growth-supporting electron donor for DNRA and suggest potential significance of this microbial process in nitrogen- and hydrogen-related environmental biogeochemical cycles.},
}
@article {pmid40366862,
year = {2025},
author = {Wang, L and Chen, X and Pollock, NR and Villafuerte Gálvez, JA and Alonso, CD and Wang, D and Daugherty, K and Xu, H and Yao, J and Chen, Y and Kelly, CP and Cao, Y},
title = {Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505269},
doi = {10.1080/19490976.2025.2505269},
pmid = {40366862},
issn = {1949-0984},
abstract = {Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.},
}
@article {pmid40366770,
year = {2025},
author = {Baba, Y and Tsuge, D and Aoki, R},
title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: A randomized, double-blind, placebo-controlled crossover trial.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf071},
pmid = {40366770},
issn = {1347-6947},
abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL+IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL+IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL+IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL+IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.},
}
@article {pmid40366182,
year = {2025},
author = {Martin Říhová, J and Vodička, R and Hypša, V},
title = {An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0022025},
doi = {10.1128/aem.00220-25},
pmid = {40366182},
issn = {1098-5336},
abstract = {The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.},
}
@article {pmid40366158,
year = {2025},
author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB},
title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174924},
doi = {10.1128/msystems.01749-24},
pmid = {40366158},
issn = {2379-5077},
abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.<br><br>IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.},
}
@article {pmid40366141,
year = {2025},
author = {Li, J and Zheng, K and Ding, W and Lu, L and Liang, Y and Xiong, Y and Wei, Z and Gao, C and Su, Y and Wang, Z and Chen, X and Bao, Z and Hu, X and McMinn, A and Wang, M},
title = {Healthy and moribund Zhikong scallops (Chlamys farreri) developed different viral communities during a mass mortality event.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0034225},
doi = {10.1128/msystems.00342-25},
pmid = {40366141},
issn = {2379-5077},
abstract = {UNLABELLED: Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves.<br><br>IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.},
}
@article {pmid40366139,
year = {2025},
author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ},
title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013725},
doi = {10.1128/msphere.00137-25},
pmid = {40366139},
issn = {2379-5042},
abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.<br><br>IMPORTANCE: The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.},
}
@article {pmid40366134,
year = {2025},
author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X},
title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/msystems.00375-25},
pmid = {40366134},
issn = {2379-5077},
abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.},
}
@article {pmid40366096,
year = {2025},
author = {Ragupathy, V and Kelley, K and Hewlett, I},
title = {Near-complete torque teno virus (TTV) genome identified in a blood donor infected with hepatitis B virus (HBV).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0117824},
doi = {10.1128/mra.01178-24},
pmid = {40366096},
issn = {2576-098X},
abstract = {We have identified a near full-length torque teno virus (TTV) genome sequence in plasma from a blood donor infected with hepatitis B virus. The consensus sequence of TTV was extracted from Nanopore metagenomic sequencing. The identified TTV open reading frame 1 is 3,062 nucleotides (nt) long and shares 90%-100% identity with other human TTVs.},
}
@article {pmid40365535,
year = {2025},
author = {Li, M and Chen, J and Zhang, L and Chen, X and Zhou, J and Liu, F and Zhou, X and Xiao, J and Yang, K and Qi, L and Han, X and Liu, T and Zhao, H and Zhou, Z and Chen, X and Sun, L},
title = {Clinicopathological characteristics and diagnostic performance of metagenomic pathogen detection technology in mycobacterial infections among HIV patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1584189},
pmid = {40365535},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; *HIV Infections/complications ; Adult ; Middle Aged ; Mycobacterium tuberculosis/isolation &amp; purification/genetics ; *Metagenomics/methods ; Sputum/microbiology ; *Mycobacterium Infections/diagnosis/microbiology/pathology ; Sensitivity and Specificity ; *Molecular Diagnostic Techniques/methods ; Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Biopsy ; },
abstract = {BACKGROUND: Mycobacterial infections represent a major cause of morbidity and mortality in HIV-infected individuals. This study evaluated diagnostic techniques for mycobacterial identification and compared clinicopathological features between HIV-positive and HIV-negative patients.<br><br>METHODS: We analyzed 88 tissue samples (with 41 matched blood and 28 sputum samples) using histopathology (HE and acid-fast staining), bacterial culture, MTB-PCR (sputum/biopsy), PCR-reverse dot blot hybridization (RDBH), and metagenomic pathogen detection technology (MetaPath&#x2122;). Logistic regression analyses were performed to identify factors affecting detection rates.<br><br>RESULTS: Mycobacterial infection was detected in 95.5% (84/88) of patients. Among HIV-positive patients (n=63), 46% (29/63) had Mycobacterium tuberculosis (MTB) infections, and 44% (28/63) had non-tuberculous mycobacteria (NTM) infections, significantly higher than the 20% (5/25) NTM rate in HIV-negative patients. Univariate analysis identified HIV-positive status (p=0.009), lymph node involvement (p=0.020), and positive MetaPath&#x2122; results (p=0.002) as significant predictors of detection, while multivariate analysis confirmed these as independent factors (p=0.036; p=0.042; p=0.006). Lymph nodes were the most common infection site in HIV-positive patients (42.9%, 27/63), while lung tissue predominated in HIV-negative patients (48%, 12/25). MetaPath&#x2122; demonstrated superior sensitivity and specificity for detecting both MTB and NTM. Biopsy samples provided higher diagnostic accuracy than sputum or blood for lung and lymph node infections, but not for brain. In HIV-positive patients, NTM infections showed significantly more granuloma formation (p=0.032) and foam cells (p=0.005), but less necrosis (p=0.0005) compared to MTB infections. No significant differences were observed in HIV-negative patients.<br><br>CONCLUSIONS: MetaPath&#x2122; is a highly effective diagnostic tool for mycobacterial infections, particularly in tissue biopsies. HIV-positive status, lymph node involvement, and MetaPath&#x2122; positivity independently predict mycobacterial detection. HIV-positive patients exhibit distinct clinicopathological features, emphasizing the need for tailored diagnostic and therapeutic approaches based on immune status.},
}
@article {pmid40365473,
year = {2025},
author = {Pu, T and Tan, Y and Zhao, Y and Zhao, Z and Zhang, N and Li, C and Song, Y},
title = {Effect of Seasonal Variations on Soil Microbial, Extracellular Enzymes, and Ecological Stoichiometry in Tea Plantations.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71362},
pmid = {40365473},
issn = {2045-7758},
abstract = {Tea plantations are important agricultural ecosystems in karst areas, yet the seasonal dynamics of soil microbial communities, functional genes, and extracellular enzyme activities (EEA) under different management practices remain poorly understood. This study investigated organic (HY), pollution-free (TS), and conventional (XY) tea plantations in Weng'an County, Southwest China, during the spring (April) and autumn (August) tea seasons via metagenomics and stoichiometric analyses. Seasonal variations significantly altered the soil physicochemical properties (e.g., SOC, TN, and TP) and EEA (p < 0.05), with higher C-acquiring enzyme activity in autumn and elevated soil C:N:P ratios in spring. The soil extracellular enzyme stoichiometry (EES C:N:P) deviated from the theoretical 1:1:1 ratio, indicating that microbial metabolism was constrained by soil resource availability rather than homeostasis. Phosphorus limitation (vector angle > 45°) persisted across seasons, contradicting initial hypotheses, with acid phosphatase (ACP) activity and EES C:P identified as critical drivers. Random forest (RF) and structural equation modeling (SEM) revealed that the spring season had stronger impacts on microbial communities and functional genes, with the soil TN, C:N, NAG, ACP, and EES C:P ratios as key predictors. Compared with conventional practices, organic management enhances microbial diversity and functional redundancy, buffering seasonal fluctuations. These findings highlight the interplay between seasonal climatic shifts and agricultural practices regulating soil nutrient cycling and microbial adaptation. Strategic interventions-such as spring carbon supplementation, autumn organic phosphorus fertilization, and intercropping-are proposed to optimize microbial resilience and ecosystem stability in fragile karst tea plantations. This study provides novel insights into soil ecological stoichiometry and microbial metabolic strategies, offering a reference for the sustainable management of agroecosystems in karst areas.},
}
@article {pmid40365061,
year = {2025},
author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L},
title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1571684},
pmid = {40365061},
issn = {1664-302X},
abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.<br><br>METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.<br><br>RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000&#xd7;) and T3 (500&#xd7;), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal &#x3b1;-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.<br><br>DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.},
}
@article {pmid40364394,
year = {2025},
author = {Cao, K and Shi, P and Xu, X and Wang, J},
title = {Self-Inhibition Effects of Litter-Mediated Plant-Phyllosphere Feedback on Seedling Growth in Invasive and Native Congeneric Species.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/plants14091355},
pmid = {40364394},
issn = {2223-7747},
abstract = {Plant-phyllosphere feedback (PPF) is an ecological process in which phyllosphere microbiota, originating from plant litter, are transmitted via aerosols and subsequently influence the growth of conspecific or heterospecific plants. However, the cross-species generality of this mechanism and its role in invasive plant success remain to be fully elucidated. This study systematically examined PPF effects using three invasive/native congeneric plant pairs from distinct families (Phytolaccaceae, Asteraceae, and Amaranthaceae) in Jiangxi Province, China. Key findings include the following: (1) Wide conspecific negative feedback across families, with four of six species exhibiting 6.2-12.7% biomass reduction under their own litter treatments (p < 0.05). (2) Comparable feedback intensity between invasive and native species, as indicated by average pairwise indices (invasive I = -0.05 vs. native I = -0.04; p = 0.15). Notably, the invasive species Phytolacca americana uniquely showed a positive biomass response (+7.1%), though underlying mechanisms (phytochemical or microbial) were not investigated. (3) Lack of correlation between PPF strength and plant functional traits or phylogenetic distance, as indicated by Mantel tests (p > 0.8), in contrast to the trait/phylogeny associations commonly observed in soil feedback systems. This study provided the first evidence of PPF universality across multiple plant families-previously documented only within Asteraceae-and highlights the potential microbial-mediated advantages in plant invasions. Future research should integrate spatiotemporal metagenomic and metabolomic approaches to decipher the dynamic pathogen/microbe networks and their phytochemical interactions.},
}
@article {pmid40363788,
year = {2025},
author = {Zhou, L and Li, J and Ding, C and Zhou, Y and Xiao, Z},
title = {Mechanistic Advances in Hypoglycemic Effects of Natural Polysaccharides: Multi-Target Regulation of Glycometabolism and Gut Microbiota Crosstalk.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {9},
pages = {},
doi = {10.3390/molecules30091980},
pmid = {40363788},
issn = {1420-3049},
support = {2024JJ8163//Hunan Natural Science Foundation/ ; C2023005//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 201923//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 2022ZYYGN06//2022 Annual Natural Drug Resources and Function Development Fund Project/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; Animals ; *Hypoglycemic Agents/pharmacology/chemistry/therapeutic use ; Signal Transduction/drug effects ; Insulin Resistance ; Glucose/metabolism ; },
abstract = {Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure-activity relationships, integration of the gut microbiota-metabolism-immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure-activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications.},
}
@article {pmid40362493,
year = {2025},
author = {Žukienė, G and Narutytė, R and Rudaitis, V},
title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094258},
pmid = {40362493},
issn = {1422-0067},
mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.},
}
@article {pmid40362462,
year = {2025},
author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R},
title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094227},
pmid = {40362462},
issn = {1422-0067},
support = {xxxxx//AFRRI/ ; },
mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; },
abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.},
}
@article {pmid40362406,
year = {2025},
author = {Krivonos, DV and Fedorov, DE and Konanov, DN and Vvedensky, AV and Sonets, IV and Korneenko, EV and Speranskaya, AS and Ilina, EN},
title = {Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094168},
pmid = {40362406},
issn = {1422-0067},
support = {24-15-00419//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Fungi/genetics/classification ; *Nanopore Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Algorithms ; Metagenome ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore amplicon sequencing data analysis often provide only taxonomy annotation without OTU sequence assembly. Conversely, tools that facilitate OTU assembly are constrained in their analysis to long reads, such as the V1-V9 regions of 16S rRNA for bacterial community studies or the full-length ITS cluster (ITS1-5.8S-ITS2) for fungal community studies. In other cases, researchers propose their own solutions without dedicated tools. In this paper, we present Pike, a novel tool for analyzing Oxford Nanopore amplicon sequencing data. Pike allows analysis without amplicon size limitations and allows de novo assembly of OTU sequences. In our research, we created mock communities of fungi and bacteria, which we then used to demonstrate the efficiency of our algorithm. Furthermore, we validated the algorithm using externally available data. We also compared our approach with similar ones to show its applicability.},
}
@article {pmid40361215,
year = {2025},
author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q},
title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {537},
pmid = {40361215},
issn = {1479-5876},
support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.<br><br>METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.<br><br>RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.<br><br>CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.},
}
@article {pmid40360994,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {475},
pmid = {40360994},
issn = {1471-2164},
support = {31900327//National Natural Science Foundation of China/ ; 2023NSFSC1153//Natural Science Foundation of Sichuan Province of China/ ; },
mesh = {Animals ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Caudata/physiology/genetics/microbiology ; Heat-Shock Response ; Transcriptome ; Gene Expression Profiling ; Energy Metabolism ; Larva ; },
abstract = {The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.},
}
@article {pmid40360555,
year = {2025},
author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S},
title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {78},
pmid = {40360555},
issn = {2055-5008},
support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; },
abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.},
}
@article {pmid40360028,
year = {2025},
author = {Fang, B and Liu, YF and Wei, HX and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Enhancing methanogenesis from long-chain fatty acids (LCFA) and enrichment of novel bacteria with resuscitation-promoting factors.},
journal = {Bioresource technology},
volume = {432},
number = {},
pages = {132663},
doi = {10.1016/j.biortech.2025.132663},
pmid = {40360028},
issn = {1873-2976},
abstract = {Long-chain fatty acids (LCFA) are important intermediate metabolites in lipid hydrolysis during anaerobic digestion for biogas production. High LCFA loads inhibit microbial activity by toxicity, impairing the coupling of β-oxidation and methanogenesis, thus reducing LCFA degradation efficiency. This study employed and tested seven stimulants, including the resuscitation-promoting factors (Rpf and YeaZ), the quorum-sensing molecules (cAMP, and AHLs), the chemical stimulants (pyruvate), the growth promoter (fumarate), and yeast extract + peptone (YP) for enhancement of methanogenic degradation of LCFA. The results indicate that the chemical stimulants and resuscitation-promoting factors enhanced maximum methane-production rate 1.58 to 2.20 fold versus the NS, reducing the lag phase by 1.46-9.76 days. Analysis of the microbial community composition revealed that the quorum sensing factors only increased species richness, while Rpf, YeaZ fumarate, and YP stimulated the growth of core members of the communities. Metagenomic analysis detected three previously unreported LCFA-degrading bacterial taxa, Marinisomatota, Thermoanaerobaculaceae and Pelomonas. Particularly, Rpf and YeaZ significantly enriched LCFA-degrading bacteria such as Syntrophomonadaceae, Leptospiraceae, and Marine Group B within the core species, while YeaZ also stimulated methanogenic bacteria, possibly due to resuscitating dormant microbes from unfavorable conditions. Syntrophic interactions between LCFA degraders and non-degraders, rather than methanogen abundance, govern methanogenic LCFA degradation. These results demonstrate that the use of stimulants is an effective approach to enhance LCFA degradation and provide a new pathway for energy recovery.},
}
@article {pmid40359864,
year = {2025},
author = {Fan, M and Li, H and Liu, C and Du, L and Xu, Y and Chen, Y},
title = {Insights into the molecular mechanism on high salt tolerance of electroactive microorganisms collaborated by biochar supported cerium dioxide.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125679},
doi = {10.1016/j.jenvman.2025.125679},
pmid = {40359864},
issn = {1095-8630},
abstract = {Electroactive microorganisms are a promising approach for treating high-salinity organic wastewater, however, they are highly susceptible to salt stress, which can compromise their metabolic activity. In this paper, biochar supported nano-cerium dioxide catalyst (BC-CeO2) was prepared to strengthen electroactive microorganisms in high salt environment. It was found that BC-CeO2 significantly improved the bioelectrochemical and metabolic activity of microorganisms in high salt environment (600 mM NaCl) compared with the Control. At the initial stage of the reaction, the maximum power density of microbial fuel cells (MFCs) reached 343.21 mW/m[2], and the degradation efficiency of norfloxacin (NOR) was 64.8 %, which was 1.7 times that of the Control. The analysis of microbial antioxidant properties demonstrated that BC-CeO2 could significantly increase the activities of superoxide dismutase (SOD) and catalase (CAT), effectively enhancing the ability of microorganisms to scavenge reactive oxygen species produced by salt stress. Metagenomic analysis revealed that the abundance of KEGG pathways conducive to microbial growth and metabolism under BC-CeO2 was relatively high, such as biosynthesis of amino acids (ko01230), microbial metabolism in diverse environments (ko01120) and so on. The enrichment of salt tolerant genes further illustrated the strengthening effect of BC-CeO2 on microbial adaptation to high salt environment, including genes related to NADH ubiquinone oxidoreductase, Na[+]/H[+] antiporter, intracellular small molecule compatible substance synthesis and transport related enzyme system and K[+] transporter related genes. Furthermore, the activity changes of Na[+]/K[+]-ATPase, which regulates cell permeability, in different environments also confirmed this point. This paper provides an effective strategy for enhancing the treatment of high-salt organic wastewater by electroactive microorganisms.},
}
@article {pmid40359746,
year = {2025},
author = {Bansal, M and Santhiya, D and Sharma, JG},
title = {Simulated dump yard microbes drive significant biodegradation of polypropylene and polyvinyl chloride microplastics.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138545},
doi = {10.1016/j.jhazmat.2025.138545},
pmid = {40359746},
issn = {1873-3336},
abstract = {Bacterial culture isolates were used to demonstrate the breakdown of polypropylene (PPs) and polyvinyl chloride (PVCs) microplastics for the first time. Using metagenomics and phylogenetic analysis, bacterial isolates were discovered from a simulated dump yard. PPs and PVCs were broken down using bacterial isolates found to be Acinetobacter baumannii and mixed culture species with a Bacillus sp. dominance. After 50 days of activity, the dry weight of microplastics decreased by 33.3 % (PPs) and 27.1 % (PVCs) due to the breakdown process aided by Acinetobacter baumannii. Weight reductions of 20.3 % for PPs and 18.2 % for PVCs have been observed in mixed bacterial cultures, respectively. Microplastics' thermal stability and transition properties changed, according to experiments like DTG NMR, Raman, and WCA. FTIR analysis captured the structural changes in PPs and PVCs. SEM, TEM, and cell hydrophobicity tests showed that microplastics were biodegrading. GC-MS identified the released byproducts, which included carboxylic acids, alkanes, esters, and aromatic chemicals. Based on these findings, it can be concluded that bacterial isolates are effective in degrading PPs and PVCs and may help create sustainable methods of handling plastic trash.},
}
@article {pmid40359745,
year = {2025},
author = {Yang, T and Gong, X and Xu, A and Wang, B and Huang, Z and Wang, C and Gao, D},
title = {Integrated evaluation for advanced removal of nitrate using novel solid carbon biochar/corncob/PHBV composite: Insight into electron transfer and metabolic pathways.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138549},
doi = {10.1016/j.jhazmat.2025.138549},
pmid = {40359745},
issn = {1873-3336},
abstract = {This study developed a novel Biochar/Corncob/PHBV (BCP) composite material, integrating the electron transfer capability of biochar, the cost-effectiveness of corncob, and the sustained carbon release performance of PHBV. The BCP system achieved a maximum nitrate removal efficiency of 97.3 %, significantly outperforming the single PHBV system (91.05 %), while effectively reducing nitrous oxide and other greenhouse gas emissions. It also demonstrated stable carbon release and enhanced electron transfer capabilities, contributing to a more sustainable denitrification process. The physical and chemical characterization of BCP confirmed that its superior performance is attributed to the uniformly distributed functional groups (e.g., CO and -COOH) on the surface and its porous structure, which facilitated electron transfer and microbial adhesion. Metagenomic and microbial analyses further revealed that BCP enriched functional genera such as Cellulomonas and Chryseobacterium and significantly increased the abundance of key functional genes related to nitrate reduction (e.g., NaR and NiR), enhancing organic matter decomposition and microbial nitrogen transformation. Beyond improving nitrate removal efficiency compared to PHBV, the BCP material offers practical engineering value by addressing carbon source limitations in long-term wastewater treatment applications. Its enhanced electron transfer and microbial enrichment suggest strong potential for application in constructed wetlands, biofilters, and other decentralized wastewater treatment systems. The study demonstrates that the BCP composite is not only a viable alternative to traditional PHBV but also a cost-effective and environmentally friendly material with broad applicability in nitrogen pollution control.},
}
@article {pmid40359589,
year = {2025},
author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN},
title = {Exploring deep learning in phage discovery and characterization.},
journal = {Virology},
volume = {609},
number = {},
pages = {110559},
doi = {10.1016/j.virol.2025.110559},
pmid = {40359589},
issn = {1096-0341},
abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.},
}
@article {pmid40359177,
year = {2025},
author = {, },
title = {Editorial Note: Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324350},
doi = {10.1371/journal.pone.0324350},
pmid = {40359177},
issn = {1932-6203},
}
@article {pmid40359062,
year = {2025},
author = {Jules, E and Decker, C and Bixler, BJ and Ahmed, A and Zhou, ZC and Arora, I and Tafesse, H and Dakanay, H and Bombin, A and Wang, E and Ingersoll, J and Bifulco, K and Frediani, JK and Parsons, R and Sullivan, J and Greenleaf, M and Waggoner, JJ and Martin, GS and Lam, WA and Piantadosi, A},
title = {Respiratory Virus Detection and Sequencing from SARS-CoV-2-Negative Rapid Antigen Tests.},
journal = {Emerging infectious diseases},
volume = {31},
number = {13},
pages = {39-44},
doi = {10.3201/eid3113.241191},
pmid = {40359062},
issn = {1080-6059},
mesh = {Humans ; *SARS-CoV-2/genetics ; Genome, Viral ; COVID-19/diagnosis/virology ; *Respiratory Tract Infections/virology/diagnosis ; Phylogeny ; Antigens, Viral ; *Viruses/genetics/isolation &amp; purification/classification ; },
abstract = {Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.},
}
@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.<br><br>OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote fran&#xe7;ais" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.<br><br>METHODS: "Le French Gut&#xa0;- Le microbiote fran&#xe7;ais" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Syst&#xe8;me National des Donn&#xe9;es de Sant&#xe9;). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.<br><br>RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.<br><br>CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.<br><br>DERR1-10.2196/64894.},
}
@article {pmid40358144,
year = {2025},
author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW},
title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0091324},
doi = {10.1128/msphere.00913-24},
pmid = {40358144},
issn = {2379-5042},
abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.},
}
@article {pmid40357419,
year = {2025},
author = {Liu, H and Xu, T and Fu, H and Dai, B and Xie, Y},
title = {Application of Metagenomic Next-Generation Sequencing in HIV-Infected Patients with Bloodstream Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2389-2399},
pmid = {40357419},
issn = {1178-6973},
abstract = {BACKGROUND: Bloodstream infections (BSI) are common complications in HIV-infected patients and are prone to septic shock and death. This study aimed to analyze the application of blood metagenomic next-generation sequencing (mNGS) in HIV-infected patients with BSI.<br><br>METHODS: Fifty-four HIV-infected patients with suspected BSI were hospitalized at the First Affiliated Hospital of the Zhejiang University School of Medicine between August 2020 and June 2023. Blood mNGS and blood culture (BC) results were retrospectively reviewed and compared to the application value of BSI.<br><br>RESULTS: The mNGS was more sensitive for detecting pathogens (82.4% versus 35.3%; P < 0.05), and when combining blood mNGS with culture results, the sensitivity increased to 88.2%. The detection rate of mNGS for blood-mixed infection was significantly higher than that of BC (P < 0.05). Among the positive results for fungi and bacteria detected by mNGS, 13.5% of the pathogenic microorganisms were consistent with the results of BC.<br><br>CONCLUSION: The mNGS combined with BC can improve pathogen detection sensitivity and the comprehensive identification of pathogenic microorganisms in HIV-infected patients with BSI.},
}
@article {pmid40357399,
year = {2025},
author = {Xing, ZC and Guo, HZ and Zhen, P and Ao, T and Hu, M},
title = {Clinical application of metagenomic next-generation sequencing in etiologic diagnosis of severe pneumonia in adults.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1561468},
pmid = {40357399},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; COVID-19/diagnosis/virology ; Risk Factors ; *Pneumonia/diagnosis/microbiology/mortality ; Aged, 80 and over ; Bacteria/genetics/isolation &amp; purification/classification ; SARS-CoV-2/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; },
abstract = {OBJECTIVE: To analyze the clinical characteristics and risk factors for death of severe pneumonia (SP) in adults and explore the application value of metagenomic next-generation sequencing in the detection of pathogens.<br><br>METHODS: A total of 132 adult patients with SP admitted from May 2021 to October 2023 were selected. Data on gender, age, smoking, underlying diseases, laboratory tests and prognosis were collected. BALF samples were sent for mNGS, smear-stained microscopy and culture. Meanwhile, conventional methods were used for pathogen detection of blood, urine and throat swab specimens. The detection efficiencies of different methods were compared and the associated pathogen profiles were analyzed.<br><br>RESULTS: Among the 132 patients, there were 92 males and 40 females, with a total of 52 deaths. Age&#x2265;65 years, heart failure, renal insufficiency, positive of COVID-19, use of vasoactive drugs, use of mechanical ventilation and use of CRRT were statistically different between the survivors and non-survivors. Heart failure (OR=4.751) and use of mechanical ventilation (OR=11.914) were risk factors of SP mortality. The bacteria detected were mainly Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. The fungi detected were mainly Candida and Aspergillus. The viruses detected were mainly COVID-19 and influenza virus. The positive rate of mNGS was higher than conventional methods in both bacteria, fungus and virus (82.58% vs 63.64%, 50.76% vs 37.88% and 67.42% vs 37.88%, respectively) (P<0.05). The sensitivity and accuracy of mNGS in bacterial detection were significantly higher than traditional methods (P<0.05). Compared to culture, mNGS detected more Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Escherichia coli, and had a significant advantage in the detection of Mycobacterium tuberculosis complex, Nontuberculous mycobacterial, Legionella pneumophila, Chlamydia psittaci, Pneumocystis jirovecii and Aspergillus. Moreover, mNGS can better indicate mixed infections of bacteria, viruses, or fungi.<br><br>CONCLUSION: Elderly people with chronic diseases were the main group of severe pneumonia in adults. The pathogenic microorganisms that caused SP are complex, and mixed infection is common. mNGS enhanced the effectiveness of pathogen detection, makes up for the shortcomings of conventional methods, especially in identifying unexpected pathogens, and provides a new means for early targeted anti-infection treatment.},
}
@article {pmid40357303,
year = {2025},
author = {Fu, C and Sun, Y and Chen, C},
title = {First reported Tannerella forsythia infection in a patient with extensive bronchiectasis: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1571506},
pmid = {40357303},
issn = {2296-858X},
abstract = {Tannerella forsythia infection was common in oral diseases but less reported in lung diseases. This report presents a patient with bronchiectasis who was infected by Tannerella forsythia and subsequently hospitalized with symptoms including fever, progressive cough, sputum production, and shortness of breath. A chest computed tomography (CT) scan revealed multiple bilateral pulmonary bronchiectasis with signs of infection. Metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid primarily detected Tannerella forsythia. Treatment with Piperacillin-tazobactam and ornidazole resulted in a favorable outcome. This case first reported a patient with extensive bronchiectasis infected by Tannerella forsythia and provided an effective treatment.},
}
@article {pmid40357282,
year = {2025},
author = {Wu, A and Gai, W and Guo, Y and Zhou, C and Xu, Y and Zhang, X and Wang, H},
title = {Clinical features of Talaromyces marneffei infection and colonization in HIV-negative patients: the role of mNGS in diagnosis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1579522},
pmid = {40357282},
issn = {2296-858X},
abstract = {BACKGROUND: Talaromycosis, caused by Talaromyces marneffei (T. marneffei), has become more common in HIV-negative and immunocompetent patients. The fungus colonizes the body through dormant spores, causing opportunistic infections. Early diagnosis is challenging. This study aims to analyze the clinical features, diagnosis, treatment, and prognosis of T. marneffei infections.<br><br>METHODS: Patients diagnosed with T. marneffei infection or colonization at the People's Hospital of Ningbo University between August 2022 and July 2024 were included. Demographic characteristics, clinical data, diagnostic approaches, and treatment outcomes were analyzed.<br><br>RESULTS: Seven patients were diagnosed with T. marneffei infection, and three with colonization. Productive cough and fever were the predominant symptoms in all patients. Nodules, cavitary lesions, and pleural effusions on chest imaging were observed exclusively in infected patients. The positivity rates for metagenomic next-generation sequencing (mNGS) and conventional microbiological testing were 100 and 10%, respectively. Of the seven infected patients, three had a single infection with T. marneffei, and four had co-infection with T. marneffei and Mycobacterium avium complex. All patients were treated with monotherapy or combination therapy using voriconazole. All but one recovered.<br><br>CONCLUSION: Early diagnosis and combination therapy are critical for T. marneffei infection. mNGS complements traditional methods, facilitating accurate diagnosis and guiding targeted treatment.},
}
@article {pmid40356662,
year = {2025},
author = {Vallejo-Espín, D and Galarza-Mayorga, J and Lalaleo, L and Calero-Cáceres, W},
title = {Beyond clinical genomics: addressing critical gaps in One Health AMR surveillance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596720},
pmid = {40356662},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) poses an escalating global threat that demands comprehensive surveillance approaches beyond traditional clinical contexts. Although next-generation sequencing (NGS), particularly whole-genome sequencing (WGS), has revolutionized AMR surveillance, current implementation predominantly targets clinical isolates, largely neglecting critical environmental and animal reservoirs. Consequently, significant gaps persist in our understanding of AMR dynamics across diverse ecosystems. This Perspective emphasizes the urgent need to adopt an integrated genomic framework, combining isolate-based WGS with shotgun metagenomics within a cohesive One Health strategy. Such an integrated approach would significantly enhance the detection, tracking, and containment of resistance determinants, facilitating proactive rather than reactive AMR management. Achieving this vision requires global standardization of sequencing methods, harmonization of bioinformatics pipelines, and strengthened cross-sectoral collaboration to ensure timely interventions against AMR threats worldwide.},
}
@article {pmid40356641,
year = {2025},
author = {Xing, Y and Xie, Y and Wang, X},
title = {Enhancing soil health through balanced fertilization: a pathway to sustainable agriculture and food security.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1536524},
pmid = {40356641},
issn = {1664-302X},
abstract = {Sustainable soil health management is pivotal for advancing agricultural productivity and ensuring global food security. This review comprehensively evaluates the effects of mineral-organic fertilizer ratios on soil microbial communities, enzymatic dynamics, functional gene abundance, and holistic soil health. By integrating bioinformatics, enzyme activity assays, and metagenomic analyses, we demonstrate that balanced fertilization significantly enhances microbial diversity, community stability, and functional resilience against environmental stressors. Specifically, the synergistic application of mineral and organic fertilizers elevates β-glucosidase and urease activities, accelerating organic matter decomposition and nutrient cycling while modulating microbial taxa critical for nutrient transformation and pathogen suppression. Notably, replacing 20-40% of mineral fertilizers with organic alternatives mitigates environmental risks such as greenhouse gas emissions and nutrient leaching while sustaining crop yields. This dual approach improves soil structure, boosts water and nutrient retention capacity, and increases microbial biomass by 20-30%, fostering long-term soil fertility. Field trials reveal yield increases of 25-40% in crops like rice and maize under combined fertilization, alongside enhanced soil organic carbon (110.6%) and nitrogen content (59.2%). The findings underscore the necessity of adopting region-specific, balanced fertilization strategies to optimize ecological sustainability and agricultural productivity. Future research should prioritize refining fertilization frameworks through interdisciplinary approaches, addressing soil-crop-climate interactions, and scaling these practices to diverse agroecosystems. By aligning agricultural policies with ecological principles, stakeholders can safeguard soil health-a cornerstone of environmental sustainability and human wellbeing-while securing resilient food systems for future generations.},
}
@article {pmid40356191,
year = {2025},
author = {Charalambous, H and Brown, C and Vogazianos, P and Katsaounou, K and Nikolaou, E and Stylianou, I and Papageorgiou, E and Vraxnos, D and Aristodimou, A and Chi, J and Costeas, P and Shammas, C and Apidianakis, Y and Antoniades, A},
title = {Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.},
journal = {Thoracic cancer},
volume = {16},
number = {9},
pages = {e70075},
pmid = {40356191},
issn = {1759-7714},
support = {//Investigator-Initiated Studies Program of Merck Sharp &amp; Dohme Corp/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology/pathology ; Male ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology ; Female ; *Lung Neoplasms/drug therapy/pathology/microbiology ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects ; Middle Aged ; Aged ; Prospective Studies ; Case-Control Studies ; *Antineoplastic Agents, Immunological/therapeutic use ; },
abstract = {BACKGROUND: The gut microbiome influences the host immune system, cancer development and progression, as well as the response to immunotherapy during cancer treatment. Here, we analyse the composition of the gut bacteriome in metastatic Non-Small Cell Lung Cancer (NSCLC) patients receiving Pembrolizumab immunotherapy within a prospective maintenance trial through opportunistic sampling during treatment.<br><br>METHODS: The gut microbiome profiles of NSCLC patients were obtained from stool samples collected during Pembrolizumab treatment and analysed with 16S rRNA metagenomics sequencing. Patient profiles were compared to a group of healthy individuals of matching ethnic group, age, sex, BMI and comorbidities.<br><br>RESULTS: A significant decrease in the treated patients was observed in two prominent bacterial families of the phylum Firmicutes, Lachnospiraceae and Ruminoccocaceae, which comprised 31.6% and 21.8% of the bacteriome in the healthy group but only 10.9% and 14.2% in the treated patient group, respectively. Species within the Lachnospiraceae and Ruminococcaceae families are known to break down undigested carbohydrates generating short chain fatty acids (SCFA), such as butyrate, acetate and propionate as their major fermentation end-products, which have been implicated in modifying host immune responses. In addition, a significant increase of the Bacteroidacaeae family (Bacteroidetes phylum) was observed from 10.7% in the healthy group to 23.3% in the treated patient group. Moreover, and in agreement with previous studies, a decrease in the Firmicutes to Bacteroidetes ratio in the metastatic NSCLC Pembrolizumab-treated patients was observed.<br><br>CONCLUSION: The observed differences indicate dysbiosis and a compromised intestinal health status in the metastatic NSCLC Pembrolizumab-treated patients. This data could inform future studies of immunotherapy treatment responses and modulation of the gut microbiome to minimise dysbiosis prior or concurrent to treatment.<br><br>TRIAL REGISTRATION: SWIPE Trial (NCT02705820).},
}
@article {pmid40356165,
year = {2025},
author = {Park, C and Park, J and Chang, D and Kim, S},
title = {Development of reference-based model for improved analysis of bacterial community.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116380},
doi = {10.1016/j.foodres.2025.116380},
pmid = {40356165},
issn = {1873-7145},
mesh = {RNA, Ribosomal, 16S/genetics ; *Probiotics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; },
abstract = {Probiotic bacteria play a vital role in maintaining gut microbial homeostasis and are widely used in various commercial products. Although 16S rRNA amplicon-based next-generation sequencing (NGS) is commonly used to analyze probiotic products, biases can arise from various 16S rRNA amplification regions, sequencing platforms, and library kits. In this study, a reference-based bias correction model was developed to correct sequencing biases. The model was validated using eight mock communities and 12 commercial products, which were analyzed across multiple NGS platforms and various 16S rRNA regions. Specific primer-probe assays were developed for accurate bacterial quantification, and their specificity was validated and used in conjunction with droplet digital PCR (ddPCR) to establish initial bacterial ratios within communities. Analysis of the mock communities revealed platform- and region-specific biases, with specific species consistently over- or under-represented. Similarly, commercial product analyses have shown biased outcomes owing to varying sequencing protocols. The correction model, based on PCR efficiencies from the reference communities, successfully corrected biased ratios across different amplification regions and platforms to achieve results that closely matched the proportions predicted by ddPCR. The model effectively corrected the biases arising from the different polymerases. Notably, partial references containing approximately 40 % of the species achieved correction results that were comparable to those of the complete references. This approach demonstrates the potential for improving microbiome analysis accuracy within predictable ranges, and could serve as a model for addressing sequencing bias in metagenomic research.},
}
@article {pmid40356145,
year = {2025},
author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q},
title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116488},
doi = {10.1016/j.foodres.2025.116488},
pmid = {40356145},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; },
abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.},
}
@article {pmid40356136,
year = {2025},
author = {Luo, Y and Tang, R and Huang, Y},
title = {Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116474},
doi = {10.1016/j.foodres.2025.116474},
pmid = {40356136},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Rubus/chemistry ; *Antioxidants/pharmacology/chemistry ; *Pectins/chemistry/pharmacology ; Prebiotics/analysis ; *Polysaccharides/chemistry/pharmacology ; *Fruit/chemistry ; Humans ; *Plant Extracts/chemistry/pharmacology ; },
abstract = {Red raspberries are associated with various health benefits, with pectic polysaccharides as their primary component and potential key contributor to these effects. This study aimed to evaluate the antioxidant and prebiotic potential of four red raspberry pectic polysaccharides (RP)-EN-RP (enzyme-assisted extraction), AC-RP (acid-assisted extraction), AL-RP (alkali-assisted extraction), and US-RP (ultrasound-assisted extraction)-and to elucidate the relationship between their structure and function. AC-RP and US-RP contained higher proportions of homogalacturonan (HG) at 50.92 % and 53.10 %, respectively, while EN-RP and AL-RP exhibited higher proportions of rhamnogalacturonan-I (RG-I) at 63.89 % and 43.37 %, respectively. All four polysaccharides demonstrated significant antioxidant and prebiotic properties. AL-RP exhibited the strongest DPPH radical scavenging activity, while US-RP showed the highest hydroxyl radical scavenging ability. These pectic polysaccharides were highly fermentable, significantly modulating gut microbiota composition and promoting the production of propionic acid, particularly EN-RP and AL-RP. Compared to the blank group, RP intervention significantly enriched Bacteroides, Phocaeicola, Bifidobacterium, Limosilactobacillus, and Paraprevotella. Carbohydrate-active enzyme genes in metagenomes revealed that glycoside hydrolases played a vital role in the degradation and utilization of red raspberry polysaccharides. Furthermore, correlation analysis indicated that a higher RG-I proportion and an elevated Rha/GalA ratio enhanced the abundance of certain beneficial microbial species and increased propionic acid production. These findings advance the understanding of the structure-function relationship of natural pectic polysaccharides and highlight their potential for tailoring gut microbiota and promoting health through precise dietary interventions.},
}
@article {pmid40355758,
year = {2025},
author = {Saeedi Saravi, SS and Pugin, B and Constancias, F and Shabanian, K and Spalinger, M and Thomas, A and Le Gludic, S and Shabanian, T and Karsai, G and Colucci, M and Menni, C and Attaye, I and Zhang, X and Allemann, MS and Lee, P and Visconti, A and Falchi, M and Alimonti, A and Ruschitzka, F and Paneni, F and Beer, JH},
title = {Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {40355758},
issn = {2662-8465},
support = {#310030_21A053//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #CRSK-3_229134//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #21A053//Novartis Stiftung f&#xfc;r Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; },
abstract = {Endothelial cell senescence is a key driver of cardiovascular aging, yet little is known about the mechanisms by which it is induced in vivo. Here we show that the gut bacterial metabolite phenylacetic acid (PAA) and its byproduct, phenylacetylglutamine (PAGln), are elevated in aged humans and mice. Metagenomic analyses reveal an age-related increase in PAA-producing microbial pathways, positively linked to the bacterium Clostridium sp. ASF356 (Clos). We demonstrate that colonization of young mice with Clos increases blood PAA levels and induces endothelial senescence and angiogenic incompetence. Mechanistically, we find that PAA triggers senescence through mitochondrial H2O2 production, exacerbating the senescence-associated secretory phenotype. By contrast, we demonstrate that fecal acetate levels are reduced with age, compromising its function as a Sirt1-dependent senomorphic, regulating proinflammatory secretion and redox homeostasis. These findings define PAA as a mediator of gut-vascular crosstalk in aging and identify sodium acetate as a potential microbiome-based senotherapy to promote healthy aging.},
}
@article {pmid40355744,
year = {2025},
author = {Schreiber, S and Waetzig, GH and López-Agudelo, VA and Geisler, C and Schlicht, K and Franzenburg, S and di Giuseppe, R and Pape, D and Bahmer, T and Krawczak, M and Kokott, E and Penninger, JM and Harzer, O and Kramer, J and von Schrenck, T and Sommer, F and Zacharias, HU and , and Millet Pascual-Leone, B and Forslund, SK and Heyckendorf, J and Aden, K and Hollweck, R and Laudes, M and Rosenstiel, P},
title = {Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40355744},
issn = {2522-5812},
support = {EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: RTF-VI//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SO1141/10-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1470, SFB1449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-2, RTF-VI, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med CKDNapp 01ZX1912A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; K126408//Christian-Albrechts-Universit&#xe4;t zu Kiel (Christian-Albrechts-University Kiel)/ ; },
abstract = {Cellular NAD[+] depletion, altered tryptophan metabolism and gut microbiome dysbiosis are associated with disease progression and unfavourable clinical outcomes in COVID-19. Here, we show that supplementing tryptophan metabolism with nicotinamide alleviates COVID-19 symptoms. We evaluate a 4-week intervention with a novel nicotinamide formulation (1,000 mg) in a prospective, double-blind, randomized, placebo-controlled trial in 900 symptomatic outpatients with PCR-proven COVID-19. In the primary analysis population of participants at risk for severe COVID-19, 57.6% of those receiving nicotinamide and 42.6% receiving placebo recover from their performance drop at week 2 (P = 0.004). Nicotinamide is also beneficial for returning to normal activities (P = 0.009). Effects on gut metagenomic signatures parallel clinical efficacy, suggesting that nicotinamide influences COVID-19-associated faecal microbiome changes. After 6 months, responders to nicotinamide in acute COVID-19 show fewer post-COVID symptoms than placebo responders (P = 0.010). No relevant safety signals are observed. Overall, our results show that nicotinamide leads to faster recovery of physical performance and modulates COVID-19-associated faecal microbiome changes.},
}
@article {pmid40355385,
year = {2025},
author = {Wang, L and Chen, Y and Wang, Q and Wang, F},
title = {Microbial imbalances linked to early pregnancy loss: a comparative analysis of vaginal microbiota.},
journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {38},
number = {1},
pages = {2496787},
doi = {10.1080/14767058.2025.2496787},
pmid = {40355385},
issn = {1476-4954},
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Case-Control Studies ; *Abortion, Spontaneous/microbiology ; Adult ; *Microbiota ; Young Adult ; },
abstract = {OBJECTIVE: To explore the role and related functions of vaginal microbiota in early pregnancy loss.<br><br>METHODS: This study was a case-control study with a comparison group (reference group). We recruited 178 women, including 73 who had experienced at least one early clinical pregnancy loss and 105 patients with one live birth and no history of pregnancy loss. Data on demographics, disease history, menstrual and reproductive history was collected. The case group patients were sampled immediately upon presenting with pregnancy loss at their first visit. The reference group patients underwent samples when they chose to participate voluntarily. All vaginal discharge was performed DNA Preparation and Metagenomics Sequencing. DNA extraction was performed using the phenol/trichloromethane method and the DNA fragments were then size-selected to 300-700 bp using magnetic beads. The selected fragments were repaired and ligated with indexed adaptors. The captured DNA was amplified again by PCR and circularized to create a single-stranded circular (ssCir) library. The ssCir library was subsequently amplified through rolling circle amplification (RCA) to produce DNA nanoballs (DNBs). The DNBs were then loaded onto a flow cell and sequenced using the DNBSEQ Platform. Nonparametric tests, including Kruskal-Wallis and Wilcoxon tests, were employed. Relative abundance between groups was compared, and differential species selection was performed using the LEfSe software with linear discriminant analysis.<br><br>RESULTS: 1. PCoA analysis based on Bray-Curtis distances at the species level revealed a difference between the groups (p = 0.011). At the genus level, &#x3b1;-diversity, assessed using the Shannon, Simpson, and Inverse Simpson indices, indicated higher bacterial richness and diversity in the control group (Shannon: mean 0.554 vs. 0.383, p = 0.0044; Simpson: mean 0.254 vs. 0.179, p = 0.0043; Inverse Simpson: mean 1.636 vs. 1.414, p = 0.0043); At the genus level, 107 microbial genera were identified, 18 of which displayed statistically significant differences. At the species level, 23 microbial species showed significant differences between the two groups. 2. We analyzed the differences in the most abundant phyla, genera, and species, with a particular focus on the top 20 most abundant genera and species. Firmicutes and Proteobacteria were significantly more prevalent among patients with pregnancy loss (PL). Among the top 20 most abundant genera, Streptococcus and Porphyromonas were significantly more abundant in patients with PL, whereas Bifidobacterium was significantly more prevalent in the reference group. Among the 20 most abundant species, Lactobacillus crispatus was significantly more prevalent in patients with PL, whereas common in the control group. 3. Principal Coordinates Analysis (PCoA) of Bray-Curtis distances, highlight their distinct clustering patterns, suggesting a notable difference between the metabolic pathways of the two groups. Key pathways with a negative correlation to PL include those related to amino acid biosynthesis, lipid metabolism, and nucleotide biosynthesis.<br><br>CONCLUSION: Our study highlights the association between vaginal microbiota dysbiosis and EPL, identifying specific microbial taxa that may contribute to pregnancy loss. These findings underscore the importance of the vaginal microbiome in reproductive health and open up new avenues for research into microbiome-based diagnostics and therapies. By integrating microbial, immune, and environmental data, future research has the potential to uncover the mechanisms underlying EPL and develop targeted interventions to improve pregnancy outcomes.},
}
@article {pmid40355358,
year = {2025},
author = {Zhang, WL and Zu, YL and Huang, ZH and Li, Z and Gui, RR and Wang, J and Wang, XJ and Wang, HL and Fan, XX and Song, YP and Fang, BJ and Zhou, J},
title = {[BK virus nephropathy after allogeneic hematopoietic stem cell transplantation: a case report and literature review].},
journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi},
volume = {46},
number = {3},
pages = {273-275},
doi = {10.3760/cma.j.121090-20240810-00298},
pmid = {40355358},
issn = {0253-2727},
mesh = {Humans ; Male ; *Hematopoietic Stem Cell Transplantation/adverse effects ; BK Virus ; Young Adult ; *Polyomavirus Infections ; *Kidney Diseases/virology/etiology ; *Tumor Virus Infections ; Transplantation, Homologous ; },
abstract = {A 20-year-old male patient with T-lymphoblastic lymphoma/leukemia received 9/10 human leukocyte antigen-compatible unrelated peripheral blood stem cell transplantation. He was transplanted with 5.91×10(8) mononuclear cells/kg and 2.88×10(6) CD34(+) cells/kg, and neutrophil engraftment was obtained at +11 days and platelet engraftment at +9 days. After transplantation, he presented with repeatedly increased serum creatinine levels, BK virus (BKV) -associated hemorrhagic cystitis, and BKV viremia. BK virus nephropathy was diagnosed based on renal biopsy and metagenomic next-generation sequencing. After adjusting the immunosuppressant, intravenous immunoglobulin, and donor lymphocyte infusion treatment, the patient's renal function deteriorated progressively, and he eventually died of multiple organ failure at +289 days.},
}
@article {pmid40354774,
year = {2025},
author = {Hu, T and He, S and Gao, Z and Feng, L and Jiang, J and Zhao, Q and Wei, L},
title = {Micro-mechanism of rhamnolipid promoting acid production during anaerobic digestion: protein structures, metagenomics and molecular dynamics simulations.},
journal = {Water research},
volume = {283},
number = {},
pages = {123795},
doi = {10.1016/j.watres.2025.123795},
pmid = {40354774},
issn = {1879-2448},
abstract = {The addition of rhamnolipid (RL) is a promising strategy to enhance volatile fatty acids (VFAs) production in anaerobic digestion (AD) systems. However, the microscopic mechanisms underlying this enhancement remain poorly understood. This study investigates the micro-mechanisms by which RL promotes VFAs production, integrating protein structural analysis, metagenomics, and molecular dynamics simulations. Experimental results revealed that adding RL at 0.08 g/g TS significantly increased VFAs production to 11,441.8 mg COD/L. Protein structural analysis revealed disruption of amide I-related C = O groups and amide II-related CN and NH bonds, indicating the release or structural alteration of sludge proteins. Metagenomic analysis indicated an increase in the abundance of microbial communities and related genes, suggesting that RL enhanced the activity of acid-producing microorganisms and related metabolic pathways. Furthermore, molecular docking and molecular dynamics simulations indicated that RL spontaneously aggregated and absorbed acetate kinase (AK), altering its conformation and reducing structural compactness, which made acetyl phosphate (AcP) more accessible to the binding site of AK. RL reduced the energy barrier associated with the polar solvation interactions, increasing the contributions of key residues (LYS176 and GLU234) to the binding free energy, which enhanced the binding affinity of AK-AcP complex. This study provides a comprehensive molecular basis for how RL promotes VFAs production in AD, offering a promising strategy for optimizing acid production.},
}
@article {pmid40354675,
year = {2025},
author = {Zhi, N and Chang, X and Zha, L and Zhang, K and Wang, J and Gui, S},
title = {Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156653},
doi = {10.1016/j.phymed.2025.156653},
pmid = {40354675},
issn = {1618-095X},
abstract = {BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.<br><br>PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.<br><br>STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.<br><br>RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.<br><br>CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.},
}
@article {pmid40354439,
year = {2025},
author = {Llarena, AK and Haverkamp, THA and Gulliksen, WS and Herstad, K and Holst-Jensen, A and Skjerve, E and Rannem, L and Rodriguez-Campos, S and Øines, &#xd8;},
title = {DNA extraction protocols for animal fecal material on blood spot cards.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0313808},
doi = {10.1371/journal.pone.0313808},
pmid = {40354439},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology/chemistry ; Dogs ; Cattle ; Metagenomics/methods ; Horses ; Swine ; Sheep ; *DNA/isolation &amp; purification ; *DNA, Bacterial/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Collecting fecal samples using dry preservatives is an attractive option in large epidemiological studies as they are easy to use, cheap and independent of cold chain logistics. Here, we test four DNA extraction methods with the aim of identifying an efficient procedure to extract high-quality DNA from fecal material of canine, sheep, equine, bovine, and pig collected on dry blood spot cards, with the goal of generating good quality shotgun metagenomics datasets. Further, the suitability of Illumina shotgun metagenomic sequencing at 20 million paired-end (PE) read depth per sample was assessed on its ability to successfully characterize the taxonomic and functional aspects of the resulting fecal microbiome.<br><br>METHODS: DNA was extracted from pig feces and mock communities collected on blood spot cards using four DNA extraction methods; two different methods of the QIAsymphony&#xae; PowerFecal&#xae; Pro DNA Kit, the ZymoBIOMICS&#x2122; DNA Miniprep Kit, and the MagNA Pure 96 DNA and Viral NA Small Volume Kit. Possible extraction bias was controlled by amplicon sequencing of mock communities. Fecal samples from canine, sheep, equine, bovine, and pig were thereafter subjected to the best performing DNA extraction method and shotgun metagenomic sequencing to determine sequencing efforts for functional and taxonomic analysis.<br><br>RESULTS: The four DNA extraction methods demonstrated similar community composition in the sequenced bacterial mock community. The QIAsymphony&#xae; PowerFecal&#xae; Pro DNA Kit was identified as the DNA extraction method of choice, and the resulting DNA was subjected to shotgun metagenomic sequencing with 20million PE reads. We found that higher number of reads increased the richness of observed genera between 100,000 and 5 million reads, after which higher sequencing effort did not increase the richness of the metagenomes. As for functional analysis, the number of low abundance functions in the metagenomes of the animals' feces increased with sequencing depth above 20 million PE reads.<br><br>CONCLUSION: Our experiments identified several methods suitable for extracting DNA from feces collected on blood spot cards. The QIAGEN's Blood and Tissue kit on the QiaSymphony platform fulfilled the criteria of high yield, quality, and unbiased DNA, while maintaining high throughput for shotgun metagenomic sequencing. A sequencing depth of 20 million PE reads proved adequate for taxonomic estimations and identifying common functional pathways. Detecting rarer traits, however, requires more sequencing effort.},
}
@article {pmid40353658,
year = {2025},
author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C},
title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0074925},
doi = {10.1128/mbio.00749-25},
pmid = {40353658},
issn = {2150-7511},
abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.},
}
@article {pmid40352947,
year = {2025},
author = {Zhong, QL and Xiong, JQ},
title = {A Globally Distributed Cyanobacterial Nitroreductase Capable of Conferring Biodegradation of Chloramphenicol.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0692},
pmid = {40352947},
issn = {2639-5274},
abstract = {Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production. Yet, the interactions between cyanobacteria and antibiotics remain unclear. This study revealed that Synechocystis sp., a cyanobacterial species, removed 94.27% of 0.1 mg l[-1] chloramphenicol (CAP) through enzyme-mediated degradation. While cytochrome P450 enzymes (CYP450s) were found unnecessary for CAP removal, a gene encoding cyanobacterial nitroreductase was significantly up-regulated (7.85-fold) under CAP exposure. The purified nitroreductase exhibited strong binding affinity to CAP (K d = 2.9 nM) and a Michaelis constant (K m) of 104.0 μM. By engineering a bacterial strain with nitroreductase, 94.43% of 0.1 mg l[-1] CAP was removed within 2 h. Metagenomic and metatranscriptomic analyses showed that nitroreductase genes and transcripts are globally distributed across diverse microbial phyla. These findings uncover a novel enzyme for CAP degradation and advance sustainable biotechnologies to mitigate antibiotic pollution, addressing critical environmental challenges in aquaculture and other industries globally.},
}
@article {pmid40351504,
year = {2025},
author = {Wilkhoo, HS and Islam, AW and Wilkhoo, HS and Hussain, S and Singh, B and Kadam, SR},
title = {Clinical Insights and Advancements in Human Metapneumovirus Management and Prognosis.},
journal = {Discoveries (Craiova, Romania)},
volume = {13},
number = {1},
pages = {e204},
pmid = {40351504},
issn = {2359-7232},
abstract = {Human metapneumovirus is a respiratory pathogen that infects children, the elderly, and immunocompromised individuals. Despite its global prevalence, underdiagnosis persists because of clinical overlap with other respiratory viruses. The current approach is mostly supportive, with oxygen therapy and hydration being crucial interventions. Ribavirin contains antiviral properties but has little clinical application. Vaccine development is moving forward, with prospects including live-attenuated, subunit-based, and virus-like particle vaccines. Molecular diagnostics, such as RT-PCR and metagenomic sequencing, have increased detection rates, which aids epidemiological monitoring. Monoclonal antibodies targeting the fusion (F) protein are being studied for passive immunity, while immunomodulatory treatments such as corticosteroids and intravenous immunoglobulins may help treat severe cases. Emerging treatments include fusion inhibitors and pan-pneumovirus vaccinations that protect against HMPV and RSV. Future research should concentrate on optimizing antiviral methods, increasing vaccination trials, and improving surveillance to detect outbreaks. A multidisciplinary approach that combines virology, immunology, and epidemiology is required to reduce HMPV's effect and improve patient outcomes. This review serves as a comprehensive literature about HMPV which provides all the crucial clinical perspectives and the latest advancements in management, antivirals, patient prognosis as well and diagnostic modalities.},
}
@article {pmid40351315,
year = {2025},
author = {Li, S and Sun, Y and Cao, S and Guo, T and Tong, X and Zhang, Z and Sun, J and Yang, Y and Wang, Q and Li, D and Min, L},
title = {Asparagopsis taxiformis mitigates ruminant methane emissions via microbial modulation and inhibition of methyl-coenzyme M reductase.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1586456},
pmid = {40351315},
issn = {1664-302X},
abstract = {INTRODUCTION: Asparagopsis taxiformis (A. taxiformis) has shown great potential to mitigate methane (CH4) emissions in recent years. This study aims to evaluate the impact of A. taxiformis on methane emissions and to fill the knowledge gap regarding its mechanisms of action in affecting CH4 metabolism and rumen fermentation.<br><br>METHODS: The experimental design consisted of a control group (CON) and test groups supplemented with 2% (Low), 5% (Mid), and 10% (High) of dried and freeze-dried treatment A. taxiformis, respectively, for 48&#x202f;h of in vitro rumen fermentation. The optimal combination strategy for mitigating CH4 emissions was confirmed by analyzing nutrient degradation, CH4 production and rumen fermentation parameters, and the mechanism of action was analyzed by metagenomic and metabolomic approaches.<br><br>RESULTS AND DISCUSSION: The results showed that freeze-dried treatment had better potential to mitigate CH4 emissions than dried treatment, and supplementation of freeze-dried treatments at Low, Mid, and High groups significantly reduced CH4 production by 32.44%, 98.53%, and 99.33%, respectively. However, the High group exhibited a huge negative impact on rumen fermentation. Therefore, subsequent analyses focused on the Low and Mid groups to explore the underlying mechanisms. Metagenomics analyses showed that supplementation of freeze-dried treatment with the Mid-level supplementation significantly increased the relative abundance of propionate-producing bacteria such as Prevotella, Ruminobacter, and Succinivibrio, while inhibited acetate-producing bacteria such as Ruminococcus, altered the pattern of volatile fatty acid (VFA) synthesis in the rumen, and reduced H2 availability for methanogenesis and promoted propionate production, indirectly alleviating CH4 production. Moreover, by suppressing the relative abundance of Methanobrevibacter, CH4 production in the rumen was directly suppressed. Furthermore, KEGG pathway analysis showed that A. taxiformis significantly inhibited the abundance of K00399, methyl-coenzyme M reductase alpha subunit, which directly inhibited CH4 synthesis. Metabolomics analysis of A. taxiformis supplementation significantly enriched ketoglutarate, malate, isocitrate, and melatonin, which may have reduced the release of rumen fermented H2, thereby mitigating CH4 emissions. In summary, freeze-dried treatment A. taxiformis at the 5% supplementation level achieved the optimal balance between CH4 mitigation and rumen fermentation efficiency.},
}
@article {pmid40350519,
year = {2025},
author = {Schultz, J and Jamil, T and Sengupta, P and Sivabalan, SKM and Rawat, A and Patel, N and Krishnamurthi, S and Alam, I and Singh, NK and Raman, K and Rosado, AS and Venkateswaran, K},
title = {Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {117},
pmid = {40350519},
issn = {2049-2618},
support = {BAS/1/1096-01-01//KAUST Baseline Grant/ ; PPR-ROSES-2006//National Aeronautical and Space Administration/ ; },
mesh = {*Spacecraft ; United States National Aeronautics and Space Administration ; *Bacteria/genetics/isolation &amp; purification/classification ; United States ; Biofilms/growth &amp; development ; Space Flight ; *Extremophiles/genetics/isolation &amp; purification/classification ; *Genome, Bacterial ; Humans ; Microbiota/genetics ; Genomics ; Metagenome ; Phylogeny ; },
abstract = {BACKGROUND: Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.<br><br>RESULTS: During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n&#x2009;=&#x2009;13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for &#x3b5;-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited&#xa0;for&#xa0;zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.<br><br>CONCLUSION: Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.},
}
@article {pmid40350492,
year = {2025},
author = {Ding, Y and Ke, J and Hong, T and Zhang, A and Wu, X and Jiang, X and Shao, S and Gong, M and Zhao, S and Shen, L and Chen, S},
title = {Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {287},
pmid = {40350492},
issn = {1471-2180},
support = {STEP 2024QZKK02010//Supported by the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2208085MC39//Natural Science Foundation of Anhui Province, China/ ; },
mesh = {China ; *Lakes/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Archaea/classification/genetics/isolation &amp; purification ; Phylogeny ; DNA, Archaeal/genetics ; Salinity ; *Biodiversity ; Alkalies/analysis ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; Sodium Chloride ; Sequence Analysis, DNA ; Bacteria/classification/genetics ; },
abstract = {Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.},
}
@article {pmid40350460,
year = {2025},
author = {Zhang, X and Zhong, R and Wu, J and Tan, Z and Jiao, J},
title = {Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {118},
pmid = {40350460},
issn = {2049-2618},
support = {32372829, 31972992//National Natural Science Foundation of China/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; 2022RC1158//The Science and Technology innovation Program of Hunan Province/ ; 2023382//Youth Innovation Promotion Association CAS/ ; },
mesh = {Animals ; *Goats/microbiology ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; Animal Feed/analysis ; Metagenomics/methods ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fibrobacter/metabolism/genetics/isolation &amp; purification ; Ruminococcus/metabolism/genetics/isolation &amp; purification ; Diet/veterinary ; Cecum/microbiology/metabolism ; Cellulose/metabolism ; Fatty Acids, Volatile/metabolism ; Polysaccharides/metabolism ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.<br><br>RESULTS: The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).<br><br>CONCLUSIONS: These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.},
}
@article {pmid40350266,
year = {2025},
author = {Ohyama, Y and Miura, T and Furukawa, M and Shimamura, M and Asami, Y and Yamazoe, A and Uchino, Y and Kawasaki, H},
title = {A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24076},
pmid = {40350266},
issn = {1347-4405},
mesh = {Chromatography, High Pressure Liquid/methods ; *Bacteria/genetics/isolation &amp; purification/classification ; Humans ; *Microbiota/genetics ; *Genome, Bacterial ; Metagenomics/methods ; Reproducibility of Results ; },
abstract = {Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.},
}
@article {pmid40350102,
year = {2025},
author = {El-Son, MAM and Elbahnaswy, S and Khormi, MA and Aborasain, AM and Abdelhaffez, HH and Zahran, E},
title = {Harnessing the Fish Gut Microbiome and Immune System to Enhance Disease Resistance in Aquaculture.},
journal = {Fish &amp; shellfish immunology},
volume = {},
number = {},
pages = {110394},
doi = {10.1016/j.fsi.2025.110394},
pmid = {40350102},
issn = {1095-9947},
abstract = {The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.},
}
@article {pmid40349998,
year = {2025},
author = {Patel, M and Patel, K},
title = {Emerging Insights of Staphylococcus spp. in Human mastitis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107685},
doi = {10.1016/j.micpath.2025.107685},
pmid = {40349998},
issn = {1096-1208},
abstract = {Human mastitis represents a prevalent and intricate condition that significantly challenges breastfeeding women, often exacerbated by pathogenic bacteria such as Staphylococcus aureus. A deep understanding of the interplay between human mastitis, the breast milk microbiome, and causative agents is imperative. This understanding must focus on the bacterium's virulence and resistance genes, which critically influence the severity and persistence of mastitis. Current methods for detecting these genes, including Polymerase Chain Reaction (PCR), 16S rRNA gene sequencing, shotgun metagenomic sequencing, multiplex PCR, whole genome sequencing (WGS), loop-mediated isothermal amplification (LAMP), CRISPR-based assays, and microarray technology, are vital in elucidating bacterial pathogenicity and resistance profiles. However, advanced attention is required to refine diagnostic techniques, enabling earlier detection and more effective therapeutic approaches for human mastitis. The involvement of Staphylococcus aureus in human infection should be a prime focus, especially in women's health, which deals directly with neonates. Essential virulence genes in Staphylococcus species are instrumental in infection mechanisms and antibiotic resistance, serving as potential targets for personalized treatments. Thus, this review focuses on Staphylococcus aureus induced mastitis, examining its virulence factors and detection techniques to advance diagnostic and therapeutic strategies.},
}
@article {pmid40349794,
year = {2025},
author = {Dai, Y and Wang, B and Zhang, M and Li, W and Wang, L and Zou, Y and Peng, Y},
title = {Thermal activation of peroxymonosulfate for enhanced volatile fatty acids production and phosphorus release during anaerobic fermentation of iron-rich sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132653},
doi = {10.1016/j.biortech.2025.132653},
pmid = {40349794},
issn = {1873-2976},
abstract = {Heat-peroxymonosulfate (PMS) pre-treatment was simultaneously used for phosphorus (P) release and volatile fatty acids (VFAs) production in this study. Maximum P concentrations increased from 10.3 ± 0.4 mg/L in PMS-0 to 246.1 ± 1.6 mg/L in PMS-0.8, with 41.4 % of total P released. VFAs production on day 5 increased from 2409.1 ± 30.8 mg chemical oxygen demand (COD)/L in PMS-0 to 2995.4 ± 86.5 mg COD/L in PMS-0.8. Metagenomic analysis showed that an increase in PMS dosage was detrimental to P release during polyphosphate hydrolysis by polyphosphate-accumulating organisms; functional genes involved in S cycling increased, suggesting that sulfate reduction was a critical cause of P release from iron-rich sludge during anaerobic fermentation (AF). These results provide important insights for the improvement of P release efficiency and acid production during AF, enhancing the potential for resource recovery from iron-rich sludge.},
}
@article {pmid40349588,
year = {2025},
author = {Zhang, S and Li, X and Li, X and Fu, Y and Chen, L and Wang, W and Lin, Q and Lou, H and Yao, Y and Chen, W and Zhong, C and Ye, J and Yao, Y and Guo, H and Yu, Y and Zhou, H},
title = {Optimisation and clinical validation of a metagenomic third-generation sequencing approach for aetiological diagnosis in bronchoalveolar lavage fluid of patients with pneumonia.},
journal = {EBioMedicine},
volume = {116},
number = {},
pages = {105752},
doi = {10.1016/j.ebiom.2025.105752},
pmid = {40349588},
issn = {2352-3964},
abstract = {BACKGROUND: Metagenomic Third Generation Sequencing (mTGS), based on nanopore technology, has emerged as a promising tool for the rapid diagnosis of pneumonia pathogens. However, this technology currently lacks standardised technical protocols, quality control measures, and comprehensive performance evaluations for the simultaneous detection of bacteria, fungi, and viruses in clinical settings.<br><br>METHODS: We optimised the mTGS workflow by refining key parameters (cell wall lysis, fragment size selection, host DNA depletion, and sequencing depth) using reference samples and bronchoalveolar lavage fluid (BALF) from eight patients with pneumonia. These optimisations formed the basis for a standardised mTGS protocol. To assess the clinical diagnostic value of the optimised mTGS, a multicentre prospective cohort study involving 313 pneumonia-suspected patients was conducted. Each BALF sample was tested using conventional microbiological testing (CMTs), metagenomic next-generation sequencing (mNGS), pre-optimised mTGS, and optimised mTGS.<br><br>FINDINGS: The optimised mTGS protocol, based on the refined cell wall lysis, fragment size selection, no host DNA depletion, and 800 MB sequencing depth, achieved a tenfold increase in sensitivity compared with pre-optimised mTGS for detecting the species of Bacillus subtilis, Mycobacterium tuberculosis, Mycobacterium avium, Cryptococcus neoformans, and Human papillomavirus in reference samples. In the prospective cohort, 274 patients with a confirmed diagnosis of pneumonia were identified, yielding 376 distinct microbes. The mTGS identified more microbes than CMTs (314 vs. 115), with a 45.30% increase in sensitivity (84.70% vs. 39.40%, P < 0.01, Chi-square test/Fisher's exact test). Compared with pre-optimised mTGS, the sensitivity of optimised mTGS increased by 32.51% (84.70% vs. 52.19%, P < 0.01, Chi-square test/Fisher's exact test). mTGS showed comparable performance to mNGS (84.70% vs. 79.90%, P = 0.14,Chi-square test/Fisher's exact test), both significantly outperforming CMTs. mNGS was more sensitive for detecting Non-tuberculous mycobacteria, Pneumocystis jirovecii, and Aspergillus spp., while mTGS demonstrated higher sensitivity for M. tuberculosis, Chlamydia psittaci, and Streptococcus pneumoniae. The overall diagnostic agreement between mTGS and clinical diagnosis was 81.80%.<br><br>INTERPRETATION: We optimised and validated a standardised mTGS protocol that significantly improved the ability to detect pathogens in the BALF of patients with pneumonia. Optimised mTGS demonstrated comparable performance to mNGS, making it a promising tool for the aetiological diagnosis of pneumonia.<br><br>FUNDING: The Research and Development Programme of Zhejiang Province (2023C03068, 2024C03187), the National Natural Science Foundation of China (82272338), the Key R&amp;D Plan of the Ministry of Science and Technology (China) of China (2022YFC2504502).},
}
@article {pmid40349412,
year = {2025},
author = {Ren, P and You, C and Chen, P and Mei, X and Yang, T and Xu, Y and Wang, X and Shen, Q and Wei, Z},
title = {Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128213},
doi = {10.1016/j.micres.2025.128213},
pmid = {40349412},
issn = {1618-0623},
abstract = {Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.},
}
@article {pmid40349120,
year = {2025},
author = {Jiang, S and Huang, S and Zhang, Z and Ma, W and Han, Z and Song, Y and Huo, D and Cui, W and Zhang, J},
title = {Gut microbiota drives structural variation of exogenous probiotics to enhance colonization.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2503371},
doi = {10.1080/19490976.2025.2503371},
pmid = {40349120},
issn = {1949-0984},
mesh = {*Probiotics/pharmacology ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Lactobacillus plantarum/genetics/growth &amp; development ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts ; Metagenomics ; },
abstract = {Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.},
}
@article {pmid40348945,
year = {2025},
author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H},
title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {114},
number = {5},
pages = {77},
pmid = {40348945},
issn = {1432-0800},
support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; },
abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.},
}
@article {pmid40348632,
year = {2025},
author = {Lotankar, M and Houttu, N and Benchraka, C and Lahti, L and Laitinen, K},
title = {Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104095},
doi = {10.1016/j.numecd.2025.104095},
pmid = {40348632},
issn = {1590-3729},
abstract = {BACKGROUND AND AIM: Gut microbiota may regulate metabolism but is incompletely characterized in pregnancy. Our objective was to investigate the relations using omics techniques.<br><br>METHODS AND RESULTS: In a cross-sectional setting, fecal and serum samples of 361 healthy pregnant women with overweight or obesity were analyzed with a combinatorial approach of metagenomics and targeted NMR-based metabolomics, with statistical and machine learning techniques to identify and analyze the extent to which the gut microbiota composition and predicted functions would be reflected in the serum metabolome. We identified five biclusters, each of which consisted of a set of gut microbial species and serum metabolites with correlated abundance profiles. Two of the biclusters included metabolites that have been linked to the cardiovascular health; one was linked with factors known to increase the risk i.e., various sizes of lipoprotein subclasses (VLDL and LDL), subclasses of relative lipoprotein lipid concentrations (VLDL, IDL, and LDL), apolipoprotein B, and an inflammation marker, glycoprotein acetylation. These metabolites were associated with abundances of species such as, Enterocloster bolteae and Ruminococcus gnavus. The second bicluster included metabolites linked with a reduced cardiovascular risk, such as different sizes of HDL (high-density lipoprotein), subclasses for relative lipoprotein lipid concentrations and mean diameter for HDL particles, and fatty acid ratios. These metabolites were associated with abundances of species, such as Bacteroides cellulosilyticus and Alistipes finegoldii. We did not observe any biclusters between predicted pathways and serum metabolites.<br><br>CONCLUSION: Overall, we identified five biclusters of co-abundant gut bacteria and serum metabolites , of which two were linked to pro-atherogenic and anti-atherogenic properties.<br><br>TRIAL REGISTRATION: www.<br><br>CLINICALTRIALS: Gov: NCT01922791.},
}
@article {pmid40348492,
year = {2025},
author = {Quigley, EMM},
title = {Microbial Influences on Irritable Bowel Syndrome.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {2},
pages = {351-365},
doi = {10.1016/j.gtc.2024.12.003},
pmid = {40348492},
issn = {1558-1942},
mesh = {*Irritable Bowel Syndrome/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolomics ; Metagenomics ; Dysbiosis ; },
abstract = {Since the description of postinfection irritable bowel syndrome (IBS), a role for gut microbes in the pathogenesis of IBS has been proposed. Molecular microbiological tools have now been applied to IBS, though data are largely derived from fecal samples with attendant limitations. Metagenomics, metabolomics, and other 'omics facilitate a comprehensive picture of the microbiome and its metabolic activity. Has a microbial signature characteristic of IBS been identified? The answer is no; this should not be a surprise given the heterogeneity of the phenotype and each individual's microbiome profile.},
}
@article {pmid40348264,
year = {2025},
author = {Hu, Z and Li, Z and Xu, Y and He, F and Zhang, J and Li, T},
title = {MgFe-LDHs/Vallisneria natans combined system for simultaneous elimination of endogenous N and P pollution in eutrophic water: Performance, synergetic mechanism, and metagenomics analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121798},
doi = {10.1016/j.envres.2025.121798},
pmid = {40348264},
issn = {1096-0953},
abstract = {Eutrophication is the main factor for the degradation of lake ecosystems. More than exogenous input, endogenous N and P nutrients are responsible for it. Although the P passivation technology with functional materials is common for alleviating endogenous P pollution, will it have the same effect for endogenous N removal? In this study, a novel MgFe-LDHs/Vallisneria natans (V. natans) combined system was established for effective eliminating endogenous N and P simultaneously. During remediation periods, MgFe-LDHs/V. natans combined system with the most obvious improvement for overlying water quality that was reflected by DO, ORP, and SS, and TP, TN, and NH4[+]-N removal efficiency were up to 99%. In sediments, TP and TN removal rate was approximately 68% and 63%, where the reduction of Org-P and NH4[+]-N accounted for the majority of it, respectively. Under stimulation of MgFe-LDHs, NH4[+]-N assimilation in V. natans could be promoted through improving the metabolizing enzymes activity. In turn, V. natans contributed to Org-P mineralization by secreting organic acid, further facilitating IP enrichment on MgFe-LDHs. Additionally, owing to the synergism between V. natans allelopathy and MgFe-LDHs, the symbiotic relationship between microbial communities was much closer and more stable, the expression of functional genes that relate to denitrification, assimilatory nitrate reduction, phosphorylation and organophosphorus mineralization processes were up-regulated prominently. That is, microorganisms acted synergistically were important for endogenous N and P elimination performance. This study proposed a high-efficiency and environmentally friendly materials/plants combined remediation technology for eutrophication, especially those where with much high endogenous N and P loading.},
}
@article {pmid40348210,
year = {2025},
author = {Lin, Z and Zhang, P and Shi, D and Zhang, Y and Wu, W and Tang, Q and Wang, Q and Wang, S},
title = {Association between the gut microbiota and cystitis: A two-sample mendelian randomization study combined with the GEO database.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107683},
doi = {10.1016/j.micpath.2025.107683},
pmid = {40348210},
issn = {1096-1208},
abstract = {BACKGROUND: Disturbances within the intestinal microbiota have emerged as a significant factor contributing to systemic inflammation, thereby rendering distant anatomical sites more vulnerable to various illnesses, including inflammatory conditions in the urinary tract such as cystitis. However, the causal relationship between dysbiosis of the gut microbiota and cystitis remains unclear. We sought to elucidate the causal relationship between the intestinal microbiota and cystitis employing Mendelian randomization (MR), offering insights into novel preventive and therapeutic strategies for managing cystitis.<br><br>METHOD: Summary statistics for the Genome-Wide Association Study (GWAS) of cystitis were sourced from the R5 release dataset provided by the FinnGen consortium, which included 8,081 cystitis cases and 195,140 controls. Single Nucleotide Polymorphisms (SNPs) that showed strong associations with 196 microbial taxa (encompassing 18,340 individuals) were selected as instrumental variables. To analyse the causal relationships between cystitis and gut microbiota, we employed four MR analysis methods: random effects, inverse variance weighting, weighted medians, and MR-Egger regression. Sensitivity analyses were performed using the Cochran's Q test, funnel plots, leave-one-out analyses, and the MR-Egger intercept test. We conducted metagenomic analysis of fecal samples from 7 patients with cystitis and 7 healthy controls to validate the findings from our MR results. To further elucidate the biological mechanisms, we conducted positional mapping of the extracted SNPs associated with the significant taxa. Additionally, we curated differentially expressed genes (DEGs) from three datasets about cystitis obtained from the Gene Expression Omnibus (GEO). Finally, we intersected the DEGs with the mapped genes to identify common genes of cystitis.<br><br>RESULTS: Our analysis revealed significant associations between specific gut microbiota and cystitis. IVW results revealed that four gut microorganisms, specifically, the genus RuminococcaceaeUCG011, genus Sutterella, family Porphyromonadaceae, and family Veillonellaceae (P&#x2009;<&#x2009;0.05), contributed to a reduction in the incidence of cystitis. Similarly, four cystitis-related bacteria, namely, the genus Marvinbryantia, the genus Odoribacter, the genus Ruminiclostridium6, and the genus Sellimonas, are thought to play a significant role in elevating the risk of cystitis (P&#x2009;<&#x2009;0.05). The metagenomic analysis revealed significant differences in the abundance of the genera Sutterella and Odoribacter in patients with cystitis compared to healthy controls. Additionally, we mapped causal SNPs to genes and identified 62 genes. Bioinformatics analysis reveals 161 common DEGs in cystitis. Through MR and bioinformatics analysis, we identified two common genes-ICAM1 and HP-as potential targets for cystitis.<br><br>CONCLUSION: Our research identified genetic connections between eight components of gut microbiota and two genes related to cystitis. These results offer important insights for subsequent studies into the complex relationship between gut microbiota and cystitis.},
}
@article {pmid40347608,
year = {2025},
author = {Ahmed, I and Zhuang, Z and Zhang, D and Li, P and Zhang, B},
title = {Temperature-driven dynamics of intracellular and extracellular antibiotic resistance genes during aerobic composting: Insights from qPCR and metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138519},
doi = {10.1016/j.jhazmat.2025.138519},
pmid = {40347608},
issn = {1873-3336},
abstract = {The widespread use of antibiotics in animal farming has accelerated the dissemination of antibiotic resistance genes (ARGs). Aerobic composting is an effective method for managing animal manure, yet its effects on intracellular (iARGs) and extracellular ARGs (eARGs) under different temperature regimes including control (LT), gradual increase temperature (GT), and initially enriched temperature (HT) remain unclear. This study investigated the dynamics of iARGs and eARGs across these temperature gradients during composting. Initial composting substrate harbored higher levels of iARGs than eARGs. After composting, ARG rebound was primarily driven by eARG enrichment. On day 40, iARGs decreased by 3.1 logs in HT, 1.2 logs in LT, and 1 log in GT, while eARGs decreased by 0.9 log only in HT but increased in LT and GT. Initially phyla Firmicutes and Proteobacteria were dominated, the microbial community shifted to Bacteroidetes in LT, Actinobacteria in GT, and retained Firmicutes dominance in HT on day 40. Metagenomic analysis revealed that 68 % ARG reduction was associated with plasmid-borne ARGs, with reductions of 83.4 % in HT, 68.2 % in GT, and 51.6 % in LT, whereas non-plasmid ARGs were reduced by up to 75 % across all treatments. Notably, plasmid conjugation was significantly inhibited under HT and GT conditions.},
}
@article {pmid40347566,
year = {2025},
author = {Jiang, J and Wu, H and Yuan, Y},
title = {Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca).},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {55},
number = {},
pages = {101529},
doi = {10.1016/j.cbd.2025.101529},
pmid = {40347566},
issn = {1878-0407},
abstract = {The influences of different bamboo species on the microbiome and metabolome of giant pandas (Ailuropoda melanoleuca) remain understudied. The aim of this study was to investigate the effects of different Phyllostachys species on the gut microbial communities and fecal metabolite profiles in giant pandas. Metagenome and metabolome were performed on the feces of giant pandas fed with different Phyllostachys species (P. edulis, P. iridescens, P. glauca, and P. violascens). The results of metagenome showed that dietary with P. glauca could notably decrease the microbial Shannon index. The relative abundances of both Cellulosilyticum and Pseudomonas were enhanced after dietary with P. iridescens, suggesting P. iridescens could enhance the cellulose-degrading function in giant pandas. However, dietary with P. glauca or P. violascens could increase the relative abundances of certain pathogenic bacteria (Escherichia, Shigella, and Klebsiella). Metabolomics analysis further revealed that all experimental groups exhibited notably elevated levels of fecal flavonoids and fatty acids. In addition, the correlation analysis showed that certain nutrients of bamboo leaves (mainly crude protein and Cu) were significantly correlated with several differential gut bacteria and fecal metabolites. Based on the present results, P. iridescens might be a substitute for the routinely used Phyllostachys species (P. edulis) in the captive management of giant pandas. The results have revealed that bamboo species is an important factor affecting the gut microbiota and fecal metabolites in giant pandas. Our results could provide important information about bamboo species-induced alterations on the microbiome and metabolome in giant pandas.},
}
@article {pmid40347421,
year = {2025},
author = {Akinbi, GO and Lin, Q and Fiola, TE and Rathore, RS and Badisa, VLD and Mwashote, B and Chen, G and Ibeanusi, V},
title = {Ecosystem assessment to support innovative advancements in soil sustainability in the major land resource areas of Mississippi through geochemical and metagenomics studies.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40347421},
issn = {1614-7499},
support = {NR204423XXXXC125-F1-SA1-21//U.S. Department of Agriculture/ ; },
abstract = {In the present study, the ecosystem of Roebuck (RF) and Nesbit blueberry plantation (NBP) farms in Mississippi state, USA that differed by type of fertilizer treatment was assessed using soil samples through geophysical-chemical parameters and metagenomics studies. Soil geophysical-chemical parameters such as pH, moisture, organic content, nutrients, and toxic metal concentrations were measured. Metagenomic analysis was performed to identify the bacterial communities in the soil samples. The results revealed that the pH of the NBP farm (organic fertilizer) was lower than that of the RF farm (chemical fertilizer). The NBP soil samples exhibited higher moisture and organic contents than the RF soil samples. The tested heavy metal concentrations in both farm soil samples were within the limits recommended by the EPA (United States Environmental Protection Agency). Different concentrations of nutrients were observed between these two farms soil samples. RF soil indicated greater species richness and a more balanced distribution of species abundances. Proteobacteria, Bacteroidota, and Actinobacteriota were the most abundant phyla observed in RF soil, whereas Proteobacteria, Acidobacteriota, and Actinobacteriota were the most abundant phyla observed in NBP soil. This study clearly demonstrated the effects of fertilizer type on the soil through variations in geophysical-chemical parameters, which subsequently changed the microbial communities. This study suggests that organic fertilizer application could be an effective method for sustainable soil quality as the organic fertilized soils exhibited higher moisture and organic content that promotes plant growth.},
}
@article {pmid40347034,
year = {2025},
author = {Song, L and He, W and Lu, H and Jiang, J and Ding, PH and He, F},
title = {Submucosal Microbiome in Peri-Implantitis: A Comparative Metagenomic Analysis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13407},
pmid = {40347034},
issn = {1600-0765},
support = {82470973;82271026;82170953//the National Natural Science Foundation of China/ ; 2024M762880//the Postdoctoral Science Foundation of China/ ; },
abstract = {Through metagenomic sequencing, this study reveals significant microbial and functional differences between peri-implant health and peri-implantitis, identifying pathogenic species, virulence genes, and antibiotic resistance markers that may contribute to disease progression.},
}
@article {pmid40346812,
year = {2025},
author = {Pryor, JC and Nieva, C and Talley, NJ and Eslick, GD and Duncanson, K and Burns, GL and Hoedt, EC and Keely, S},
title = {Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2500063},
doi = {10.1080/19490976.2025.2500063},
pmid = {40346812},
issn = {1949-0984},
mesh = {Humans ; *Celiac Disease/microbiology/enzymology ; *Gastrointestinal Microbiome ; *Glutens/metabolism ; *Duodenum/microbiology ; *Dyspepsia/microbiology ; *Peptide Hydrolases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.},
}
@article {pmid40346542,
year = {2025},
author = {Gao, H and Xu, L and Liu, Y and Wang, X and Zhu, S and Lin, H and Gao, Y and Mao, D and Lu, X and Luo, Y},
title = {Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {178},
pmid = {40346542},
issn = {1465-993X},
support = {2022BKY015//the Tianjin Graduate Research and Innovation Projects/ ; 42377426//the National Natural Science Foundation of China/ ; 18ZXDBSY00100//the Tianjin Science and Technology Plan Project/ ; 21JCYBJC01200//the Tianjin Municipal Natural Science Foundation/ ; 2023220//the Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; 2020YFC1806904//the National Key R&amp;D Program of China/ ; 41831287//the Key Projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; Animals ; *Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics ; Mice ; *Burkholderia cenocepacia/genetics/isolation &amp; purification/pathogenicity ; *Gastrointestinal Microbiome/genetics ; Male ; *Intensive Care Units/trends ; Female ; *Bacterial Translocation/physiology/genetics ; *Lung/microbiology ; Middle Aged ; Aged ; *Whole Genome Sequencing/methods ; *Genome, Bacterial ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Identifying the sources of pathogenic bacteria causing ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients is crucial for developing effective prevention and treatment strategies. However, the scarcity of reported cases with confirmed sources limits the ability to evaluate and manage VAP, which remains a major challenge for healthcare systems globally.<br><br>METHODS: Pathogens were isolated from endotracheal aspirate (ETA) samples of VAP patients using conventional culture techniques. Whole-genome comparisons, based on average nucleotide identity (ANI), were performed to identify genetically identical strains by comparing pulmonary isolate genomes with gut metagenome-derived bacterial genomes. Mouse models of pneumonia and colitis were used to validate the translocation of pathogenic bacteria from the gut to the lungs. Metagenomic analysis was performed to characterize the gut microbiome and resistome.<br><br>RESULTS: Pathogenic isolates were obtained from the ETA samples of seven VAP patients, with one isolate per sample. Among these, Escherichia coli (Ec1) and Burkholderia cenocepacia (Bc1) from two patients were genetically identical to strains in their respective gut microbiota, with ANI values above 99%, indicating gut-to-lung translocation. The Ec1 strain demonstrated increased resistance to cefazolin while remaining susceptible to gentamicin, amikacin, and kanamycin, compared to previously reported pneumonia-associated E. coli strains. The Bc1 strain showed elevated resistance to macrolides, chloramphenicols, and tetracyclines relative to pneumonia-associated B. cenocepacia strains. Metagenomic analysis revealed a highly individualized gut microbiota composition among VAP patients. Notably, the translocated bacteria were not dominant within their gut microbiota. Additionally, these patients showed a marked increase in the total abundance of antibiotic resistance genes (ARGs) in their gut microbiota. The translocation ability of the Ec1 strain was validated in a mouse pneumonia model, where it caused more severe lung damage. Furthermore, elevated levels of Escherichia-Shigella were detected in the lung tissues of colitis mice, suggesting that gut-to-lung bacterial translocation may occur in a severely inflamed host, potentially leading to pneumonia.<br><br>CONCLUSIONS: This study demonstrates the gut-to-lung translocation of E. coli and B. cenocepacia, highlighting their role in the development and progression of VAP in ICU patients. These findings provide valuable insights for implementing targeted prevention and treatment strategies for VAP in ICU settings.},
}
@article {pmid40346475,
year = {2025},
author = {Yuan, T and Ren, W and Zhang, J and Mahmood, M and Jia, Z and Zhang, S and Wang, M and Liang, S and Yuan, F and Liu, Y},
title = {Synergistic effect of grassland plants and beneficial rhizosphere bacteria helps plants cope with overgrazing stress.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {614},
pmid = {40346475},
issn = {1471-2229},
support = {32060407//Natural Science Foundation of China/ ; 2021ZD00804//Major Special Foundation of Science and Technology Plan of Inner Mongolia/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Grassland ; Plant Roots/microbiology ; *Poaceae/microbiology/physiology/growth &amp; development ; Stress, Physiological ; Plant Growth Regulators/metabolism ; },
abstract = {BACKGROUND: Overgrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.<br><br>RESULT: This study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.<br><br>CONCLUSION: This study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40346456,
year = {2025},
author = {Cao, M and Huang, L and Zhang, R},
title = {Community-acquired pneumonia associated with influenza co-infection caused by fusobacterium necrophorum: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {686},
pmid = {40346456},
issn = {1471-2334},
mesh = {Humans ; *Community-Acquired Infections/microbiology/drug therapy/diagnosis ; *Influenza, Human/complications/diagnosis/drug therapy/microbiology ; *Fusobacterium Infections/drug therapy/microbiology/diagnosis/complications ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology/drug therapy/diagnosis ; *Fusobacterium necrophorum/isolation &amp; purification/genetics/drug effects ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; Male ; Adult ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Fusobacterium necrophorum is a rare pathogen associated with community-acquired pneumonia (CAP), particularly among healthy adults. This case report presents a rare documented case of CAP caused by F. necrophorum in a young individual, providing valuable insights for the diagnosis and treatment of similar cases.<br><br>CASE PRESENTATION: The patient was initially diagnosed with influenza, and subsequently developed CAP caused by F. necrophorum. Despite one week of outpatient treatment with moxifloxacin, the symptoms persisted, leading to hospitalisation. Treatment with piperacillin tazobactam/imipenem and doxycycline, which target atypical pathogens, did not result in improvement after admission. Conventional diagnostic methods failed to identify the causative pathogen; however, metagenomic next-generation sequencing of bronchoalveolar lavage fluid confirmed it to be F. necrophorum. The patient showed significant improvement after ten days of targeted treatment with ornidazole and imipenem/piperacillin tazobactam, and was discharged.<br><br>CONCLUSION: Uncommon pathogens, such as F. necrophorum, should be considered as potential culprits in young individuals with CAP when conventional cultures yield negative results but there is a strong suspicion of infection, especially if initial antibiotic therapy is ineffective.},
}
@article {pmid40346111,
year = {2025},
author = {Song, W and Yang, Q and Lv, H and Lv, Y and Jiang, Y and Qu, J and Li, Y},
title = {Prospective multicenter study identifying prognostic biomarkers and microbial profiles in severe CAP using BALF, blood mNGS, and PBMC transcriptomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16252},
pmid = {40346111},
issn = {2045-2322},
support = {No. 82200005//National Natural Science Foundation of China/ ; No. 82470002//National Natural Science Foundation of China/ ; 2023ZD0506200//National Key Research and Development Program of China/ ; SHDC2020CR5010//the three-year action plan of Shanghai Shenkang Hospital Development Center/ ; shslczdzk02202//Shanghai Municipal Key Clinical Specialty/ ; 2017ZZ02014//Shanghai Top-Priority Clinical Key Disciplines Construction Project/ ; 20dz2261100//Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases/ ; },
mesh = {Humans ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *Biomarkers/blood ; Prospective Studies ; Prognosis ; Middle Aged ; Aged ; *Transcriptome ; *Leukocytes, Mononuclear/metabolism/microbiology ; High-Throughput Nucleotide Sequencing ; *Pneumonia/microbiology/genetics ; Severity of Illness Index ; Metagenomics/methods ; Adult ; Gene Expression Profiling ; },
abstract = {To identify potential biomarkers associated with the prognosis and severity of severe community-acquired pneumonia (SCAP), we conducted a multi-center prospective study from January 1, 2022, to December 31, 2023, enrolling 14 mild CAP and 75 SCAP patients in Shanghai, China. Patients underwent bronchoalveolar lavage fluid (BALF) and blood metagenomic next-generation sequencing (mNGS) as well as peripheral blood mononuclear cell (PBMC) transcriptomics. Among the 75 SCAP patients, 32 died within 30 days, with older age, a history of allergies, and comorbidities like cerebrovascular disease linked to worse outcomes. BALF mNGS showed greater microbial diversity, revealing a higher prevalence of pathogens, including Acinetobacter baumannii, Klebsiella pneumoniae, and Candida albicans, compared to mild CAP patients. RNA sequencing identified 431 differentially expressed genes in deceased SCAP patients, with significant alterations in immune pathways. Notably, microbial markers such as Pneumocystis jirovecii and viral markers like Human cytomegalovirus were associated with poor outcomes. Transcriptomic biomarkers, including otoferlin (OTOF), MS4A4A, and SIGLEC1, were identified as potential prognostic indicators for SCAP severity. GSEA and traditional GO/KEGG analyses identified key immune and metabolic pathways in SCAP (death) patients, including upregulation of complement activation, oxidative phosphorylation, nitrogen metabolism, while downregulation of adaptive immune response, hematopoietic cell lineage, and antigen processing pathways. These findings underscore the superiority of BALF mNGS over blood mNGS for pathogen detection, revealing microbial differences and transcriptomic alterations between mild and severe cases while identifying prognostic markers for SCAP treatment strategies.},
}
@article {pmid40345996,
year = {2025},
author = {Eyssautier-Chuine, S and Besaury, L and Vaillant-Gaveau, N and Villaume, S and Habrant, A and Franco Castillo, I and Rondeau, M and Aggad, D and Gommeaux, M and Fronteau, G and Mitchell, SG},
title = {Controlling Lampenflora in Heritage Sites: In Situ Testing of POM-ILs in the Pommery Champagne Cellar.},
journal = {ChemPlusChem},
volume = {},
number = {},
pages = {e202500043},
doi = {10.1002/cplu.202500043},
pmid = {40345996},
issn = {2192-6506},
abstract = {Artificial lighting, essential for geotouristic purposes in subterranean sites, has facilitated the growth of colored photosynthetic organisms (lampenflora) on two monumental 19th-century bas-reliefs of the Pommery Champagne cellar - a UNESCO-protected heritage site - causing significant aesthetic and physical deterioration. To sustainably preserve these stone artworks, biocidal polyoxometalate-ionic liquids (POM-ILs) were tested alongside the commercial biocide Preventol RI80® on three trial zones, cleaned and colonized areas of a wall, and clean stone samples positioned on a testing station within the cellar. After one year, untreated control areas exhibited growth/regrowth of green biofilms, whereas surfaces treated with POM-ILs or Preventol RI80® remained biofilm-free. Measurements of colorimetry and chlorophyll fluorescence confirmed the effectiveness of both biocides in controlling photosynthetic microorganisms. However, confocal fluorescence microscopy highlighted a reduced long-term inhibition by Preventol RI80® compared to POM-ILs, despite the latter being applied at lower concentrations. Metagenomic analysis validated the performance of POM-ILs, showing a notable decrease in microbial richness and diversity in treated areas. While both products effectively inhibited phototrophs and fungi, their efficacy against Pseudomonadota was limited, due to microbial adaptation via antibiotic resistance genes. This study underscores the potential of POM-ILs as a sustainable alternative for preserving cultural heritage against microbial colonization.},
}
@article {pmid40345059,
year = {2025},
author = {Yao, H and Romans-Casas, M and Vassilev, I and Rinta-Kanto, JM and Puig, S and Rissanen, AJ and Kokko, M},
title = {Selective butyrate production from CO2 and methanol in microbial electrosynthesis - influence of pH.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {165},
number = {},
pages = {109000},
doi = {10.1016/j.bioelechem.2025.109000},
pmid = {40345059},
issn = {1878-562X},
abstract = {Methanol assisted microbial electrosynthesis (MES) enables butyrate production from carbon dioxide and methanol using external electricity. However, the effects of operational parameters on butyrate formation remain unclear. By running three flat plate MES reactors with fed-batch mode at three controlled pH values (5.5, 6 and 7), the present study investigated the influence of pH on methanol assisted MES by comparing the process performance, microbial community structure, and genetic potential. The highest butyrate selectivity (87 % on carbon basis) and the highest butyrate production rate of 0.3 g L[-1] d[-1] were obtained at pH 6. At pH 7, a comparable butyrate production rate was achieved, yet with a lower selectivity (70 %) accompanied with acetate production. Butyrate production rate was considerably hindered at pH 5.5, reaching 0.1 g L[-1] d[-1], while the selectivity reached was up to 81 %. Methanol and CO2 consumption increased with pH, along with more negative cathodic potential and more negative redox potential. Furthermore, pH affected the thermodynamical feasibility of involved reactions. The results of metagenomic analyses suggest that Eubacterium callanderi dominated the microbial communities at all pH values, which was responsible for methanol and CO2 assimilation via the Wood-Ljungdahl pathway and was likely the main butyrate producer via the reverse β-oxidation pathway.},
}
@article {pmid40344981,
year = {2025},
author = {Lin, F and Tang, W and Zeng, L and Peng, L and Li, Z and Fang, Z},
title = {A rare case of severe pneumonia caused by leptospirosis complicated with Jarisch-Herxheimer reaction.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {1},
pages = {116891},
doi = {10.1016/j.diagmicrobio.2025.116891},
pmid = {40344981},
issn = {1879-0070},
abstract = {BACKGROUND: Leptospirosis, a zoonotic disease caused by Leptospira species, presents significant diagnostic challenges due to its diverse clinical manifestations. Jarisch-Herxheimer reaction (JHR), an acute inflammatory response triggered by antibiotic therapy, can complicates disease management. Reports of leptospirosis with JHR remain rare, emphasizing the need for early diagnosis and appropriate treatment.<br><br>CASE PRESENTATION: An 80-year-old male presented with severe pneumonia, septic shock, and acute respiratory distress syndrome (ARDS). Diagnosis of leptospirosis was confirmed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, identifying Leptospira species. The patient was treated with piperacillin-tazobactam and supportive care, leading to full recovery.<br><br>CONCLUSIONS: This case highlights the importance of mNGS in diagnosing rare infections and the need for vigilance in managing JHR. Clinicians should consider leptospirosis in patients with unexplained severe pneumonia and systemic inflammation.},
}
@article {pmid40344830,
year = {2025},
author = {Hou, X and Gu, J and Chen, J and Ullah, H and Mamtimin, T and Wang, X and Li, X and Jiang, Y and Fan, J and Han, H and Li, X},
title = {Identification and functional characterization of a novel CaSrpA enzyme for selenite reduction and selenium nanoparticle formation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138486},
doi = {10.1016/j.jhazmat.2025.138486},
pmid = {40344830},
issn = {1873-3336},
abstract = {Selenite reductases are widely distributed across various oxidoreductase families (e.g., ThxR, OYE, and FccA enzymes) [1]. The ability of short-chain dehydrogenase/reductase (SDR) family enzymes for selenite reduction remains unknown. Using metagenomic and metatranscriptomic analyses, 40 putative selenite reductases were identified from selenium-rich regions based on catalytic domain homology and transcriptional upregulation. These enzymes mainly belong to the SDR family and metalloenzymes. Enzyme activity analysis indicated that CaSrpA possessed the ability (Vmax, 18.85 μM/min/g) to reduce selenite to selenium nanoparticles (SeNPs). Phylogenetic analysis showed that CaSrpA was clustered in the clade of SDR enzymes, with the typical Rossmann fold. CaSrpA also oxidized S-1-phenylethanol to phenylacetone (Vmax, 15.4 μM/min/mg), sharing 53 % sequence similarity with the alcohol dehydrogenase RasADH. Molecular docking and structural superposition identified sixteen key residues associated with CaSrpA activity. Site-directed mutagenesis revealed that over 14 mutants exhibited a 30-90 % reduction in relative activity. Mutant M206A enhanced catalytic efficiency towards selenite by 2.4-fold and S-1-phenylethanol by 5.4-fold via a lid-opening mechanism. Molecular dynamics simulation elucidated that the mutant M206A utilized lid opening mechanism to accommodate more substrate and co-factor for catalysis via altering the conformation of the α7-α8 loop. This study helps understand the intrinsic connection between the SDR family and selenite-reducing capability, broadening the repertoire of selenite reductases.},
}
@article {pmid40344797,
year = {2025},
author = {Chen, Y and Liu, Q and Xu, XW},
title = {Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118121},
doi = {10.1016/j.marpolbul.2025.118121},
pmid = {40344797},
issn = {1879-3363},
abstract = {Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3[-]]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.},
}
@article {pmid40344252,
year = {2025},
author = {Crawford, MS and Ulu, A and Ramirez, BM and Santos, AN and Chatterjee, P and Canale, V and Manz, S and Lei, H and Soriano, SM and Nordgren, TM and McCole, DF},
title = {Respiratory Exposure to Agriculture Dust Extract Alters Gut Commensal Species and Key Metabolites in Mice.},
journal = {Journal of applied toxicology : JAT},
volume = {},
number = {},
pages = {},
doi = {10.1002/jat.4808},
pmid = {40344252},
issn = {1099-1263},
support = {2R01DK091281/NH/NIH HHS/United States ; 1R01AI153314/NH/NIH HHS/United States ; 1R01DK130373/NH/NIH HHS/United States ; R00ES025819/NH/NIH HHS/United States ; R01HL158926/NH/NIH HHS/United States ; T34GM062756/NH/NIH HHS/United States ; U54OH007550//The University of California, Davis-Western Center for Agricultural Health and Safety/ ; //University of California Presidential Postdoctoral Fellowship Program/ ; //National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Exposure to agricultural dust containing antimicrobial-resistant pathogens poses significant health risks for workers in animal agriculture production. Beyond causing severe airway inflammation, pollutants are linked to intestinal diseases. Swine farm dust is rich in ultrafine particles, gram-positive and gram-negative bacteria, and bacterial components such as lipopolysaccharides (LPS; endotoxins). In our previous study, we demonstrated that intranasal exposure of male and female C57BL/6J mice to 12.5% hog dust extract (HDE, containing 22.1-91.1 EU/mL) for 3 weeks resulted in elevated total cell and neutrophil counts in bronchoalveolar lavage fluid and increased intestinal permeability compared to saline controls. Now, we report that 16S and metagenomic analyses of Week 3 stool samples from HDE-treated mice indicate a reduced abundance of the beneficial species Akkermansia muciniphila and Clostridium sp. ASF356 and Lachnospiraceae bacterium. Bacterial alpha diversity showed increased species evenness in fecal samples from HDE-treated mice (Pielou's evenness, p = 0.047, n = 5-6/group). Metabolomic analysis also indicated significant reductions in key metabolites involved in energy metabolism, including riboflavin (p = 0.027, n = 11) and nicotinic acid (p = 0.049, n = 11), as well as essential amino acids, such as inosine (p = 0.043, n = 11) and leucine (p = 0.018, n = 11). While HDE exposure does not robustly alter overall microbial abundance or community structure, it leads to specific reductions in beneficial bacterial species and critical metabolites necessary for maintaining intestinal homeostasis by supporting energy metabolism, gut barrier function, microbiota balance, and immune regulation. The results of this study underscore the potential risks for gut health posed by inhalation of agricultural dust.},
}
@article {pmid40344212,
year = {2025},
author = {Zhao, Y and Song, L and Li, HY and Liu, SX and Mao, FF and Li, XJ and Ding, PH},
title = {Metagenomic Insights Into the Subgingival Microbiome in Periodontal Health and Different Grades of Periodontitis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13408},
pmid = {40344212},
issn = {1600-0765},
support = {//Postdoctoral Science Foundation of China/ ; //National Natural Science Foundation of China/ ; //the Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; //National Key Research and Development Program of China/ ; //Key Research and Development Program of Zhejiang Province/ ; //Fundamental Research Funds for the Central Universities/ ; },
abstract = {AIM: This cross-sectional study compared the subgingival microbiome in periodontal health (PH) and periodontitis, focusing on distinguishing Stage III Grade B periodontitis (PD-S3gB) and Stage III Grade C periodontitis (PD-S3gC) as defined by the 2018 Classification of Periodontitis.<br><br>METHODS: Subgingival samples from subjects with PH, PD-S3gB, and PD-S3gC were analyzed using metagenomic sequencing. Taxonomic and functional annotations were performed, followed by analyses of microbial diversity, differential abundance, interspecies networks, predictive modeling, and functional pathway enrichment.<br><br>RESULTS: Significant differences in both alpha and beta diversity were observed between PH and periodontitis. Several periodontal pathogens were more abundant in disease states, with Capnocytophaga granulosa and Capnocytophaga sp. CM59 enriched in PD-S3gC compared to PD-S3gB. The PD-S3gC group also exhibited a more complex microbial network with increased interspecies connectivity. An 11-species diagnostic model effectively distinguished PH, PD-S3gB, and PD-S3gC. Furthermore, pathways related to motility, chemotaxis, and methane metabolism were significantly enriched in periodontitis.<br><br>CONCLUSION: Distinct structural and functional differences in the subgingival microbiome characterize periodontal health and periodontitis. Periodontitis with a rapid rate of progression is marked by specific pathogen overgrowth and enhanced microbial interactions, supporting the development of microbiome-based diagnostics and personalized therapies.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registration: ChiCTR2000039426.},
}
@article {pmid40343892,
year = {2025},
author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM},
title = {Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323382},
doi = {10.1371/journal.pone.0323382},
pmid = {40343892},
issn = {1932-6203},
abstract = {Potato (Solanum tuberosum L.) is an important food crop in Kenya, providing a source of nutrition and income for many farmers. However, potato cyst nematodes (PCN) cause significant damage to potato plants, leading to substantial economic losses and threatening the nation's food security. Understanding the composition and functional potential of bacterial communities in the soil is important for developing sustainable biological control strategies against PCN and improving soil health. This cross-sectional purposive study examined the bacterial communities associated with PCN-suppressive and conducive potato rhizosphere from two major potato-producing counties in Kenya. We analyzed 180 soil samples from symptomatic and asymptomatic potato plants using shotgun metagenomics, followed by functional analysis to identify genes and metabolic pathways relevant to soil and plant health. Taxonomic classification revealed Enterobacteriaceae and Pseudomonadaceae as the most dominant bacterial families present. Within these families, the genera Pseudomonas and Enterobacter were highly abundant, both known for their plant growth-promoting traits, including biological control of soil pathogens and nutrient solubilization. KEGG and Pfam database analysis revealed pathways associated with nutrient cycling, transport systems, and metabolic functions. The abundance of iron-acquisition, chemotaxis, and diverse transport genes across analyzed samples suggests the presence of beneficial bacterial communities. This study provides the first report on bacterial ecology in PCN-infested rhizosphere in Kenya and its implications for soil health and PCN management.},
}
@article {pmid40343328,
year = {2025},
author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G},
title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.},
journal = {Plant direct},
volume = {9},
number = {5},
pages = {e70078},
doi = {10.1002/pld3.70078},
pmid = {40343328},
issn = {2475-4455},
abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.},
}
@article {pmid40343031,
year = {2025},
author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP},
title = {Metagenomic analysis reveals extreme complexity of Plasmodium spp. infections in high transmission in West Africa.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.29.25326533},
pmid = {40343031},
abstract = {Mixed-species, mixed-strain Plasmodia infections are known to occur in humans in malaria endemic areas. To date, the true extent of this complexity has not been explored in high- burden countries of sub-Saharan Africa. Here we take a metagenomic lens to infections obtained by sampling variable blood volumes from residents living in high, seasonal transmission in northern Ghana. We identified significantly higher prevalence of Plasmodium spp. and inter-/intra-species complexity in larger blood volumes. Overall, malaria infections displayed high levels of metagenomic complexity comprising single-, double-, and triple- species infections with varying levels of complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We present evidence of individuals with greater susceptibility to highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in Ghana.},
}
@article {pmid40342956,
year = {2025},
author = {Yang, Z and Liu, Q and Hu, Y and Geng, S and Ni, JX},
title = {Application of Metagenomic and Targeted Next-Generation Sequencing in Diagnosis of Pulmonary Tuberculosis in Bronchoalveolar Lavage Fluid.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2229-2241},
doi = {10.2147/IDR.S514090},
pmid = {40342956},
issn = {1178-6973},
abstract = {PURPOSE: To explore the application value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in the diagnosis of pulmonary tuberculosis (PTB) in bronchoalveolar lavage fluid (BALF).<br><br>PATIENTS AND METHODS: Data from 202 patients with suspected PTB at Wuhan Central Hospital (Jan 2022 - Jan 2024) were retrospectively analyzed. BALF samples were collected and examined using mNGS and tNGS, comparing their sensitivity to traditional methods like acid-fast staining, TB culture, and TB-DNA. Mixed microbial species were identified from the BALF using mNGS and tNGS, and the pros and cons of tNGS were evaluated against mNGS.<br><br>RESULTS: Of the 202 patients evaluated, 94 were diagnosed with PTB. The BALF mNGS and tNGS exhibited a sensitivity of 77.66% and a specificity of 100%, with positive and negative predictive values of 100% and 83.72%, respectively, outperforming conventional diagnostic methods. It was possible to compare the AUC values of the ROC curves of the BALF mNGS and tNGS with the corresponding values of the other three assay methods (0.89 vs 0.56, p < 0.05), MTB culture (0.89 vs 0.71, p < 0.05), and TB-DNA (0.89 vs 0.68, p < 0.05). Additionally, these techniques identified mixed microbial species in 52.13% of the BALF samples. Although both mNGS and tNGS demonstrated similar diagnostic rates, tNGS proved to be faster, more cost-effective, and incorporated a tuberculosis-specific wall-breaking technology, thereby suggesting greater clinical utility.<br><br>CONCLUSION: BALF mNGS and tNGS technologies quickly and accurately detect PTB patients with greater sensitivity and specificity than traditional MTB methods. While both mNGS and tNGS demonstrate enhanced capacity for polymicrobial detection, the clinical significance of co-detected microorganisms requires integration with clinical context to differentiate colonization from active infection. Compared to mNGS, tNGS provides distinct advantages in clinical utility.},
}
@article {pmid40342698,
year = {2025},
author = {Kang, X and Shao, M and Jiang, J and He, L and Lu, Y and Song, J and Xu, J and Fan, Z},
title = {The Gut Microbiome of the Asiatic Toad (Bufo gargarizans) Reflects Environmental Changes and Human Activities.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71394},
doi = {10.1002/ece3.71394},
pmid = {40342698},
issn = {2045-7758},
abstract = {Amphibians are extremely sensitive to environmental changes, and their gut microbiome may have different responses to environmental changes. Here, metagenomic sequencing was used to investigate the intestinal microbiota of the Asiatic toad (Bufo gargarizans) from three different habitats (city areas, transition areas, and wild areas) of Sichuan Province, China. The results showed that Proteobacteria, Firmicutes, and Fusobacteria were the main bacteria in the gut of B. gargarizans. There were significant differences in the composition and function of the gut microbiome among the samples from the three different habitats. Enterobacteriaceae showed significant changes in the three habitats and occupied a high relative abundance in the city areas, especially for Citrobacter. Especially, antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly increased in city areas. We performed de novo assembly of the metagenome-assembled genomes (MAGs). In total, 322 nonredundant MAGs were reconstructed, 304 of which might be potential novel genomes. Among the 13 species-level genome bins (SGBs) belonging to Enterobacteriaceae, the one belonging to Citrobacter portucalensis annotated the most types of ARGs and VFs. Phylogenetic and functional analyses of the assembled C. portucalensis MAG and public genome data were carried out, suggesting that it may play a potential role in intestinal diseases in amphibians. Our study revealed the differences in the gut microbiome of B. gargarizans across different habitats and suggests that amphibian intestinal microbiota could serve as environmental indicators to reflect environmental changes and human activities. The reconstructed MAGs expanded our understanding of the gut microbiota in amphibians, which may serve as a substantial reservoir for microbiome resources.},
}
@article {pmid40342619,
year = {2025},
author = {Sakiyama, Y and Yuan, JH and Yoshimura, A and Takeuchi, M and Maki, Y and Mori, T and Takei, J and Ando, M and Hiramatsu, Y and Nozuma, S and Higuchi, Y and Yonezawa, H and Kirishima, M and Suzuki, M and Kano, T and Tarisawa, M and Hashiguchi, S and Kunii, M and Sato, S and Takahashi-Iwata, I and Hashiguchi, A and Matsuura, E and Izumo, S and Tanimoto, A and Takashima, H},
title = {Brain biopsy and metagenomic sequencing enhance aetiological diagnosis of encephalitis.},
journal = {Brain communications},
volume = {7},
number = {3},
pages = {fcaf165},
doi = {10.1093/braincomms/fcaf165},
pmid = {40342619},
issn = {2632-1297},
abstract = {Identifying the aetiology of CNS diseases, regardless of their infectious or non-infectious nature, is often intricate. Next-generation sequencing (NGS) has emerged as a powerful tool for sensitive and unbiased screening of tissue or body fluid specimens. This study aimed to investigate the underlying aetiology of patients with suspected infectious CNS diseases. Between April 2013 and October 2021, we collected brain tissue samples from 33 patients diagnosed with encephalitis or encephalitis-like CNS diseases, obtained via biopsy or autopsy, and underwent metagenomic NGS (mNGS) in conjunction with pathological evaluations. Moreover, we employed PCR-based assays and pathogen-specific immunostaining to corroborate the presence of pathogens within the tissue samples. Among the 33 patients, mNGS elucidated pathogen-specific genomic sequences in 7 cases (21.2%), including halobacteria (archaea), Balamuthia mandrillaris, Epstein-Barr virus, Toxoplasma gondii and herpes simplex virus. Additionally, brain tissue mNGS ruled out known pathogens, identifying 14 cases (42.4%) of non-infectious CNS diseases, which included neoplastic, autoimmune/inflammatory and amyloid angiopathy conditions. The adjustment of therapeutic strategies based on these findings led to improvements in clinical symptoms, imaging outcomes and patient prognosis. Brain biopsy serves as both a direct pathological research target and a valuable source of samples for unbiased high-throughput sequencing. Our study illustrates the reliability of mNGS on brain tissue, which significantly improves the diagnostic rate for suspected encephalitis or encephalitis-like diseases of unknown aetiology. These findings underscore the importance of mNGS in guiding more precise and effective therapeutic interventions for patients in clinical practice.},
}
@article {pmid40342595,
year = {2025},
author = {Sun, Y and Cai, Q and Li, T and Chen, J and Fang, Y},
title = {Genome assembly of Klebsiella michiganensis based on metagenomic next-generation sequencing reveals its genomic characteristics in population genetics and molecular epidemiology.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1546594},
doi = {10.3389/fmicb.2025.1546594},
pmid = {40342595},
issn = {1664-302X},
abstract = {INTRODUCTION: Klebsiella michiganensis, a significant member of the Klebsiella oxytoca complex, has emerged as a potential pathogen in clinical settings. Despite extensive research on the Klebsiella pneumoniae complex, the pathogenicity and drug resistance of the K. oxytoca complex remain understudied, particularly regarding the reconstruction of whole genomes from metagenomic next-generation sequencing (mNGS) data.<br><br>METHODS: In this study, bronchoalveolar lavage fluid (BALF) from a 55-year-old woman with a suspected right lung infection in Anhui Province, China, was analyzed using mNGS.<br><br>RESULTS: Three distinct assembly strategies were employed to reconstruct the genome of K. michiganensis, leading to the identification of a novel ST452 strain, KMLRT2206. Comprehensive genomic analysis of this strain and 206 clinical isolates (genomes downloaded from public databases) revealed the population structure, distribution of drug resistance genes, and virulence factors of K. michiganensis. The results demonstrated significant genetic diversity, with the species divided into three major clades, each exhibiting distinct patterns of drug resistance and virulence genes. Notably, 38.6% of the strains harbored the bla OXY-1-1 gene, highlighting a potential threat of drug resistance. While virulence gene distribution was not correlated with sequence type (ST), significant differences were observed among clades.<br><br>CONCLUSION: This study underscores the value of mNGS combined with optimized assembly strategies for accurate species identification within the K. oxytoca complex, providing critical insights for clinical pathogen detection and epidemiological surveillance.},
}
@article {pmid40341642,
year = {2025},
author = {Humińska-Lisowska, K and Michałowska-Sawczyn, M and Kosciolek, T and Łabaj, PP and Kochanowicz, A and Mieszkowski, J and Proia, P and Cięszczyk, P and Zielińska, K},
title = {Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16061},
pmid = {40341642},
issn = {2045-2322},
support = {2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; 2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Biomarkers/blood ; *Exercise/physiology ; Young Adult ; Feces/microbiology ; Exercise Test ; Athletes ; Anaerobiosis ; Adult ; },
abstract = {The gut microbiome influences physiological responses to exercise by modulating inflammatory markers and metabolite production. Athletes typically exhibit greater microbial diversity, which may be associated with improved performance, but the mechanisms linking different exercise modalities to the gut microbiome are not fully understood. In this study, blood and stool samples were collected from endurance athletes, strength athletes, and non-athletic controls performing two maximal exercise tests (the anaerobic Wingate test and the aerobic Bruce Treadmill Test) to integrate serum biomarker data with gut bacterial metagenomic profiles. While most biochemical markers showed similar post-exercise trends across groups, SPARC (secreted protein acidic and rich in cysteine) and adiponectin levels showed modality-specific responses. Strength-trained participants showed unique microbiome-biomarker associations after the Wingate test. In addition, baseline enrichment of certain bacterial taxa, including Clostridium phoceensis and Catenibacterium spp., correlated with reduced Bruce Treadmill test response in strength-trained individuals. These findings, while requiring further validation, indicate the complex interplay between exercise type, training background, and the gut microbiome, and suggest that specific microbial species may help shape recovery and adaptation.},
}
@article {pmid40341309,
year = {2025},
author = {Coimbra, A and D'arc, M and Moreira, FRR and Cosentino, MAC and Schiffler, FB and Miranda, TDS and Mouta, R and Girardi, DL and Wanderkoke, V and Medeiros, G and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and Santos, AFD},
title = {Fecal Virome of Southeastern Maned Sloth (Bradypus crinitus) (Pilosa: Bradypodidae).},
journal = {Genetics and molecular biology},
volume = {48},
number = {2},
pages = {e20240183},
doi = {10.1590/1678-4685-GMB-2024-0183},
pmid = {40341309},
issn = {1415-4757},
abstract = {We report a viral metagenomic analysis of fecal samples from Bradypus crinitus (Pilosa: Bradypodidae), a recently described sloth species that occurs in the Atlantic Forest of Espírito Santo and Rio de Janeiro states, Southeast Brazil. Through Illumina sequencing, we generated a total of 2,065,344 raw reads, of which 945,386 reads (45.77%) passed the quality and size filter. The highest proportion of them was assigned to Eukarya, followed by Bacteria and only a small proportion to Virus. However, we identified 24 viral families using distinct taxonomic assignment tools, including phages and vertebrate viruses, such as retroviruses and papillomaviruses. Also, we identified four bacterial genus already associated with disease in sloths. Our study sheds light on the microbiome of a previously unexplored species, further contributing to the comprehension of metagenomic global diversity.},
}
@article {pmid40341174,
year = {2025},
author = {Kalwasińska, A and Królikiewicz, I and Tirkey, SR and Szabó, A and Kumar, SB},
title = {Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16079},
pmid = {40341174},
issn = {2045-2322},
support = {101038072//European Commission/ ; 101038072//European Commission/ ; },
mesh = {*Polyvinyls/chemistry ; Triticum/microbiology ; *DNA, Bacterial/isolation &amp; purification/genetics ; Rhizosphere ; Soil Microbiology ; *Nitrogen-Fixing Bacteria/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Nitrogen Fixation ; Fluorocarbon Polymers ; },
abstract = {The rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26 °C for 24 h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).},
}
@article {pmid40340931,
year = {2025},
author = {Niu, BB and Xu, JJ and Li, JA and Zhu, LD},
title = {Case report: Cervical suppurative lymphadenitis caused by burkholderia multivorans in a healthy child.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {678},
pmid = {40340931},
issn = {1471-2334},
support = {ZR2024QH132//Natural Science Foundation of Shandong Province/ ; },
mesh = {Humans ; Male ; *Lymphadenitis/microbiology/diagnosis/drug therapy/pathology ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; *Burkholderia Infections/diagnosis/microbiology/drug therapy ; Neck/pathology/microbiology ; Lymph Nodes/pathology/microbiology ; Meropenem/therapeutic use ; },
abstract = {BACKGROUND: Cervical suppurative lymphadenitis in children is commonly caused by Staphylococcus aureus or Streptococcus pyogenes. However, cases caused by Burkholderia multivorans (BM) are rare. The clinical presentation lacks specificity, making it difficult for clinicians to recognize, which may delay diagnosis and treatment.<br><br>CASE PRESENTATION: We report a case of a 5-year-old boy admitted with recurrent fever and neck swelling. Initial treatment with meropenem and linezolid was ineffective, and symptoms persisted after 24 days of conservative therapy. Aspiration of pus yielded negative culture results. Definitive diagnosis was achieved through surgical biopsy of cervical lymph nodes, pathological examination, and metagenomic next-generation sequencing (mNGS), which identified BM as the causative pathogen. The patient was successfully treated with a combination of trimethoprim-sulfamethoxazole and meropenem. The cervical lesion exhibited granulomatous inflammation and was managed with adjunctive vacuum-assisted closure (VAC) therapy, resulting in complete wound healing without recurrence.<br><br>CONCLUSIONS: This study aims to raise awareness among all specialists about BM as a potential causative agent in cervical suppurative lymphadenitis. Early recognition and timely intervention can reduce misdiagnosis and missed diagnoses, improving patient outcomes.},
}
@article {pmid40340823,
year = {2025},
author = {Shen, Y and An, Z and Gao, L and Gu, M and Xia, S and Ding, Q and Li, Y and Cao, S and Li, J and Huang, J and Zhong, J and Chen, K and Wang, X and Wang, H},
title = {Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {456},
pmid = {40340823},
issn = {1471-2164},
support = {2021YFD1200404//National Key R &amp; D Program of China/ ; ZR2023QC252//Shandong Provincial Natural Science Foundation/ ; },
mesh = {Animals ; *Buffaloes/genetics/growth &amp; development/metabolism ; *Ribosomal Proteins/genetics/metabolism ; Quantitative Trait Loci ; Transcriptome ; Genomics ; Metabolomics ; Metabolome ; Multiomics ; },
abstract = {BACKGROUND: Asian water buffaloes (Bubalus bubalis) in the Yangtze River Basin of China are the important meat provider for local residents because of its outstanding body size. Several previous studies have highlighted their genetic basis of growth characteristics, but the crucial genes regulating growth traits via multi-layer omics are still rarely investigated.<br><br>RESULTS: We conducted a comprehensive multi-omics analysis integrating blood and muscle transcriptome, plasma metabolome, rumen fluid metagenome, and genome of Haizi water buffaloes. Of note, ribosomal protein L26 (RPL26) located in the evolutionary selection regions associated with body sizes is the top differentially expressed gene (DEG) in both blood and muscle tissues. Further metabolomics and metagenomics identified growth-related molecular biomarkers (myristicin and Bacteroidales) and microbiological composition (Bacteroides and Prevotella). Leveraging cattle quantitative trait loci (QTLs) and genotype-tissue expression (CattleGTEx) databases, we found the significant correlations of QTL_180979 on RPL26 and two identified cis-eQTLs in muscle tissue in the upstream of RPL26 with weight gain. The follow-up cell assay validations confirmed the regulation roles of RPL26 in cell cycle, apoptosis, and differentiation, where the low RPL26 expressions enhanced the antiapoptotic ability and promoted the differentiation of myoblasts into myotubes markedly.<br><br>CONCLUSIONS: Our study illustrates RPL26 roles in regulating growth traits via both integrated multi-omics analysis and functional validations that suggests the further applications of RPL26 for growth trait selection of water buffaloes.},
}
@article {pmid40340756,
year = {2025},
author = {Laue, HE and Willis, AD and Wang, F and MacDougall, MC and Xu, Y and Karagas, MR and Madan, JC and Fleisch, AF and Lanphear, BP and Cecil, KM and Yolton, K and Chen, A and Buckley, JP and Braun, JM},
title = {Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {50},
pmid = {40340756},
issn = {1756-994X},
support = {K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; R35GM133420/GM/NIGMS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Adolescent ; Female ; Male ; Child ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Metagenomics/methods ; },
abstract = {BACKGROUND: The microbiome of adolescents is poorly understood, as are factors influencing its composition. We aimed to describe the healthy adolescent microbiome and identify early-life and concurrent predictors of its composition.<br><br>METHODS: We performed metagenomic sequencing of 247 fecal specimens from 167 adolescents aged 11-14&#xa0;years participating in the Health Outcomes and Measures of the Environment (HOME) Study, a longitudinal pregnancy and birth cohort (Cincinnati, OH). We described common features of the adolescent gut microbiome and applied self-organizing maps (SOMs)-a machine-learning approach-to identify distinct microbial profiles (n&#x2009;=&#x2009;4). Using prospectively collected data on sociodemographic characteristics, lifestyle, diet, and sexual maturation, we identified early-life and concurrent factors associated with microbial diversity and phylum relative abundance with linear regression models and composition with Kruskal-Wallis and Fisher's exact tests.<br><br>RESULTS: We found that household income and other sociodemographic factors were consistent predictors of the microbiome, with higher income associated with lower diversity and differential relative abundances of Firmicutes (increased) and Actinobacteria (decreased). Sexual maturation, distinct from chronological age, was related to higher diversity in females and differences in phylum relative abundances and compositional profiles in both males and females.<br><br>CONCLUSIONS: Our study suggests that adolescence is a unique window for gut microbial composition and that it may be shaped by both early-life and concurrent exposures, highlighting its potential in future epidemiologic research.},
}
@article {pmid40340623,
year = {2025},
author = {Deng, J and Zhang, J and Su, M and Li, J and Su, Y and Zhong, Q and Hu, J and Chen, Y and Liao, S and Lin, D and Guo, X},
title = {Fusobacterium mortiferum and its metabolite 5-aminovaleric acid promote the development of colorectal cancer in obese individuals through Wnt/β-catenin pathway by DKK2.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2502138},
doi = {10.1080/19490976.2025.2502138},
pmid = {40340623},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology ; Animals ; Humans ; Mice ; Gastrointestinal Microbiome ; *Fusobacterium/metabolism ; *Wnt Signaling Pathway/drug effects ; *Obesity/microbiology/metabolism/complications ; *Intercellular Signaling Peptides and Proteins/metabolism/genetics ; Male ; Female ; Cell Line, Tumor ; Cell Proliferation ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, with high incidence and mortality rates. An increasing body of research suggests that obesity is a significant risk factor for the development of CRC. Moreover, recent findings have highlighted the close association between the gut microbiota and both obesity and CRC. Despite this, the specific mechanisms by which the gut microbiota influences obesity and CRC remain unclear. This study aims to explore the role of the gut bacterium Fusobacterium mortiferum and its metabolite 5-aminovaleric acid (5-AVA) in the development of obesity and CRC. Our study found that the metabolite 5-aminovaleric acid produced by Fusobacterium mortiferum significantly inhibits the expression of the tumor suppressor DKK2. This inhibition leads to enhanced proliferation of CRC cells. Furthermore, we discovered that Fusobacterium mortiferum and 5-AVA can activate the Wnt/β-catenin signaling pathway by inhibiting DKK2, thereby promoting tumor growth. This finding was validated in CRC mouse models and in vitro experiments. Additional mechanistic studies revealed that 5-AVA interacts with the demethylase KDM6B, affecting the demethylation process of DKK2 and subsequently activating the Wnt/β-catenin signaling pathway. Our study retrospectively collected fecal samples from patients who underwent gastrointestinal endoscopy at the Sixth Affiliated Hospital of Sun Yat-sen University over the past five years. Participants were stratified into a healthy control group and an adenoma group based on the outcomes of their colonoscopies. Following this, we conducted metagenomic analysis to identify differential bacteria, and based on the results, we performed bacterial cultivation and metabolomic profiling. The roles of the targeted bacteria and their metabolites were further validated through animal models and cellular assays, employing techniques such as Western Blot, qPCR, immunohistochemistry, molecular docking simulations, and gene overexpression studies. This study uncovers the potential carcinogenic effects of Fusobacterium mortiferum and 5-AVA in the development of obesity and CRC. Our research emphasizes the complex interplay between the gut microbiota and host metabolism and suggests new directions for future research to explore how modulation of the gut microbiota could prevent and treat CRC.},
}
@article {pmid40340466,
year = {2025},
author = {Javornik Cregeen, S and Tisza, MJ and Hanson, B and Cook, M and Surathu, A and Schneider, R and Wu, J and Short, K and Domakonda, K and Hopkins, L and Ross, MC and Petrosino, JF and Deegan, J and Stadler, LB and Boerwinkle, E and Maresso, A},
title = {Sequencing-Based Detection of Measles in Wastewater: Texas, January 2025.},
journal = {American journal of public health},
volume = {},
number = {},
pages = {e1-e5},
doi = {10.2105/AJPH.2025.308146},
pmid = {40340466},
issn = {1541-0048},
abstract = {Measles is a potentially deadly viral infection spread via respiratory droplets from infected individuals. Outbreaks occur when vaccine coverage drops below the threshold of herd, or community, immunity. Using a sequencing-based approach, we report the prospective (January 7, 2025) detection of measles in nucleic acid extracts from 2 wastewater treatment plants in Houston, Texas, with a population of more than 218 000 residents. The sequencing data from 2 samples contained 53 unique reads mapping to 11 different regions of the measles virus genome with a 99.4% match to genotype B3. Importantly, no detections were observed from 821 previous samples from the same city spanning nearly 3 years of monitoring. The findings were confirmed using droplet digital polymerase chain reaction. A concomitant investigation identified 2 unvaccinated measles-positive travelers living within the same sewershed as the wastewater detection event. This work suggests that sequencing-based wastewater analysis is valuable as a comprehensive early detection warning system that facilitates more targeted epidemiological investigation. (Am J Public Health. Published online ahead of print May 8, 2025:e1-e5. https://doi.org/10.2105/AJPH.2025.308146).},
}
@article {pmid40340458,
year = {2025},
author = {Bay, L and Barnes, CJ and Fritz, BG and Ravnborg, N and Ruge, IF and Halling-Sønderby, A-S and Søeborg, SR and Langhoff, KH and Lex, C and Hansen, AJ and Thyssen, JP and Bjarnsholt, T},
title = {Unique dermal bacterial signature differentiates atopic dermatitis skin from healthy.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0015625},
doi = {10.1128/msphere.00156-25},
pmid = {40340458},
issn = {2379-5042},
abstract = {UNLABELLED: Gaining a deeper understanding of the variation in skin microbiota across habitats and layers provides critical insights into the complex host-microbial interactions that drive inflammatory skin diseases. Our study investigated dermal versus epidermal microbiota in lesional and non-lesional skin of 37 adult atopic dermatitis (AD) patients and 37 healthy controls. Skin biopsies were partitioned into epidermal and dermal compartments, while serial tape strips collected the superficial epidermis. Bacterial communities were analyzed by cultivation, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confocal laser scanning microscopy, and metagenomic sequencing. We found that the effects of AD were evident across skin layers. The natural variation between skin layers and habitats diminishes in AD-affected skin, intensifying the impact of the microenvironment and host factors. A remarkably distinct dermal bacterial community was discovered among AD patients, being more conserved and providing a clearer difference between skin habitats, while the epidermis varied substantially. Importantly, comparisons between AD patients and controls revealed more genera differed when studying the dermal samples than the epidermal ones. Staphylococcus, Corynebacterium, and Cutibacterium genera differed with AD status across all samples, but Prevotella and Mitsuokella only differed in the dermis. In the dry and moist dermis, this translated into 14 and 61 gene pathways significantly varying with AD status, including many related to the biosynthesis of menaquinones (vitamin K2). These results suggest dermal sampling would allow for the role of the skin microbiome within AD pathogenesis to be better resolved since these communities are simpler and less prone to environmental contamination.<br><br>IMPORTANCE: This study sheds light on the profound impact of skin microbiota's complex composition and distribution in atopic dermatitis (AD). The distinctive bacterial profile and activity, especially within the dermal skin compartment, vividly mirrored the cutaneous conditions in this inflamed microenvironment. The striking similarity in bacterial communities across different skin habitats in atopic skin underscores the high influence of atopic dermatitis-the genetic predisposition to an amplified immune response. This finding suggests that the dermal bacterial profile could be a valuable tool for longitudinally monitoring changes during the disease's relapsing phases, allowing for a precise categorization of patients into specific AD endotypes. Broadening the focus throughout the entire eczema-affected skin paves the way for treatments capable of modulating dermal biological factors, offering more effective management of AD. By further centering the interest in host-microbial interactions, we can refine personalized treatments, ultimately improving the lives of millions suffering from atopic dermatitis.},
}
@article {pmid40340444,
year = {2025},
author = {Richtsmeier, P and Nedielkov, R and Haring, M and Yücel, O and Elsner, L and Lülf, RH and Wöhlbrand, L and Rabus, R and Moeller, H and Philipp, B and Mueller, FM},
title = {7β-Hydroxysteroid dehydratase Hsh3 eliminates the 7-hydroxy group of the bile salt ursodeoxycholate during degradation by Sphingobium sp. strain Chol11 and other Sphingomonadaceae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018525},
doi = {10.1128/aem.00185-25},
pmid = {40340444},
issn = {1098-5336},
abstract = {Bile salts are steroids with distinctive hydroxylation patterns that are produced and excreted by vertebrates. In contrast to common human bile salts, ursodeoxycholate (UDCA) has a 7-hydroxy group in β-configuration and is used in large amounts for the treatment of diverse gastrointestinal diseases. We isolated the 7β-hydroxysteroid dehydratase Hsh3 that is involved in UDCA degradation by Sphingobium sp. strain Chol11. Hsh3 eliminates the 7β-hydroxy group as water, leading to a double bond in the B-ring. This is similar to 7α-hydroxysteroid dehydratases in this and other strains, but Hsh3 is evolutionarily different from these. Purified Hsh3 accepted steroids with and without side chains as substrates and had minor activity with 7α-hydroxy groups. The deletion mutant strain Chol11 Δhsh3 had impacted growth with UDCA and accumulated a novel compound. The compound was identified as 3',5-dihydroxy-H-methyl-hexahydro-5-indene-1-one-propanoate, consisting of steroid rings C and D with a C3-side chain carrying the former 7β-hydroxy group, indicating that Hsh3 activity is important especially for the later stages of bile salt degradation. Hsh3 homologs were found in other sphingomonads that were also able to degrade UDCA as well as in environmental metagenomes. Thus, Hsh3 adds to the bacterial enzyme repertoire for degrading a variety of differently hydroxylated bile salts.IMPORTANCEThe bacterial degradation of different bile salts is not only important for the removal of these steroidal compounds from the environment but also harbors interesting enzymes for steroid biotechnology. The 7β-hydroxy bile salt ursodeoxycholate (UDCA) naturally occurs in high concentration in the feces of black bears and has important pharmaceutical relevance for the treatment of different liver-related diseases, for which it is administered in high and increasing amounts. Additionally, it is present in the bile salt pool of humans in trace amounts. While UDCA degradation is environmentally important, the enzyme Hsh3 modifies the hydroxy group that confers the medically relevant properties and thus might be interesting for microbiome analyses and biotechnological applications.},
}
@article {pmid40339985,
year = {2025},
author = {Xavier, RGC and Santana, CH and de Castro, YG and Carvalho, RDO and da Silva, TF and Azevedo, V and Aburjaile, FF and Dorneles, EMS and Santos, RL and Silva, ROS},
title = {Metagenomic and 16S rRNA analysis of culture-negative uterine samples identifies Brucella spp. in a female dog with pyometra.},
journal = {Topics in companion animal medicine},
volume = {},
number = {},
pages = {100981},
doi = {10.1016/j.tcam.2025.100981},
pmid = {40339985},
issn = {1946-9837},
abstract = {Canine pyometra is the most prevalent reproductive disease in female dogs and involves a complex interplay of hormonal and microbial factors. Although Enterobacteriaceae are known to be the main cause of pyometra, up to 25% of samples remain negative when classic culture methods are used. The lack of growth in conventional media raises the intriguing possibility that non-cultivable microorganisms participate in the disease. Our study aimed to address this knowledge gap by investigating the microbiota in culture-negative uterine samples from dogs with pyometra. The purulent uterine contents of dogs with pyometra (n=79) were subjected to bacterial culture. Most of the samples showed bacterial growth of Escherichia coli (48/79, 60.7%) or other bacterial species (25/79, 31.8%). Samples that tested negative using the classic culture method (6/79=7.5%) were further analyzed using 16S rRNA gene sequencing, high-throughput 16S rRNA sequencing, and shotgun metagenomics. Only three of these provided DNA of sufficient quality for further analysis, which revealed a mixture of Haemophilus/Aggregatibacter and Fusobacterium/Porphyromonas in two uterine content. In the third sample, Brucella spp. was identified as the main genus. This study suggests that pathogens that are not easily isolated by classical culture methods, including zoonotic species, may be present in the uterus of dogs with pyometra.},
}
@article {pmid40339893,
year = {2025},
author = {Zhang, L and Wang, S and Jia, Y and Liu, Z and Yao, J and Chen, Y},
title = {Alterations in microbial communities and antibiotic resistance genes pre- and post-sludge bulking in a wastewater treatment plant.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126391},
doi = {10.1016/j.envpol.2025.126391},
pmid = {40339893},
issn = {1873-6424},
abstract = {Sludge bulking is a common issue in wastewater treatment plants (WWTPs) that can disrupt microbial communities and potentially impact the abundance and spread of antibiotic resistance genes (ARGs) within treatment systems. This study employed high-throughput 16S rRNA gene sequencing and metagenomic sequencing to examine the changes in microbial communities and ARGs in a WWTP during non-bulking and bulking periods. The results indicated that bacterial diversity decreased in bulking sludge while maintaining a high removal efficiency of conventional pollutants. Significant differences were detected at the bacterial genus level between non-bulking and bulking sludge (p < 0.05). The proliferation of Candidatus_Microthrix contributed to sludge bulking, while Micropruina improved sludge settleability. When treating wastewater with the same water quality and quantity, anaerobic/anoxic/oxic (A[2]/O) exhibited the highest resistance to sludge bulking, followed by Bardenpho and the Carrousel oxidation ditch. The abundance of ARGs in bulking sludge (28.15-43.63 ppm) was lower than that in non-bulking sludge (51.72-59.01 ppm). The ARGs removal efficiency reached 96.24% and 94.34% during bulking and non-bulking periods, respectively. Network analysis revealed that Candidatus_Microthrix was positively correlated with aadS and tetX, and norank_f_Saprospiraceae exhibited positive correlations with vanRO and ANT(3'')-Iia. These findings provide valuable insights into the impacts of sludge bulking on WWTP performance and ARGs dynamics, informing evidence-based policies for sustainable wastewater treatment.},
}
@article {pmid40339368,
year = {2025},
author = {Zhang, X and Liu, T and Sun, W and Zhang, C and Jiang, X and You, X and Wang, X},
title = {The fate and ecological risk of typical diamide insecticides in soil ecosystems under repeated application.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138440},
doi = {10.1016/j.jhazmat.2025.138440},
pmid = {40339368},
issn = {1873-3336},
abstract = {Diamide insecticides are the third most widely used class of pesticides worldwide. However, the long-term impacts of repeated diamide applications on soil ecosystems remain unclear. This study investigated chlorantraniliprole (CLP) and cyantraniliprole (CYP) effects on soil ecosystems through simulated repeated exposures. Results showed both exhibited slow degradation in the soil, with repeated applications extending their persistence, particularly for CLP. Both significantly inhibited soil alkaline nitrogen and organic matter accumulation, while reducing urease and sucrase activities, with CLP exerting stronger inhibitory effects. Metagenomic analysis indicated that CLP and CYP notably reduced soil microbial diversity. Additionally, the two insecticides altered the soil microbial community structure and inhibited carbon-nitrogen metabolic pathways. Further analysis revealed that CLP treatment significantly decreased the relative abundances of Mesorhizobium and Marmoricola, whereas CYP treatment primarily reduced Clostridium_sensu_stricto_1. All of these genera exhibited significant positive correlations with key metabolic pathways in soil carbon and nitrogen cycling. Notably, the relative abundance of Sphingomonas increased significantly following CLP and CYP treatments, demonstrating potential degradation capabilities. Overall, both CLP and CYP posed ecological risks to soil ecosystems, with CLP exhibiting more severe impacts. These findings revealed the need for strengthened scientific management in actual production.},
}
@article {pmid40339316,
year = {2025},
author = {Cuzman, OA and Raio, A and Galeotti, M and Striova, J and Chaban, A and Innocenti, S and Penoni, S and de Luca, F and Cantini, B and Petrocchi, D},
title = {Pink discoloration due to pigmented Archaea on the walls of the so-called Michelangelo's "secret room" (Medici Chapel, Florence, Italy).},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179494},
doi = {10.1016/j.scitotenv.2025.179494},
pmid = {40339316},
issn = {1879-1026},
abstract = {Pink discolorations are often observed on heritage buildings mainly in areas affected by salt weathering, where the development of halotolerant and halophilic microorganisms is favored. Part of these extremophilic microorganisms contains carotenoids, reason for which their colonization becomes visible by naked eye on large surfaces. This work investigates the pink alteration of the walls with drawings attributed to Michelangelo, located in the basement room of the Medici Chapel (Florence, Italy). The results of in-depth multidisciplinary investigations are discussed in the context of a thorough literature review on pink alterations of heritage buildings. For the first time, we combined culture-based approaches with metagenomic analyses that revealed the pink pigmented archaea Halalkalicoccus sp. as dominant, pointing their role in the pink discoloration present on the wall. Raman spectroscopy was exploited for the characterization of the biogenic pigments and Fourier Transform infrared spectroscopy and scanning electron microscopy to analyze the salt formations present on the walls.},
}
@article {pmid40339249,
year = {2025},
author = {Shi, Z and Zeng, W and Liu, Z and Yao, F and Guo, J and Chen, Y and Qin, Z and Zhang, J},
title = {Invasive apple snails with their core microbes are underestimated hotspots for disseminating antibiotic resistance genes and virulence factors in aquatic habitats.},
journal = {Journal of environmental management},
volume = {385},
number = {},
pages = {125575},
doi = {10.1016/j.jenvman.2025.125575},
pmid = {40339249},
issn = {1095-8630},
abstract = {Antibiotic resistance in pathogens is a threat to human health. The invasive apple snail (Pomacea canaliculata), widely distributed and linked to human activities, is a potential vector for human pathogens. However, its role in spreading antibiotic resistance genes (ARGs) is poorly understood. This study assessed the microbiological risk of this snail by sampling from five interconnected habitats: feces of invasive apple snails and native snails, ditch water, sediment, and soil. Using metagenomic and 16S rRNA sequencing, we analyzed the microbial communities and quantified the ARGs and virulence factors (VFs). Results showed that invasive apple snails carried significantly higher levels of ARGs and VFs compared with the native snails and environmental samples. ARGs and VFs were primarily found co-occurring in Aeromonas and Citrobacter freundii, with Aeromonas identified as the core microbe selected by invasive apple snails. Furthermore, the abundance and community dissimilarity of Aeromonas positively correlated with those of ARGs and VFs, both directly and indirectly through mobile genetic elements. This suggests Aeromonas may play a key role in disseminating ARGs and VFs across habitats. Overall, this study highlights the invasive apple snail as a significant vector for ARGs and virulent pathogens, providing critical insights for risk assessment and targeted management within the One Health framework.},
}
@article {pmid40338610,
year = {2025},
author = {Gan, X and Yu, Q and Hu, X and Qian, Y and Mu, X and Li, H},
title = {Metagenomic and metatranscriptomic analysis reveals the enzymatic mechanism of plant polysaccharide degradation through gut microbiome in plateau model animal (Ochotona curzoniae).},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf045},
pmid = {40338610},
issn = {1574-6968},
abstract = {Herbivorous animals can obtain energy by decomposing plant polysaccharides through gut microbiota, but the mechanism of gut microbiota decomposing plant polysaccharides in high-altitude model animals is still unclear. Plateau pika (Ochotona curzoniae) is a key model animal native to the Qinghai-Tibet Plateau with a high intake of grass. Thus, Plateau pika is an excellent animal model for studying how herbivorous animals digest and metabolize grass polysaccharides. Here, we used 16S rDNA, 16S rRNA, metagenomic and metatranscriptomic sequencing to characterize gut microbial composition, gene potential and expressed function in pikas from different altitudes. Unlike total bacteria, Oscillospira and Ruminococcus were main active bacterial genera in pika's gut. The metabolic pathways of cellulose and hemicellulose were up-regulated in the middle and high-altitude groups, those genes encoding polysaccharide enzymes were enriched. Notably, the proportion of lignin metabolic genes expressed in pika's gut was the highest, followed by cellulase and hemicellulase genes. According to comparative metagenomics of different animals, the number and relative abundance of cellulase and hemicellulase genes in pika's gut were at higher level compared with steer, etc. These results indicated that plateau pika obtained sufficient energy from grass-based diet by increasing the expression of related metabolic enzymes.},
}
@article {pmid40338446,
year = {2025},
author = {Mei, S and Deng, Z and Meng, FY and Guo, QQ and Tao, HY and Zhang, L and Xi, C and Zhou, Q and Tian, XF},
title = {Sini Powder Alleviates Stress Response and Suppresses Hepatocellular Carcinoma Development by Restoring Gut Microbiota.},
journal = {Chinese journal of integrative medicine},
volume = {},
number = {},
pages = {},
pmid = {40338446},
issn = {1993-0402},
abstract = {OBJECTIVES: To explore the underlying pharmacological mechanisms and its potential effects of Chinese medicine herbal formula Sini Powder (SNP) on hepatocellular carcinoma (HCC).<br><br>METHODS: The active components of SNP and their in vivo distribution were identified using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Construction of component-target-disease networks, protein-protein interaction network, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and molecular docking were employed to analyze the active components and anti-HCC mechanisms of SNP. Cell viability assay and wound healing assay were utilized to confirm the effect of SNP-containing serum (2.5%, 5.0%, 10%, 20%, and 40%), isoprenaline or propranolol (both 10, 100, and 1,000 &#xb5; mol/L) on proliferation and migration of HepG 2 or Huh7 cells. Meanwhile, the effect of isoprenaline or propranolol on the &#x3b2; 2 adrenergic receptor (ADRB2) mRNA expression on HepG2 cells were measured by real-time quantitative reverse transcription (RT-qPCR). Mice with subcutaneous tumors were either subjected to chronic restraint stress (CRS) followed by SNP administration (364 mg/mL) or directly treated with SNP (364 mg/mL). These two parallel experiments were performed to validate the effects of SNP on stress responses. Stress-related proteins and hormones were quantified using RT-qPCR, enzyme-linked immunosorbent assay, and immunohistochemistry. Metagenomic sequencing was performed to confirm the influence of SNP on the gut microbiota in the tumor-bearing CRS mice.<br><br>RESULTS: The distribution of the 12 active components of SNP was confirmed in various tissues and feces. Network pharmacology analysis confirmed the anti-HCC effects of the 5 active components. The potential anti-HCC mechanisms of SNP may involve the epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase Src (SRC) and signal transducer and activator of transcription 3 (STAT3) pathways. SNP-containing serum inhibited the proliferation of HepG2 and Huh7 cells at concentrations of 2.5% and 5.0%, respectively, after 24 h of treatment. Furthermore, SNP suppressed tumor progression in tumor-bearing mice exposed to CRS. SNP treatment also downregulated the expressions of stress-related proteins and pro-inflammatory cytokines, primarily by modulating the gut microbiota. Specifically, the abundance of Alistipes and Prevotella, which belong to the phylum Bacteroidetes, increased in the SNP-treated group, whereas Lachnospira, in the phylum Firmicutes, decreased.<br><br>CONCLUSION: SNP can combat HCC by alleviating stress responses through the regulation of gut microbiota.},
}
@article {pmid40338094,
year = {2025},
author = {Tanaka, M and Toyonaga, T and Nakagawa, F and Iwamoto, T and Hasegawa, Y and Komatsu, A and Sumiyoshi, N and Shibuya, N and Minemura, A and Ariyoshi, T and Matsumoto, A and Oka, K and Shimoda, M and Saruta, M},
title = {Dietary 3-Aminobenzoic Acid Enhances Intestinal Barrier Integrity and Attenuates Experimental Colitis.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00406.2024},
pmid = {40338094},
issn = {1522-1547},
support = {21K15985//Kaken Pharmaceutical (Kaken)/ ; },
abstract = {Disruption of intestinal epithelial integrity and increased permeability is central to the pathogenesis of ulcerative colitis (UC). In this study, we identified 3-aminobenzoic acid (3-ABA), a dietary component abundant in azuki beans, soybeans and chickpeas as a regulator of epithelial permeability and inflammation in the colon. Screening 119 gut microbial metabolites revealed the ability of 4-ABA, a structural isomer of 3-ABA, to enhance barrier function in Caco2 cells. Further analysis of structural isomers identified 3-ABA as the most effective, significantly increasing transepithelial electrical resistance and reducing epithelial permeability. Using liquid chromatography-mass spectrometry, 3-ABA was detected in dietary beans and human fecal samples. Fecal 3-ABA levels were significantly lower in UC patients compared to healthy individuals. Metagenomic and functional prediction analyses revealed dysbiosis in UC patients, characterized by an enrichment of bacterial genes involved in ABA degradation. Gene expression analysis of 3-ABA-stimulated Caco2 cells demonstrated upregulation of tight junction molecules, such as CLDN1 and TJP1, enhancing epithelial barrier integrity. In a dextran sodium sulfate-induced colitis mouse model, rectal 3-ABA administration ameliorated colitis by enhancing epithelial barrier function and reducing inflammation. These findings highlight 3-ABA's potential as a dietary therapeutic agent for UC, offering a novel strategy to enhance intestinal integrity and mitigate inflammation.},
}
@article {pmid40337776,
year = {2025},
author = {Li, Y and Li, C and Fang, Y and Zhang, L and Ying, X and Ren, R and Zang, Y and Ying, D and Zhu, S and Liu, J and Cao, X},
title = {Comprehensive Analysis of Pathogen Diversity and Diagnostic Biomarkers in Patients with Suspected Pulmonary Tuberculosis Through Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2215-2227},
pmid = {40337776},
issn = {1178-6973},
abstract = {BACKGROUND: This study aimed to investigate the co-infecting pathogens and lung microbiomes in patients with clinically confirmed pulmonary tuberculosis (TB) and explore potential diagnostic biomarkers to differentiate between varied infection patterns.<br><br>METHODS: We conducted a retrospective cohort study by analyzing 198 bronchoalveolar lavage fluid (BALF) samples collected from patients with suspected pulmonary TB. All BALF samples were sequenced using metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: A total of 63 pathogens were detected in all samples. The TB group exhibited a higher diversity of pathogens (n=51) than the Non-TB group (n=37). The analysis revealed that TB patients had significantly higher pathogen counts (P=0.014), and specific microorganisms, such as Mycobacterium tuberculosis complex (MTBC), MTB, Streptococcus infantis, and Campylobacter curvus, were significantly enriched. Furthermore, the abundance of MTBC was negatively correlated with hemoglobin levels (R=-0.17, P=0.015) and positive correlated with C-reactive protein (CRP) levels (R=0.16, P=0.029). The random forest model combined eight differential microbes and five clinical parameters, yielding an area under the curve (AUC) of 0.86 for differentiating TB from Non-TB cohorts, whereas subgroup differentiation yielded an AUC of 0.571, demonstrating the potential for targeted diagnostics in pulmonary infections.<br><br>CONCLUSION: Our findings highlight the complexity of co-infection patterns in pulmonary TB and emphasize the potential of integrating microbial and clinical markers to improve diagnostic accuracy. This study provides valuable insights into the role of the lung microbiome in TB and informs future research on targeted therapies for this disease.},
}
@article {pmid40336613,
year = {2025},
author = {Yusuf, A and Li, M and Zhang, SY and Odedishemi-Ajibade, F and Luo, RF and Wu, YX and Zhang, TT and Yunusa Ugya, A and Zhang, Y and Duan, S},
title = {Harnessing plant-microbe interactions: strategies for enhancing resilience and nutrient acquisition for sustainable agriculture.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1503730},
pmid = {40336613},
issn = {1664-462X},
abstract = {The rhizosphere, a biologically active zone where plant roots interface with soil, plays a crucial role in enhancing plant health, resilience, and stress tolerance. As a key component in achieving Sustainable Development Goal 2, the rhizosphere is increasingly recognized for its potential to promote sustainable agricultural productivity. Engineering the rhizosphere microbiome is emerging as an innovative strategy to foster plant growth, improve stress adaptation, and restore soil health while mitigating the detrimental effects of conventional farming practices. This review synthesizes recent advancements in omics technologies, sequencing tools, and synthetic microbial communities (SynComs), which have provided insights into the complex interactions between plants and microbes. We examine the role of root exudates, composed of organic acids, amino acids, sugars, and secondary metabolites, as biochemical cues that shape beneficial microbial communities in the rhizosphere. The review further explores how advanced omics techniques like metagenomics and metabolomics are employed to elucidate the mechanisms by which root exudates influence microbial communities and plant health. Tailored SynComs have shown promising potential in enhancing plant resilience against both abiotic stresses (e.g., drought and salinity) and biotic challenges (e.g., pathogens and pests). Integration of these microbiomes with optimized root exudate profiles has been shown to improve nutrient cycling, suppress diseases, and alleviate environmental stresses, thus contributing to more sustainable agricultural practices. By leveraging multi-disciplinary approaches and optimizing root exudate profiles, ecological engineering of plant-microbiome interactions presents a sustainable pathway for boosting crop productivity. This approach also aids in managing soil-borne diseases, reducing chemical input dependency, and aligning with Sustainable Development Goals aimed at global food security and ecological sustainability. The ongoing research into rhizosphere microbiome engineering offers significant promise for ensuring long-term agricultural productivity while preserving soil and plant health for future generations.},
}
@article {pmid40335921,
year = {2025},
author = {Jia, S and Mi, H and Su, Y and Liu, Y and Ming, Z and Lin, J},
title = {Changes of intestinal microbiome and its relationship with painful diabetic neuropathy in rats.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {281},
pmid = {40335921},
issn = {1471-2180},
support = {22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/microbiology/pathology ; Rats ; Male ; Rats, Sprague-Dawley ; Diabetes Mellitus, Experimental/microbiology/complications ; Interleukin-1beta/metabolism ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Tumor Necrosis Factor-alpha/metabolism ; Diabetes Mellitus, Type 2/microbiology/complications ; Colon/pathology/microbiology ; Spinal Cord/pathology/metabolism ; },
abstract = {OBJECTIVE: To analyze the gut bacterial microbiome in rats with painful diabetic neuropathy (PDN) compared to normal rats.<br><br>METHODS: Type 2 diabetes was induced in rats via a high-fat and high-sugar diet combined with a low dose of streptozotocin. Glucose metabolism and insulin sensitivity were evaluated using intraperitoneal glucose tolerance tests and insulin tolerance tests. The progression of peripheral neuropathy was assessed using the mechanical withdrawal threshold and thermal withdrawal latency. Histopathological analysis of rat colon tissues was performed using hematoxylin-eosin staining to observe morphological changes. The expression levels of pro-inflammatory cytokines TNF-&#x3b1; and IL-1&#x3b2; in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were then collected for metagenomic sequencing and analysis.<br><br>RESULT: Behavioral tests revealed reduced mechanical withdrawal threshold and thermal withdrawal latency in PDN rats. Histological analysis showed significant colonic mucosal damage and inflammatory cell infiltration, suggesting impaired intestinal barrier function. Elevated TNF-&#x3b1; and IL-1&#x3b2; levels in spinal cord tissues further highlight peripheral inflammation's role in PDN. Sequencing analysis revealed significant differences in gut microbiota composition between PDN and control rats, with altered Bacillota/Bacteroidota ratios and increased Lactobacillus abundance. Functional annotation analysis, based on the KEGG, EggNOG, and CAZy databases, indicated significant enrichment of metabolic pathways related to carbohydrate and amino acid metabolism, energy metabolism, and cell structure biogenesis in PDN rats. Cluster analysis identified higher functional clustering in Metabolism and Genetic Information Processing pathways in PDN rats.<br><br>CONCLUSION: This study demonstrates that PDN leads to altered gut microbiota composition, disrupted metabolic pathways, and increased inflammation, contributing to the pathological progression of diabetic neuropathy. This study provides new insights into the interplay between gut microbiota and diabetic neuropathy, offering potential avenues for therapeutic interventions targeting microbiome and metabolism.},
}
@article {pmid40335750,
year = {2025},
author = {Deepali, D and Tejoprakash, N and Sudhakara Reddy, M},
title = {Diversity of Bacterial Communities in Seleniferous Soils and Their Impact on Plant Growth and Selenium Toxicity.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {285},
pmid = {40335750},
issn = {1432-0991},
mesh = {*Selenium/toxicity/metabolism ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism/drug effects ; *Soil/chemistry ; *Zea mays/growth &amp; development/microbiology/drug effects ; Biodiversity ; *Microbiota ; Plant Roots/microbiology/growth &amp; development ; *Soil Pollutants/toxicity ; Phylogeny ; },
abstract = {The present study aimed to investigate the diversity of bacterial communities in seleniferous soils using Illumina Mi-Seq Next-Generation Sequencing. This study also compared seleniferous soils (SE) with non-seleniferous (NS) soils to evaluate Selenium (Se) impact on microbial communities and soil properties. Metagenomic analysis identified Proteobacteria as the predominant phylum in both environments, with SE soils exhibiting a higher dominance (48%) than NS soils (31%). The most dominant operational taxonomic unit (OTU) across both soil types belonged to the genus Bacillus. Se altered microbial community composition, increasing the abundance of the Bacillaceae family (30%) and Pseudomonadaceae family (25%) compared to NS soil. Bacillus was the dominant genus in the SE environment indicating its tolerance to selenium. Diversity indices indicated that control soils had higher species richness, while SE soils exhibited a more stressed microbial structure. A consortium of bacterial isolates (Proteus terrae Se3, Halopseudomonas formosensis Se5, and Corynebacterium glutamicum Se38) was inoculated in maize plants cultivated in natural seleniferous soils. Plants inoculated with bacterial consortium grew more healthy and had greater biomass in their roots, shoots, and seeds. Bacterial inoculation results in lesser selenium accumulation in the roots, shoots and seeds of maize plants compared to non-inoculated plants. These results suggest that bacterial species from seleniferous soils may be employed as biofertilizers to enhance plant growth and help plants tolerate Se toxicity in seleniferous soils.},
}
@article {pmid40335687,
year = {2025},
author = {Zhang, J and Feng, X and Li, M and Liu, Y and Liu, M and Hou, LJ and Dong, HP},
title = {Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40335687},
issn = {1476-4687},
abstract = {Research on the morphology, physiology and genomics of Asgard archaea has provided valuable insights into the evolutionary history of eukaryotes[1-3]. A previous study suggested that eukaryotes are nested within Heimdallarchaeia[4], but their exact phylogenetic placement within Asgard archaea remains controversial[4,5]. This debate complicates understanding of the metabolic features and timescales of early eukaryotic ancestors. Here we generated 223 metagenome-assembled nearly complete genomes of Asgard archaea that have not previously been documented. We identify 16 new lineages at the genus level or higher, which substantially expands the known phylogenetic diversity of Asgard archaea. Through sophisticated phylogenomic analysis of this expanded genomic dataset involving several marker sets we infer that eukaryotes evolved before the diversification of all sampled Heimdallarchaeia, rather than branching with Hodarchaeales within the Heimdallarchaeia. This difference in the placement of eukaryotes is probably caused by the previously underappreciated chimeric nature of Njordarchaeales genomes, which we find are composed of sequences of both Asgard and TACK archaea (Asgard's sister phylum). Using ancestral reconstruction and molecular dating, we infer that the last Asgard archaea and eukaryote common ancestor emerged before the Great Oxidation Event and was probably an anaerobic H2-dependent acetogen. Our findings support the hydrogen hypothesis of eukaryogenesis, which posits that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-producing protomitochondrion.},
}
@article {pmid40335510,
year = {2025},
author = {Zhi, J and Liang, Y and Zhao, W and Qiao, J and Zheng, Y and Peng, X and Li, L and Wei, X and Wang, W},
title = {Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {74},
pmid = {40335510},
issn = {2055-5008},
support = {82403470//National Natural Science Foundation of China/ ; 82401333//National Natural Science Foundation of China/ ; 21JCYBJC01570//Tianjin Municipal Science and Technology Committee/ ; 24JCQNJC01170//Tianjin Municipal Science and Technology Project/ ; TJWJ2023XK013//Tianjin Municipal Health Commission/ ; TJYXZDXK-046A//Tianjin Municipal Health Commission/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; *Microbiota ; Male ; Cross-Sectional Studies ; Middle Aged ; Female ; *Head and Neck Neoplasms/diagnosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Metagenomics ; Dysbiosis/microbiology ; *Mouth/microbiology ; Adult ; Biomarkers/analysis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Machine Learning ; Biomarkers, Tumor ; },
abstract = {Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.},
}
@article {pmid40335465,
year = {2025},
author = {Romano, S and Wirbel, J and Ansorge, R and Schudoma, C and Ducarmon, QR and Narbad, A and Zeller, G},
title = {Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4227},
pmid = {40335465},
issn = {2041-1723},
support = {BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; SEG 9093//European Molecular Biology Organization (EMBO)/ ; EMBO ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; 395357507 - SFB 1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Parkinson Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Machine Learning ; Metagenome ; },
abstract = {There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (4489 samples). Within most studies, microbiome-based machine learning models accurately classify PD patients (average AUC 71.9%). However, these models are study-specific and do not generalise well across other studies (average AUC 61%). Training models on multiple datasets improves their generalizability (average LOSO AUC 68%) and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Moreover, meta-analysis of shotgun metagenomes delineates PD-associated microbial pathways potentially contributing to gut health deterioration and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, microbial pathways for solvent and pesticide biotransformation are enriched in PD. These results align with epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbes modulate their toxicity. Here, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.},
}
@article {pmid40335388,
year = {2025},
author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R},
title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.004},
pmid = {40335388},
issn = {1878-4372},
abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.},
}
@article {pmid40335001,
year = {2025},
author = {Li, G and Liu, R and Chen, Y and Liang, H and Liang, Y and Li, X and Ke, Y and Lin, B and Zhong, J and Guo, X and Che, J and Luo, J},
title = {Evolutionary dynamics and codon bias analysis of canine circovirus: Insights into global spread and host adaptability.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108369},
doi = {10.1016/j.ympev.2025.108369},
pmid = {40335001},
issn = {1095-9513},
abstract = {Circoviruses are relatively new pathogens, and new circoviruses are constantly being discovered, with a growing range of hosts. Recently, canine circovirus (CanineCV) was reported to infect cats and badgers, further broadening its host range. Previous studies on the evolution and dissemination of CanineCV were fragmented. Here, when conducting a metagenomic analysis of shelter dogs, we identified a canine circovirus positivity rate of 32.4% and obtained three new viral strains. Furthermore, we integrated publicly available viral sequences and employed multiple bioinformatic software tools to analyze the evolution, codon usage bias, recombination, origin, spatiotemporal distribution and host adaptability of CanineCV. In this study, CanineCV could be divided into five distinct phylogenetic clades, named as China-I, China-II, Cosmopolitan, EA, and SEA clades. The extensive inter-clade recombination was observed, which plays an important role in viral evolution, while based on existing sequence information, CanineCV most likely originated in Norway from Vulpes vulpes in 1950.7. Notably, CanineCV exhibits greater adaptability to human hosts compared to previously documented hosts, as indicated by host adaptability indices, suggesting that this virus may possess zoonotic potential. In summary, our study elucidates the phylogeography and evolutionary dynamics of CanineCV and underscores the importance of investigating its potential for zoonotic transmission.},
}
@article {pmid40334798,
year = {2025},
author = {Zhu, X and Chen, L and Yang, P and Luo, S and Teng, M and Zhu, W and Li, Y and Zhao, D and Wang, N and Chen, X and Cheng, M and Tu, H and Huang, W and Yang, F and Wang, L and Liu, X and Ning, K},
title = {Microbiome catalog and dynamics of the Chinese liquor fermentation process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132620},
doi = {10.1016/j.biortech.2025.132620},
pmid = {40334798},
issn = {1873-2976},
abstract = {Fermented food remains poorly understood, largely due to the lack of knowledge about microbes in food fermentation. Here, this study constructed Moutai Fermented Grain Catalog (MTFGC), a representative liquor fermented by one of the most complex fermentations. MTFGC comprised 8,379,551 non-redundant genes and 5,159 metagenome-assembled genomes, with 20% species and 20% genes being novel. Additionally, 25,625 biosynthetic gene clusters (BGCs) and 28 BGC-enriched species were identified. Moreover, the microbial community assembly was deterministic, with significant species and gene changes in early fermentation stages, while stabilizing in later stages. Further BGC-knockout experiments verified Bacillus licheniformis, a BGC-enriched species, employed its BGCs for synthesizing the aroma-related lipopeptide lichenysin. This study has established the largest genetic resource for fermented food, uncovering its uniqueness and high metabolic potential. These findings facilitate the transition potential from traditional fermentation to precision-driven synthetic biology in food systems.},
}
@article {pmid40254113,
year = {2025},
author = {Bartáková, V and Bryjová, A and Polačik, M and Alila, DO and Nagy, B and Watters, B and Bellstedt, D and Blažek, R and Žák, J and Reichard, M},
title = {Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108357},
doi = {10.1016/j.ympev.2025.108357},
pmid = {40254113},
issn = {1095-9513},
mesh = {Animals ; Tanzania ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Genetics, Population ; Genetic Variation ; Sequence Analysis, DNA ; Metagenomics ; Killifishes ; },
abstract = {Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.},
}
@article {pmid40333210,
year = {2025},
author = {Trujillo, HA and Komeili, A},
title = {Revealing the diversity of bacterial and archaeal organelles via comparative genomics.},
journal = {Molecular biology of the cell},
volume = {36},
number = {5},
pages = {pe4},
doi = {10.1091/mbc.E20-08-0564},
pmid = {40333210},
issn = {1939-4586},
mesh = {*Archaea/genetics/metabolism ; Genomics/methods ; *Bacteria/genetics/metabolism ; *Organelles/genetics/metabolism ; Metagenomics/methods ; Magnetosomes/genetics/metabolism ; Genome, Archaeal ; },
abstract = {Like eukaryotes, bacteria and archaea rely on intracellular organelles to manage biological activities. Despite their prevalence, the understanding of the diversity of these organelles and the molecular mechanisms governing their function remain limited. In this review, we examine the potential of genomics and metagenomics to augment classical approaches for the study and discovery of microbial organelles. First, we highlight how the intimate interplay between model system studies and metagenomics have been critical in illuminating the function, diversity, and ancient evolutionary origins of the lipid-bounded magnetosome organelles of magnetotactic bacteria. We next discuss the central role of open genome databases and mechanistic studies in identification and characterization of protein-bounded encapsulin organelles with novel roles in sulfur metabolism and other cellular processes. Finally, we focus on the mostly uncultured Asgard archaea superphylum, whose metagenomes are challenging our views on organelle evolution and eukaryogenesis.},
}
@article {pmid40333159,
year = {2025},
author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F},
title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040358},
pmid = {40333159},
issn = {2076-0817},
support = {22LCYY-QH10//Jinling Hospital/ ; },
mesh = {Humans ; *Psoriasis/microbiology/therapy ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Dysbiosis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.},
}
@article {pmid40333137,
year = {2025},
author = {McHugh, JW and Challener, DW and Tabaja, H},
title = {Change of Heart: Can Artificial Intelligence Transform Infective Endocarditis Management?.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040371},
pmid = {40333137},
issn = {2076-0817},
mesh = {Humans ; *Artificial Intelligence ; *Endocarditis/diagnosis/therapy/diagnostic imaging ; Echocardiography ; Machine Learning ; Disease Management ; },
abstract = {Artificial intelligence (AI) has emerged as a promising adjunct in the diagnosis and management of infective endocarditis (IE), a disease characterized by diagnostic complexity and significant morbidity. Machine learning (ML) models such as SABIER and SYSUPMIE have demonstrated strong predictive accuracy for early IE diagnosis, embolic risk stratification, and postoperative mortality, surpassing traditional clinical scoring systems. In imaging, AI-enhanced echocardiography and advanced modalities like FDG-PET/CT offer improved sensitivity, specificity, and reduced inter-observer variability, potentially transforming clinical decision making. Additionally, AI-powered microbiological techniques, including MALDI-TOF mass spectrometry combined with ML and neural network-based metagenomic classifiers, show promise in rapidly identifying pathogens and predicting antimicrobial resistance. Despite encouraging early results, widespread adoption faces barriers, including data limitations, interpretability issues, ethical concerns, and the need for robust validation. Future directions include leveraging generative AI as clinical consultative tools, provided their capabilities and limitations are carefully managed. Ultimately, collaborative efforts addressing these challenges could transform IE care, enhancing diagnostic accuracy, clinical outcomes, and patient safety.},
}
@article {pmid40333054,
year = {2025},
author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and da Silva, MS and Weber, MN and de Barros, MP and Spilki, FR},
title = {Virome of Terrestrial Mammals and Bats from Southern Brazil: Circulation of New Putative Members of the Togaviridae Family and Other Findings.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040310},
pmid = {40333054},
issn = {2076-0817},
support = {405786/2022-0//CNPQ/ ; },
mesh = {Animals ; Brazil/epidemiology ; *Chiroptera/virology ; *Virome ; *Mammals/virology ; Phylogeny ; Metagenomics ; Humans ; },
abstract = {The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic sequencing. Akodon montensis (n = 15 individuals) and Coendou spinosus (n = 4) harbored Chikungunya virus (ChikV, Togaviridae), marking its first detection in these hosts. Molossus molossus (n = 17) presented Coronaviridae and Orthoherpesviridae, while Eptesicus furinalis (n = 1) also carried Coronaviridae. A broad virome diversity, including Togaviridae and Adenoviridae members, was identified in Didelphis albiventris (n = 43), with significant relevance to human health. Additional species, such as Callithrix jacchus (n = 1), Leopardus guttulus (n = 1), Myocastor coypus (n = 1), Monodelphis iheringi (n = 1), Thaptomys nigrita (n = 1), Sooretamys angouya (n = 1), Brucepattersonius iheringi (n = 1), and Lasiurus blossevillii (n = 1), contributed to insights into viral reservoirs. These results underscore the importance of virome studies in regions harboring high biodiversity, emphasizing genomic surveillance as a vital tool for monitoring zoonotic viruses and safeguarding global health.},
}
@article {pmid40332920,
year = {2025},
author = {Liu, H and Chen, W and Fang, X and Li, D and Xiong, Y and Xie, W and Chen, Q and You, Y and Lin, C and Wang, Z and Wang, J and Chen, D and Li, Y and Cai, P and Nie, C and Hong, Y},
title = {Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management.},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040412},
pmid = {40332920},
issn = {2075-4450},
support = {2023XQ019//Key Technological Innovation and Industrialization Project/ ; 2022J011198//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01917//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01916//Project of Fujian Provincial Natural Science Fund/ ; N2023Z007//Nanping Academy of Resource Industrialization Chemistry Project/ ; N2023J004//Key Project of the Nanping Natural Fund/ ; 202410397010//National College Student Innovation and Entrepreneurship Project/ ; },
abstract = {The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.},
}
@article {pmid40332799,
year = {2025},
author = {Bai, C and Duan, Y and Zhao, C and Yan, L and Suthisut, D and Lü, J and Bai, Y and Zeng, F and Zhang, M},
title = {Abundance of the Dominant Endosymbiont Rickettsia and Fitness of the Stored-Product Pest Liposcelis bostrychophila (Psocoptera: Liposcelididae).},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040349},
pmid = {40332799},
issn = {2075-4450},
support = {32172260//National Natural Science Foundation of China/ ; },
abstract = {Endosymbiotic bacteria are key factors that regulate the biological traits of Liposcelis bostrychophila. This study employed metagenomic methods to analyze the dominant species of symbiotic microorganisms associated with L. bostrychophila. By controlling the environmental temperature, we were able to manipulate the abundance of endosymbionts and establish populations with high, medium, and low levels of these bacteria. This allowed us to examine the fitness parameters of L. bostrychophila under different levels of endosymbiont abundance. The experimental results revealed that L. bostrychophila hosts 51 genera of symbiotic microorganisms, with Rickettsia being the dominant genus, accounting for 84.11% to 98.16% of the total share. Environmental temperature significantly affected the abundance of Rickettsia, with notable differences observed during the adult stage of L. bostrychophila. A temperature gradient of 28 °C, 35 °C, and 37 °C was established, allowing for the classification of populations based on Rickettsia abundance into three categories: high-abundance populations (LBhp), medium-abundance populations (LBmp), and low-abundance populations (LBlp). The abundance of Rickettsia had a significant impact on the fitness of L. bostrychophila. Specifically, a high abundance of Rickettsia contributed positively to population fitness by increasing egg production, prolonging egg hatching time, enhancing lifespan, and improving both survival and reproductive rates. Therefore, the endosymbiont Rickettsia plays a crucial role in the growth and development of L. bostrychophila. In the future, our research will help further uncover the interactions between Rickettsia and its host, providing new perspectives for pest control and offering a better understanding of insect biology and ecology.},
}
@article {pmid40331433,
year = {2025},
author = {Meyer, F and Robertson, G and Deng, ZL and Koslicki, D and Gurevich, A and McHardy, AC},
title = {CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf369},
pmid = {40331433},
issn = {1362-4962},
support = {//NFDI4Microbiota consortium/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and best practices. Since 2015, CAMI has provided comprehensive datasets, benchmarking guidelines, and challenges. However, benchmarking had to be conducted offline, requiring substantial time and technical expertise and leading to gaps in results between challenges. We introduce the CAMI Benchmarking Portal-a central repository of CAMI resources and web server for the evaluation and ranking of metagenome assembly, binning, and taxonomic profiling software. The portal simplifies evaluation, enabling users to easily compare their results with previous and other users' submissions through a variety of metrics and visualizations. As a demonstration, we benchmark software performance on the marine dataset of the CAMI II challenge. The portal currently hosts 28 675 results and is freely available at https://cami-challenge.org/.},
}
@article {pmid40331220,
year = {2025},
author = {Wang, Y and Wei, C and Chen, Z and Zhou, M and Huang, L and Chen, C},
title = {Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1582122},
pmid = {40331220},
issn = {2297-1769},
abstract = {Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAss-like phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs. Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.},
}
@article {pmid40330784,
year = {2025},
author = {Krivonos, D and Pavlenko, A and Lukina-Gronskaya, A and Korneenko, E and Speranskaya, A and Ilina, E},
title = {Case Report: Fatal case of dual infection Metapneumovirus complicated by Streptococcus pyogenes.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1576583},
pmid = {40330784},
issn = {2296-858X},
abstract = {Human Metapneumovirus (hMPV) is a common cause of acute respiratory viral infection in humans, typically occurring in children and causing no serious complications. However, the severity of the disease can be exacerbated by certain bacterial pathogens that lead to severe illness and even death. This report details a fulminant case of dual infection with hMPV and group A Streptococcus (Streptococcus pyogenes) in a three-year-old child. The whole genome sequencing of isolated clinical S. pyogenes strains was conducted, followed by an analysis of the genomic characteristics of the pathogen. Also, potential viral and bacterial pathogens were identified by qPCR and 16S rRNA metagenomic sequencing in any autopsy materials obtained from the patient. Children who had contact with the patient and began to exhibit symptoms of a cold were also tested and confirmed to have uncomplicated hMPV infection. The S. pyogenes strain has been found to contain five genes for various streptococcal exotoxins (speA, speB, speJ, speG and smeZ). In addition, the speA gene is situated in close proximity to the prophage, which may suggest that it is encoded and transferred specifically by the bacteriophage. We hypothesize that it was the cumulative effects of different streptococcal exotoxins that led to the patient's death.},
}
@article {pmid40330742,
year = {2025},
author = {Liu, C and Cai, Y and Yuan, K and Lu, M and Deng, Y and Chen, X and Ye, L and Cui, S and Lyu, J and Ling, Y},
title = {Confirmation of Tuberculous Meningitis Using Metagenomic Next-Generation Sequencing: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2209-2214},
pmid = {40330742},
issn = {1178-6973},
abstract = {BACKGROUND: Tuberculous meningitis (TBM) remains a significant clinical challenge due to limitations in traditional diagnostic methods, such as cerebrospinal fluid (CSF) analysis and tuberculosis culture, which often have long turnaround times and low sensitivity and specificity. This case report highlights the pivotal role of metagenomic next-generation sequencing (mNGS) in enhancing clinical knowledge for the diagnosis and management of TBM, supplementing insights into its clinical presentation and treatment.<br><br>CASE PRESENTATION: A 56-year-old male patient was admitted to the hospital with a chief complaint of "unconsciousness for 4 days". Following five days of antimicrobial therapy, the patient showed significant improvement with no fever or headache, but exhibited a suspicious left-sided Babinski sign (+). MRI revealed evidence of cerebral infarction, while spiral CT imaging showed hydrocephalus accompanied by interstitial cerebral edema. A lumbar puncture revealed elevated intracranial pressure, increased protein levels in CSF, reduced glucose and chloride concentrations, and negative results for CSF smear, CSF culture, and blood culture. T-SPOT testing was positive, and mNGS of CSF detected Mycobacterium tuberculosis (M. tuberculosis) Based on clinical and etiological findings, a diagnosis of tuberculous meningitis was confirmed. The patient was treated with quadruple anti-tuberculosis therapy combined with linezolid, resulting in clinical improvement. He was subsequently transferred to a specialized chest hospital for further management.<br><br>CONCLUSION: The patient's condition improved after 5 days of treatment. TBM is notoriously challenging to diagnose and treat. Traditional diagnostic methods, such as smear microscopy and tuberculosis culture, often yield low positive rates, delaying timely diagnosis and intervention. Early detection, accurate diagnosis, and prompt treatment are crucial for improving patient outcomes. mNGS of CSF has proven to be a powerful tool in TBM diagnosis, enabling early and precise identification of the pathogen, thereby facilitating timely treatment and reducing TBM-related mortality.},
}
@article {pmid40330288,
year = {2025},
author = {Bhowmik, S and Hajra, A and Bandyopadhyay, D},
title = {Genetic insights in infectious diseases: Insights from a case report and implications for personalized medicine.},
journal = {World journal of clinical cases},
volume = {13},
number = {13},
pages = {101438},
pmid = {40330288},
issn = {2307-8960},
abstract = {The relationship between genetics and infectious diseases is important in shaping our understanding of disease susceptibility, progression, and treatment. Recent research shows the impact of genetic variations, such as heme-oxygenase promoter length, on diseases like malaria and sepsis, revealing both protective and inconclusive effects. Studies on vaccine responses highlight genetic markers like human leukocyte antigens, emphasizing the potential for personalized immunization strategies. The ongoing battle against drug-resistant tuberculosis (TB) illustrates the complexity of genomic variants in predicting resistance, highlighting the need for integrated diagnostic tools. Additionally, genome-wide association studies reveal antibiotic resistance mechanisms in bacterial genomes, while host genetic polymorphisms, such as those in solute carrier family 11 member 1 and vitamin D receptor, demonstrate their role in TB susceptibility. Advanced techniques like metagenomic next-generation sequencing promise detailed pathogen detection but face challenges in cost and accessibility. A case report involving a highly virulent Mycobacterium TB strain with the pks1 gene further highlights the need for genetic insights in understanding disease severity and developing targeted interventions. This evolving landscape emphasizes the role of genetics in infectious diseases, while also addressing the need for standardized studies and accessible technologies.},
}
@article {pmid40330019,
year = {2025},
author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S},
title = {Investigation of dynamic microbial migration patterns in the respiratory tract.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542562},
pmid = {40330019},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.<br><br>METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.<br><br>RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.<br><br>CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.},
}
@article {pmid40330015,
year = {2025},
author = {Manimaran, A and Desingu, PA and Kumaresan, A and Singh, P and Subramanya, K and Dodamani, P and Dineshbhai, PA},
title = {The metagenomic and whole-genome metagenomic detection of multidrug-resistant bacteria from subclinical mastitis-affected cow's milk in India.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1549523},
pmid = {40330015},
issn = {2235-2988},
mesh = {Animals ; India ; *Milk/microbiology ; Cattle ; *Drug Resistance, Multiple, Bacterial/genetics ; Female ; *Mastitis, Bovine/microbiology ; *Metagenomics/methods ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/drug effects/classification ; Whole Genome Sequencing ; Virulence Factors/genetics ; Humans ; },
abstract = {Multidrug-resistant (MDR) bacteria in farm animal products threaten human health by causing zoonotic infections. The complete genome sequences of MDR bacteria from subclinical mastitis-affected cow's milk have not yet been comprehensively documented in India. In this study, using a bacterial metagenomic sequencing approach, we detected the nearly complete genome sequences of Pseudomonas veronii and Staphylococcus xylosus from subclinical mastitis-affected cow's milk. Furthermore, we sequenced the nearly complete genome sequences of Escherichia coli, Klebsiella pneumoniae, Staphylococcus hominis, and S. xylosus from subclinical mastitis-affected cow's milk using a whole-genome metagenomic sequencing method. Our analysis subsequently revealed that the complete genome sequences of the identified bacteria contained MDR genes and genes for multiple virulence factors. These MDR bacteria may pose a public health risk through exposure to milkers, milk handlers, and farm workers or through the handling and consumption of unpasteurized milk.},
}
@article {pmid40329854,
year = {2025},
author = {Buddle, S and Torres, O and Morfopoulou, S and Breuer, J and Brown, JR},
title = {The use of metagenomics to enhance diagnosis of Encephalitis.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2500655},
pmid = {40329854},
issn = {1744-8352},
abstract = {INTRODUCTION: Encephalitis has a broad etiology, including infectious and auto-immune causes. In infectious encephalitis the breadth of causative organisms results in incomplete testing and low diagnostic yields.Metagenomics sequences all DNA and RNA allows untargeted detection of all organisms in a single specimen; this is of particular use in diagnosis of encephalitis with a broad etiology.<br><br>AREAS COVERED: We review the literature and discuss metagenomics workflows, host depletion and pathogen enrichment methods, bioinformatics analysis and potential analysis of the host transcriptome to aid diagnosis. We discuss the clinical use of metagenomics for diagnosis of neurological infection including time to result, cost, quality assurance, patient cohorts in whom metagenomics adds the most value, recommended specimen types, limitations and review published cases in which metagenomics has been used to diagnose encephalitis.<br><br>EXPERT OPINION: There is good evidence for the utility of metagenomics to diagnose infection in encephalitis. Due to infections with rare, unexpected or novel pathogens, metagenomics adds most value to diagnosis in immunocompromised patients and the greatest diagnostic yield is in brain biopsies. Technical advances are needed to reduce the complexity, cost and time to result which will enable wider adoption in clinical laboratories and use as a first line test.},
}
@article {pmid40329496,
year = {2025},
author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B},
title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70039},
pmid = {40329496},
issn = {1556-4029},
abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).},
}
@article {pmid40329426,
year = {2025},
author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M},
title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {115},
pmid = {40329426},
issn = {2049-2618},
support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&amp;D Program of China/ ; 2022YFA1304300//National Key R&amp;D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; Female ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Male ; Adult ; Metagenomics/methods ; *Oropharynx/microbiology ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Family Characteristics ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.<br><br>RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p&#x2009;<&#x2009;0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.<br><br>CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.},
}
@article {pmid40329425,
year = {2025},
author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M},
title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {48},
pmid = {40329425},
issn = {2524-6372},
support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.<br><br>RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.<br><br>CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.},
}
@article {pmid40329403,
year = {2025},
author = {Huang, Y and Cheng, S and Shi, J and He, P and Ma, Y and Yang, R and Zhang, X and Cao, Y and Lei, Z},
title = {Enhancing Holstein steers growth performance: oregano essential oil's impact on rumen development, functionality and microorganism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {44},
pmid = {40329403},
issn = {2524-4671},
support = {GSA-XMLZ-2021-01//Beef Cattle Quality Fattening Project of Gansu Province/ ; GSSLCSX-2020-1//Major Science and Technology Special Project of Gansu Province/ ; 2024CYZC-36//Industry Support Project of Gansu Province/ ; },
abstract = {BACKGROUND: Dietary supplementation with oregano essential oil (OEO), a natural plant extracts, is an effective and acceptable method to improve growth, beef quantity and quality, but the undergoing mechanism in rumen has not yet been reported in Holstein steers. This study investigated the effects of oregano essential oil (OEO) on growth performance, fermentation parameters, digestive enzymes activity, rumen development and microbiota in Holstein steers. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CCK) or the same diet supplemented with 20 g/(d·head) OEO (CEO) for 270 days.<br><br>RESULTS: OEO increased the rumen contents of volatile fatty acids (VFA, acetate (P&#x2009;=&#x2009;0.011), propionate (P&#x2009;=&#x2009;0.008), butyrate (P&#x2009;=&#x2009;0.018)) and digestive enzymes activity (cellulase (P&#x2009;=&#x2009;0.018), protease and &#x3b2;-glucosidase (P&#x2009;<&#x2009;0.001)), and improved rumen development (papillae width (P&#x2009;=&#x2009;0.008) and micropapillary density (P&#x2009;=&#x2009;0.001)), which reasons contribute to increase body weight (BW, P&#x2009;=&#x2009;0.022), average daily gain (ADG, P&#x2009;=&#x2009;0.021), carcass weight (P&#x2009;=&#x2009;0.001), dressing percentage (P&#x2009;<&#x2009;0.001), and net meat production (P&#x2009;=&#x2009;0.001) of steers. Meanwhile, metagenomic and metabolomic analysis revealed OEO significantly reduced abundance of rumen microorganisms, especially methanogenic archaea and viruses while beneficial bacteria (Bifidobacterium) and virulence factors were not affected. KEGG analysis revealed that OEO significantly reduces the host risk of disease, improves the digestive system, and reduces the energy basic metabolism level. A correlation analysis indicated fourteen kinds key microbiome and six downregulated metabolites interfere with each other and together influence the growth performance of steers.<br><br>CONCLUSION: These results suggest that feed with 20&#xa0;g/(d&#xb7;head) OEO in steers diets could improve growth performance, and reduces virus abundance and disease risk. And the findings provide fundamental insights into OEO, as an alternative source of natural bioactive compounds, how effect on rumen development, composition and function of microorganisms.},
}
@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.<br><br>RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).<br><br>CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}
@article {pmid40329334,
year = {2025},
author = {Lu, D and Kalantar, KL and Glascock, AL and Chu, VT and Guerrero, ES and Bernick, N and Butcher, X and Ewing, K and Fahsbender, E and Holmes, O and Hoops, E and Jones, AE and Lim, R and McCanny, S and Reynoso, L and Rosario, K and Tang, J and Valenzuela, O and Mourani, PM and Pickering, AJ and Raphenya, AR and Alcock, BP and McArthur, AG and Langelier, CR},
title = {Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {46},
pmid = {40329334},
issn = {1756-994X},
support = {5R01HL155418//NIH/NHLBI/ ; 5R01HL155418//NIH/NHLBI/ ; 5R01HL155418//NIH/NHLBI/ ; PJT-156214/CAPMC/CIHR/Canada ; PJT-156214/CAPMC/CIHR/Canada ; PJT-156214/CAPMC/CIHR/Canada ; David Braley Chair in Computational Biology//McMaster University/ ; },
mesh = {Humans ; *Cloud Computing ; *Drug Resistance, Bacterial/genetics ; Software ; Whole Genome Sequencing ; *Bacteria/genetics/drug effects ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {BACKGROUND: Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next-generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences.<br><br>RESULTS: To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and single-isolate whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes from Illumina data. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and single-isolate WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections.<br><br>CONCLUSIONS: In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and single-isolate WGS data. Its development represents an important step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.},
}
@article {pmid40329323,
year = {2025},
author = {Duarte, B and Feijão, E and Cruz-Silva, A and Pascoal, P and Nunes, M and Pereira, M and Figueiredo, A and Dias, RP and Tanner, SE and Fonseca, VF},
title = {Reveal your microbes, and i'll reveal your origins: geographical traceability via Scomber colias intestinal tract metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {43},
pmid = {40329323},
issn = {2524-4671},
support = {http://doi.org/10.54499/UIDB/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.11260.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UI/BD/153050/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
abstract = {The commercial demand for small pelagic fish, such as Atlantic chub mackerel (Scomber colias), renders them susceptible to provenance fraud. Scomber colias specimens intestinal tract bacteriome from five distinct fishing areas along the Portuguese Atlantic coastline were analyzed by 4th-generation sequencing. Bacteria diversity indices and differential abundance revealed dissimilarities in operational taxonomic unit (OTU) abundance among specimens from distinct fishing sites. Random forest-based model yielded an 85% accuracy rate in attributing sample provenance based on intestinal tract bacteriome OTU relative abundance. Further refinement of microbial features using Indicator Species Analysis, Linear Discriminant Analysis Effect Size (LEfSe) and OTU Gini scores enabled the identification of 3-5 bacterial OTU location biomarkers per fishing site. The intestinal tract bacteriome revealed sequences linked to pathogenic bacteria, particularly in specimens from Center-North and Center-South fishing areas. While this doesn't imply active pathogens, it highlights potential public health concerns and complements efforts to improve seafood microbiological quality and traceability.},
}
@article {pmid40328980,
year = {2025},
author = {Liébana-García, R and López-Almela, I and Olivares, M and Romaní-Pérez, M and Manghi, P and Torres-Mayo, A and Tolosa-Enguís, V and Flor-Duro, A and Bullich-Vilarrubias, C and Rubio, T and Rossini, V and Segata, N and Sanz, Y},
title = {Gut commensal Phascolarctobacterium faecium retunes innate immunity to mitigate obesity and metabolic disease in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40328980},
issn = {2058-5276},
abstract = {The gut microbiota may protect against obesity and chronic metabolic conditions by regulating the immune response to dietary triggers. Yet the specific bacteria that control the overactivation of the immune system in obesity and their mode of action remain largely unknown. Here we surveyed 7,569 human metagenomes and observed an association between the gut symbiont Phascolarctobacterium faecium and non-obese adults regardless of nationality, sex or age. In a mouse model of diet-induced obesity, we confirmed the specificity of P. faecium DSM 32890 anti-obesogenic properties compared with other species of the same genus. P. faecium reversed the inflammatory phenotype associated with obesity. Specifically, P. faecium promoted polarization of alternatively activated macrophages (M2), which reversed the obesity-induced increase in gut-resident type 1 innate lymphoid cells. This resulted in mitigation of glucose intolerance, adiposity and body weight gain irrespective of treatment with live or pasteurized bacteria. The metabolic benefits were independent of the adaptive immune system, but they were abolished by an inhibitor of M2 polarization in mice. P. faecium directly promoted M2-macrophage polarization through TLR2 signalling and these effects seemed to be independent of gut microbiota changes. Overall, we identify a previously undescribed gut commensal bacterium that could help mitigate obesity and metabolic comorbidities by retuning the innate immune response to hypercaloric diets.},
}
@article {pmid40328944,
year = {2025},
author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE},
title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1184-1197},
pmid = {40328944},
issn = {2058-5276},
support = {R35GM143056//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01DK121822//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Feces/microbiology ; Female ; *Metagenomics/methods ; Bayes Theorem ; Longitudinal Studies ; Escherichia coli/genetics/isolation &amp; purification/classification ; Infant ; Algorithms ; Enterococcus faecalis/genetics/isolation &amp; purification/classification ; Adult ; *Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.},
}
@article {pmid40328731,
year = {2025},
author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y},
title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4211},
pmid = {40328731},
issn = {2041-1723},
support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.},
}
@article {pmid40328237,
year = {2025},
author = {Teitelbaum, J and Madan, S and Patel, S and Coyle, C and Chiu, CY and Thwe, PM and Uehara, M and Jermyn, R and Hemmige, V},
title = {Chagas Meningoencephalitis Diagnosed in Heart Transplant Patient Using Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0553},
pmid = {40328237},
issn = {1476-1645},
abstract = {Chagas meningoencephalitis can present in immunocompromised patients after organ transplantation. We present the first reported instance in which metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid diagnosed Chagas meningoencephalitis in a patient. The diagnosis of Chagas in this case underscores the role of mNGS in identifying rare or unexpected pathogens.},
}
@article {pmid40328153,
year = {2025},
author = {Chu, Y and Dong, X and Fang, S and Gan, L and Lee, X and Zhou, L},
title = {Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks.},
journal = {Water research},
volume = {282},
number = {},
pages = {123750},
doi = {10.1016/j.watres.2025.123750},
pmid = {40328153},
issn = {1879-2448},
abstract = {Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.},
}
@article {pmid40328090,
year = {2025},
author = {Xia, Y and Lan, Y and Xu, Y and Liu, F and Chen, X and Luo, J and Xu, H and Liu, Y},
title = {Effects of microplastics and tetracycline induced intestinal damage, intestinal microbiota dysbiosis, and antibiotic resistome: metagenomic analysis in young mice.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109512},
doi = {10.1016/j.envint.2025.109512},
pmid = {40328090},
issn = {1873-6750},
abstract = {Microplastics (MPs) and antibiotic tetracycline (TC) are widespread in the environment and constitute emerging combined contaminants. Young individuals are particularly vulnerable to agents that disrupt intestinal health and development. However, the combined effects of MPs and TC remain poorly understood. In this study, we developed a young mouse model exposed to polystyrene MPs, either alone or in combination with TC for 8 weeks to simulate real-life dietary exposure during early life. Our findings revealed that concurrent exposure to MPs and TC caused the most severe intestinal barrier dysfunction driven by inflammatory activation and oxidative imbalance. Moreover, exposure to MPs and TC reduced the abundance of potential probiotics while promoting the growth of opportunistic pathogens. Metagenomic analysis further indicated that co-exposure to MPs and TC enhanced the abundance of bacteria carrying either antibiotic resistance genes (ARGs) or virulence factor genes (VFGs), contributing to the widespread dissemination of potentially harmful genes. Finally, a strong positive correlation was observed between microbiota dysbiosis, ARGs, and VFGs. In general, this study highlighted the hazards of MPs and antibiotics to intestinal health in young mice, which provided a new perspective into the dynamics of pathogens, ARGs, and VFGs in early-life intestinal environments.},
}
@article {pmid40328065,
year = {2025},
author = {Ye, Y and Yan, X and Jiang, Y and Wang, S and Liu, D and Ren, Y and Li, D and Ngo, HH and Guo, W and Cheng, D and Jiang, W},
title = {Optimized feeding schemes of heterotrophic anodic denitrification coupled with cathodic phosphate recovery from wastewater using a microbial fuel cell.},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179590},
doi = {10.1016/j.scitotenv.2025.179590},
pmid = {40328065},
issn = {1879-1026},
abstract = {Enhanced water quality standards and increasing resource scarcity have prompted extensive research into low-cost nitrogen removal and phosphate recovery from wastewater. Microbial fuel cells (MFCs) offer a viable solution by simultaneously removing nitrogen, recovering phosphorus, and generating electrical energy. This study employed MFCs to achieve simultaneous nitrogen removal and phosphorus recovery, investigating the impact of different feeding schemes. The experimental results indicated that replacing the entire anode chamber solution and recycling the anode effluent to the cathode chamber effectively prevented the accumulation of nitrifying bacteria while achieving the highest pollutant removal performance. Under closed circuit conditions, the system consistently maintained low nitrite concentrations, achieving an average nitrate removal efficiency of 68.09 ± 1.86 % and phosphate recovery efficiency of 83.46 ± 5.30 %. Furthermore, this feeding scheme facilitated microbial growth and reproduction while also improving operational convenience. The study utilized metagenomics and other technologies to comprehensively analyze the system's operation mechanism and reasons for its excellent performance.},
}
@article {pmid40327993,
year = {2025},
author = {Grafakou, ME and Pferschy-Wenzig, EM and Aziz-Kalbhenn, H and Kelber, O and Moissl-Eichinger, C and Bauer, R},
title = {Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {187},
number = {},
pages = {118111},
doi = {10.1016/j.biopha.2025.118111},
pmid = {40327993},
issn = {1950-6007},
abstract = {Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.},
}
@article {pmid40327934,
year = {2025},
author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Yin, H and Dang, Z},
title = {Degradation mechanisms of isodecyl diphenyl phosphate (IDDP) and bis-(2-ethylhexyl)-phenyl phosphate (BEHPP) using a novel microbially-enriched culture.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138453},
doi = {10.1016/j.jhazmat.2025.138453},
pmid = {40327934},
issn = {1873-3336},
abstract = {Organophosphate esters (OPEs) pose significant environmental concerns due to their widespread presence, potential toxicity, and persistence. This study investigated the degradation of the isodecyl diphenyl phosphate (IDDP) and bis-(2-ethylhexyl)-phenyl phosphate (BEHPP) using a novel enrichment culture, which could degrade 85.4 % and 78.2 % of 1 mg/L IDDP and BEHPP after 192 h and 172 h, respectively, under extremely low bacterial dosage (the initial OD600 nm= 0.0075, biomass was approximately 1 mg/L). The identification of intermediate products suggested that the degradation reactions likely included hydrolysis, hydroxylation, methylation, carboxylation, and glycosylation. Metagenomic analysis highlighted the crucial role of enzymes in degrading IDDP and BEHPP, including phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase. Pure strains Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 were isolated, and their efficient individual degradation abilities were confirmed. These efficiencies were lower compared to the enrichment culture, emphasizing the importance of microbial interactions for effective degradation. The pathways identified for these strains illustrated their involvement in different degradation steps, reinforcing the synergy between different degraders. Molecular dynamics simulations provided insights into the interactions between alkaline phosphatase (ALP), cytochrome P450 (CYP450), and hydroxylase with OPEs. These enzymes demonstrated a strong binding capacity with both BEHPP and IDDP, exhibiting distinct binding site preferences that may contribute to varied metabolic pathways. These findings comprehensively reveal the transformation mechanisms of OPEs.},
}
@article {pmid40327666,
year = {2025},
author = {Yang, X and Zhang, Y and Xu, Y and Xu, Y and Zhang, M and Guan, Q and Hu, W and Tun, HM and Xia, Y},
title = {Microbial Disturbances Caused by Pesticide Exposure and Their Predictive Implications for Gestational Diabetes Mellitus.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01076},
pmid = {40327666},
issn = {1520-5851},
abstract = {Previous studies have suggested that pesticide exposure and gut microbiome alterations are associated with gestational diabetes mellitus (GDM) risk. Understanding the complex interactive effect of these factors on GDM is essential. In a cohort of 852 pregnant women, we assessed pesticide levels in serum and analyzed the gut microbiota using 16S rRNA and shotgun metagenomic sequencing. We explored the interactions between pesticides and gut microbiota, assessed their roles in GDM development, and proposed a predictive model based on identified biomarkers. We identified an environmental risk score (ERS), denoting the pesticide mixture level significantly associated with GDM, with the gut microbiota, particularly involving the Dorea branch, playing a crucial mediating role. In addition, we found an interactive effect of pesticide exposure and gut microbiota on GDM risk. Notably, low Prevotella enrichment combined with high ERS arisen from pesticide levels led to a 10.36-fold increased GDM risk. The identified pesticide and gut microbial biomarkers achieved high predictive accuracy for GDM (AUC: 0.833, 95% CI: 0.748-0.918). Collectively, maternal pesticide exposure may induce disrupted microbiome-dependent glycemic alteration, necessitating future assessment of clinical implications. Potential GDM markers can serve as targets for therapeutic intervention caused by pesticides, leading to prevention.},
}
@article {pmid40327160,
year = {2025},
author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z},
title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {282},
pmid = {40327160},
issn = {1432-0991},
support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal &amp; Child Research Fund Project" of Biostime Institute of Nutrition &amp; Care/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.},
}
@article {pmid40327041,
year = {2025},
author = {Hao, Q and Wang, O and Gong, X and Liu, F and Zhang, Y and Xie, Z and Tang, J and Sang, Y and Li, F and Liu, F},
title = {Cadmium-Induced Responses and Tolerance Mechanisms of Aerobic Methanotrophs in Rice Paddy Soils.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00031},
pmid = {40327041},
issn = {1520-5851},
abstract = {Paddy fields are major sources of atmospheric methane and are at risk of cadmium (Cd) contamination. Aerobic methanotrophs, which serve as biological methane sinks, play a key role in methane cycling, but their responses to Cd stress remain poorly understood. Here, we examined the relationship between Cd pollution levels and aerobic methane oxidation potential in paddy soils. We evaluated methanotrophic enrichments under Cd exposure, applied metagenomic sequencing to identify functional microbes, and investigated Cd tolerance mechanisms in pure culture. Aerobic methane oxidation rates were positively correlated with Cd levels in paddy soils from South China, with Methylocystis and Methylomonas emerging as dominant genera possessing diverse Cd tolerance genes. Notably, interspecific differences in Cd tolerance were observed among methanotrophic strains. The faster-growing Methylomonas sp., endowed with more robust antioxidant defenses and extracellular polymeric substances synthesis genes, exhibited Cd resistance through markedly enhanced loosely bound extracellular polymeric substances production, in contrast to the Cd-sensitive Methylobacter sp. Gene knockout experiments confirmed the essential roles of glutathione synthase, glutathione peroxidase, and exosortase in exopolysaccharide extrusion for Cd detoxification. These findings advance our understanding of the methane cycle in Cd-contaminated rice paddies and suggest potential strategies to mitigate methane emissions while addressing Cd detoxification.},
}
@article {pmid40326928,
year = {2025},
author = {Wang, R and Deng, P and Hu, X and Shen, C and Dong, X and Hu, K and Li, R},
title = {Optimizing Watershed Land Use to Achieve the Benefits of Lake Carbon Sinks while Maintaining Water Quality.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00190},
pmid = {40326928},
issn = {1520-5851},
abstract = {Greenhouse gas emissions and water quality decline are two major issues currently affecting lakes worldwide. Determining how to control both greenhouse gas emissions and water quality decline is a long-term challenge. We compiled data on the annual average carbon dioxide (CO2) flux and water quality parameters for 422 global lakes, revealing that 82.42% of the lakes act as carbon sources and that 66.56% have experienced water quality deterioration. Carbon sources and eutrophication trends were observed for lakes from the 1990s to 2020s, with further deterioration expected over the next 80 years. Unmanaged land use change in lake watersheds could exacerbate the CO2 flux into lakes and water quality degradation. In this study, a watershed land use planning (WLUP) framework was established, and a 24.83% reduction in the CO2 flux into lake water, a 5.07% reduction in chlorophyll a (Chl-a), a 4.70% reduction in total phosphorus, and a 12.92% increase in Secchi depth were achieved. The WLUP framework identifies Asia and Europe as the regions experiencing the greatest demands for land use transformation, where optimization leads to the most significant improvements. Metagenomic analysis revealed that forests enhance carbon fixation and that grasslands reduce carbon degradation and phosphorus metabolism in lake watersheds, explaining and supporting the possibility of WLUP. This work provides a win-win solution for improving CO2 fluxes and water quality in global lakes to mitigate the effects of climate change and promote lake protection.},
}
@article {pmid40326765,
year = {2025},
author = {Lindner, BG and Graham, KE and Phaneuf, JR and Hatt, JK and Konstantinidis, KT},
title = {SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03603},
pmid = {40326765},
issn = {1520-5851},
abstract = {Methodologies utilizing metagenomics are attractive to fecal source tracking (FST) aims for assessing the presence and proportions of various fecal inputs simultaneously. Yet, compared to established culture- or PCR-based techniques, metagenomic approaches for these purposes are rarely benchmarked or contextualized for practice. We performed shotgun sequencing experiments (n = 35) of mesocosms constructed from the water of a well-studied recreational and drinking water reservoir spiked with various fecal (n = 6 animal sources, 3 wastewater sources, and 1 septage source) and synthetic microbiome spike-ins (n = 1) introduced at predetermined cell concentrations to simulate fecal pollution events of known composition. We built source-associated genome databases using publicly available reference genomes and metagenome assembled genomes (MAGs) recovered from short- and long-read sequencing of the fecal spike-ins, and then created an associated bioinformatic tool, called SourceApp, for inferring source attribution and apportionment by mapping the metagenomic data to these genome databases. SourceApp's performance varied substantially by source, with cows being underestimated due to under sampling of cow fecal microbiomes. Parameter tuning revealed sensitivity and specificity near 0.90 overall, which exceeded all alternative tools. SourceApp can assist researchers with analyzing and interpreting shotgun sequencing data and developing standard operating procedures on the frontiers of metagenomic FST.},
}
@article {pmid40326511,
year = {2025},
author = {Zhu, Y and Liu, Q and Alffenaar, JW and Wang, S and Cao, J and Dong, S and Zhou, X and Li, X and Li, X and Xiong, H and Zhu, L and Hu, Y and Wang, W},
title = {Gut Microbiota in Patients with Tuberculosis Associated with Different Drug Exposures of Antituberculosis Drugs.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.3687},
pmid = {40326511},
issn = {1532-6535},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-03//Shanghai New Three-year Action Plan for Public Health/ ; 82073612//National Natural Science Foundation of China/ ; },
abstract = {Interindividual variability in drug exposure can significantly influence treatment outcomes and may lead to drug concentration-related side effects during tuberculosis (TB) treatment. Although the gut microbiota is known to affect drug metabolism, its impact on anti-TB drugs has not been thoroughly explored. This study sought to elucidate the relationship between pre-treatment gut microbiota and drug exposure levels among patients with pulmonary TB. Two cohorts were analyzed: a discovery cohort (N = 99) and a validation cohort (N = 32), both comprising patients undergoing anti-TB therapy with rifampicin, isoniazid, pyrazinamide, and ethambutol. The gut microbiota patterns of participants from the discovery cohort and the validation cohort were profiled by 16S rRNA gene sequencing and metagenomics, respectively. Analyses of both cohorts robustly established a positive association between pre-treatment microbial diversity and drug exposure, as well as significant differences in gut microbiota composition across various drug exposure groups. At the species level, Faecalibacterium prausnitzii was positively associated with drug exposure to rifampicin. Moreover, functional analysis revealed that starch and sucrose metabolism and secondary bile acid biosynthesis were more abundant in the high drug exposure group. To identify biomarkers capable of stratifying patients based on their drug exposure levels, 11 taxa, represented by Faecalibacterium, were selected in the discovery cohort (AUC = 0.992) and were confirmed in the validation cohort with high predictive accuracy (AUC = 0.894). This study demonstrated a correlation between microbial dysbiosis and reduced exposure to anti-TB medications. Optimizing treatment by regulating gut microbiota to improve drug exposure levels requires further validation through larger scale multicenter clinical trials.},
}
@article {pmid40326136,
year = {2025},
author = {Wu, B and Wang, J and Zhang, LN and Tang, W and Chen, KL},
title = {[Value of Pathogenic Detection by Next-Generation Sequencing in Bronchoalveolar Lavage Fluid on Children with Hematological Malignancies].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {2},
pages = {569-574},
doi = {10.19746/j.cnki.issn.1009-2137.2025.02.039},
pmid = {40326136},
issn = {1009-2137},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Hematologic Neoplasms/microbiology/complications ; Child ; Child, Preschool ; Infant ; Retrospective Studies ; Male ; Female ; Adolescent ; *High-Throughput Nucleotide Sequencing ; *Pneumonia/diagnosis/microbiology ; },
abstract = {OBJECTIVE: To investigate the application value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in etiological diagnosis of children with hematological malignancies complicated with pneumonia.<br><br>METHODS: We retrospectively analyzed the clinical data of children with hematological malignancies who underwent BALF mNGS pathogenic detection due to pneumonia. All patients underwent mNGS detection of bronchoalveolar lavage fluid as well as traditional methods(including sputum culture, bronchoalveolar lavage fluid culture, blood culture, serological detection of pathogens, etc.). By analyzing the results of mNGS and traditional methods, we compared key indicators such as the positive rate, etiological distribution.<br><br>RESULTS: A total of 26 children with hematological malignancies enrolled in the study, including 12 males and 14 females, with a median age of 4.9 (1.8-14.9) years, underwent bronchoalveolar lavage (BAL) 35 times. A total of 17 pathogenic microorganisms were detected in BALF mNGS, including 9 cases of bacterial infection, 10 cases of viral infection, 3 cases of fungal infection, 2 cases of mycoplasma infection and 8 cases of mixed infection, and the most commonly detected bacteria, viruses and fungi were streptococcus pneumoniae, cytomegalovirus and pneumocystis jirovecii, respectively. The positive rate of mNGS detection (91.43%) was significantly higher than that of traditional methods detection (20%, P <0.001). A total of 25 cases were adjusted according to BALF mNGS results.<br><br>CONCLUSION: The application of BALF mNGS technology can improve the detection rate of the pathogens in children with hematological malignancies complicated with pneumonia, initially revealed the pathogen spectrum of pulmonary infection in this group, and effectively guide clinical medication, improve treatment outcomes.},
}
@article {pmid40325896,
year = {2025},
author = {Ikegwuoha, NPP and Hanekom, T and Booysen, E and Jason, C and Parker-Nance, S and Davies-Coleman, MT and van Zyl, LJ and Trindade, M},
title = {Fimsbactin Siderophores From a South African Marine Sponge Symbiont, Marinomonas sp. PE14-40.},
journal = {Microbial biotechnology},
volume = {18},
number = {5},
pages = {e70155},
doi = {10.1111/1751-7915.70155},
pmid = {40325896},
issn = {1751-7915},
support = {//South African Medical Research Council (Self-Initiated grant)/ ; 87326//DSI/NRF SARChI research chair in Microbial Genomics/ ; 312184//European Union PharmaSea Consortium/ ; 129660//National Research Foundation/ ; },
mesh = {*Siderophores/chemistry/metabolism/genetics/isolation &amp; purification ; Multigene Family ; Animals ; Biosynthetic Pathways/genetics ; *Porifera/microbiology ; Symbiosis ; Hydroxamic Acids/metabolism/chemistry ; },
abstract = {Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1-6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.},
}
@article {pmid40325616,
year = {2025},
author = {Xu, HY and Jiang, MT and Yang, YF and Huang, Y and Yang, WD and Li, HY and Wang, X},
title = {Microalgae-Based Fucoxanthin Attenuates Rheumatoid Arthritis by Targeting the JAK-STAT Signaling Pathway and Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c12474},
pmid = {40325616},
issn = {1520-5118},
abstract = {Fucoxanthin, an abundant carotenoid in marine algae, has garnered attention for its diverse health benefits, including anti-inflammatory and anticancer properties. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation and damage. This study investigated the therapeutic potential of fucoxanthin extracted from Phaeodactylum tricornutum in collagen-induced RA. Our results demonstrated that fucoxanthin significantly alleviated RA symptoms, including weight loss, joint swelling, and decreased appetite. Histological analysis revealed that fucoxanthin mitigated synovial inflammation, cartilage damage, and bone erosion. Mechanistically, transcriptomic analysis and cell experiments indicated that fucoxanthin suppressed the JAK-STAT signaling pathway by downregulating the expression of inflammatory cytokines, such as IL-6 and IL-1β. Furthermore, metagenomic analysis suggested that fucoxanthin restored the altered gut microbiota composition associated with RA. These findings highlight the therapeutic potential of fucoxanthin from P. tricornutum in the management of RA by targeting multiple pathways, including inflammation and gut microbiota.},
}
@article {pmid40325428,
year = {2025},
author = {Liu, H and Zhu, Y and Huang, Y and Jiang, H},
title = {The application of metagenomic next generation sequencing in diagnosing tuberculous otitis media: a case report and review of the literature.},
journal = {Journal of medical case reports},
volume = {19},
number = {1},
pages = {207},
pmid = {40325428},
issn = {1752-1947},
support = {LQ24H130002//Natural Science Foundation of Zhejiang Province/ ; 2024C03238//Key Research and Development Program of Zhejiang Province/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Otitis Media/diagnosis/microbiology/drug therapy ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Tuberculosis/diagnosis/drug therapy/microbiology ; Antitubercular Agents/therapeutic use ; Tomography, X-Ray Computed ; Mastoidectomy ; },
abstract = {BACKGROUND: Tuberculous otitis media is a chronic Mycobacterium tuberculosis infection of the middle ear tissues. Diseases with varied and insidious clinical features can make diagnosis difficult and delay treatment.<br><br>CASE PRESENTATION: Here, we document a case of tuberculous otitis media in a 46-year-old ethnic Han woman that manifested as nonspecific chronic otitis media. A mastoidectomy and tympanoplasty were performed for the initial diagnosis of cholesteatoma. The histopathology of the tissue specimen revealed granuloma formation with necrosis. Staining for acid-fast bacilli and the polymerase chain reaction method for Mycobacterium tuberculosis yielded negative results. However, the chest computed tomography scan demonstrated a pulmonary miliary nodule. Next, metagenomic next-generation sequencing was applied and the Mycobacterium tuberculosis was identified. The patient recovered after receiving antituberculous treatment.<br><br>CONCLUSION: This report highlights the application of novel diagnostic tools such as metagenomic next-generation sequencing as a supplementary method for the diagnosis of tuberculous otitis media in highly suspected patients.},
}
@article {pmid40325409,
year = {2025},
author = {Herbert, J and Thompson, S and Beckett, AH and Robson, SC},
title = {Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {47},
pmid = {40325409},
issn = {2524-6372},
support = {Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; },
abstract = {INTRODUCTION: Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.<br><br>AIM AND METHODS: Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~&#x2009;97% accuracy) LSK109 chemistry, and newer more accurate (~&#x2009;99% accuracy) LSK112 Q20&#x2009;+&#x2009;chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.<br><br>RESULTS: Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20&#x2009;+&#x2009;nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits.<br><br>CONCLUSION: Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20&#x2009;+&#x2009;sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT's adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.},
}
@article {pmid40325330,
year = {2025},
author = {Panicucci, C and Casalini, S and Fiorito, G and Rinaldi, AB and Biagioli, V and Cangelosi, D and Brolatti, N and Principi, E and Baratto, S and Pedemonte, M and Morando, S and Riva, A and Venturino, C and Striano, P and Uva, P and Bruno, C},
title = {Exploratory Analysis of Gut Microbiota Profile in Duchenne Muscular Dystrophy (DMD) Patients with Intellectual Disability.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40325330},
issn = {1559-1182},
abstract = {This study investigates the differences in gut microbiota composition between DMD patients with (DMD +) and without (DMD -) intellectual disability (ID) and its potential role in cognitive outcomes. In this study, we assessed the gut microbiota in 50 genetically confirmed DMD patients (median age 13.1 years) using 16S rRNA gene sequencing. Cognitive assessment was performed using the Wechsler Intelligence Scales, with ID defined as an IQ < 70. Stool samples were analyzed, and statistical methods were used to assess alpha- and beta-diversity. Thirty-four percent of patients had ID. No significant differences were found in alpha-diversity or in the Firmicutes/Bacteroidetes ratio. However, beta-diversity analysis revealed significant differences between DMD + and DMD - groups, including, in DMD + , an increased abundance of Propionibacterium and Bifidobacterium, and a reduction in Bulleidia. These bacteria are involved in metabolic pathways that can influence neurological health through the gut-brain axis, particularly via the production of short-chain fatty acids. While these preliminary findings suggest a possible association between gut microbiota profile and cognitive impairment in DMD, further research is needed to explore a causal relationship and consider microbiota-targeted therapeutic strategies.},
}
@article {pmid40325116,
year = {2025},
author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S},
title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15683},
pmid = {40325116},
issn = {2045-2322},
support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation &amp; purification/genetics ; },
abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.},
}
@article {pmid40324989,
year = {2025},
author = {Gibbs, AJ and Fuentes, S and Adams, I and Hajizadeh, M and Ben Mansour, K and Guy, PL and Fribourg, C and Ziebell, H and Kreuze, J and Fox, A and Jones, RAC},
title = {A phylogeny of the tymoviruses, sensu stricto, and its global interpretation in space and time.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-25-0061-RE},
pmid = {40324989},
issn = {0191-2917},
abstract = {Maximum likelihood (ML) phylogenies of 109 tymoviruses, including three obtained directly from metagenomes, were calculated from all three open reading frames separately, but the concatenated sequences of their replicase and coat protein genes gave the most representative trees. ML phylogenies were also calculated from all recorded tymomvirus coat protein genes, and from datasets of the turnip yellow mosaic virus cluster, and separately of tomato yellow blotch, Andean potato latent and Andean potato mild mosaic viruses. These phylogenies showed that the basal divergence of tymoviruses occurred in a population infecting Eurasian brassicas (rosids), and more recently, one of the basal lineages diversified and adapted to infect some solanaceous (asterid) plants and crops of Central and South America. Heterochronous dating of the phylogenies failed, but heuristic comparisons based on patristic distances, branching patterns and external events suggested that the 'most recent common ancestor' of all known tymoviruses existed before the last Ice Age. Some lineages reached the Americas about 15,000 years ago. However, most spread of the few tymoviruses now found on more than one continent occurred during the past two centuries. The only recombinants were two sequences of Chiltepin yellow mosaic virus both with Nemesia ring necrosis virus as minor parent. Population genetic analysis found significant evidence of population contraction in the tymovirus populations infecting asterid hosts in the Americas. It also found the replicase and coat protein genes were significantly negatively selected. By contrast, the overlapping movement protein genes were positively selected which may help them adapt to new host species, including infecting economically significant crops. This knowledge about tymoviruses is important to plant biosecurity authorities.},
}
@article {pmid40324646,
year = {2025},
author = {Shen, H and Wang, D and Huang, Y and Yang, Y and Ji, S and Zhu, W and Liu, Q},
title = {2,3,7,8-tetrachlorodibenzofuran modulates intestinal microbiota and tryptophan metabolism in mice.},
journal = {Life sciences},
volume = {373},
number = {},
pages = {123679},
doi = {10.1016/j.lfs.2025.123679},
pmid = {40324646},
issn = {1879-0631},
abstract = {Persistent organic pollutants (POPs) are known to disrupt gut microbiota composition and host metabolism, primarily through dietary exposure. In this study, we investigate the impact of 2,3,7,8-tetrachlorodibenzofuran (TCDF) on gut microbiota and host metabolic processes. RNA-seq analysis revealed that TCDF exposure significantly affected tryptophan metabolism, lipid metabolic pathways, and immune system function. Metagenomic and metabolomic analyses further showed that TCDF reduced the abundance of Mucispirillum schaedleri and levels of two key tryptophan metabolites, indole-3-carboxaldehyde (3-IAld) and Indole acrylic acid (IA). Supplementation with 3-IAld and IA alleviated TCDF-induced liver toxicity in mouse, as evidenced by reduced Cyp1a1 expression, and mitigated intestinal inflammation, reflected by lower pro-inflammatory cytokines (Ifn-γ and Il-1β) in the colon. Additionally, 3-IAld and IA supplementation enhanced intestinal barrier function, as demonstrated by increased Mucin 2 (MUC2) expression in the gut mucosa of mouse. These findings suggest that TCDF exposure disrupts the gut microbiome and host metabolic balance, and highlight the potential therapeutic role of tryptophan-derived metabolites in mitigating environmental pollutant-induced damage.},
}
@article {pmid40324616,
year = {2025},
author = {Zhao, X and Chen, Y and Hu, J and Wang, H and Ye, Z and Zhang, J and Meng, J and Li, J and Dahlgren, RA and Zhang, S and Gao, H and Chen, Z},
title = {Efficacy of nitrate and biochar@birnessite composite microspheres for simultaneous suppression of As(III) mobilization and greenhouse gas emissions in flooded paddy soils.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121757},
doi = {10.1016/j.envres.2025.121757},
pmid = {40324616},
issn = {1096-0953},
abstract = {Elevated As(III) pollution and greenhouse gas (GHG) emissions are two primary environmental concerns associated with flooded paddy soils. Herein, a novel biochar@birnessite composite microsphere was engineered using a biochar, birnessite and sodium alginate formulation. The microspheres were applied along with nitrate to examine their efficacy in suppressing As(III) mobilization and GHG emissions in an As-contaminated flooded paddy soil. After a 10-day incubation period, the combined nitrate+microsphere treatment achieved desirable remediation effects versus a nitrate-alone treatment, with mobile As(III) (initially 0.1 mM in flooded layer) completely immobilized and N2O, CH4 and CO2 emissions declining by 89%, 73% and 31%, respectively. As(III) immobilization was ascribed to oxidation/adsorption/coprecipitation by FeOx/MnOx regenerated from successive cycles of Feammox/Mnammox and nitrate-reduction coupled with Fe(II) oxidation (NRFO)/nitrate-reduction coupled with Mn(II) oxidation (NRMO). Moreover, NRFO/NRMO-derived full denitrification displayed high thermodynamic feasibility, leading to full denitrification with the generation of N2 rather than N2O. The co-occurrence of anaerobic oxidation of methane (AOM) driven by biochar-shuttling and coupled reduction of nitrate/FeOx/MnOx fostered anaerobic oxidation of CH4 to CO2. A portion of the resulting CO2 was incorporated into poorly-soluble carbonate minerals leading to lower CO2 emission and soil carbon sequestration. Metagenomic sequencing revealed that the nitrate+microsphere treatment enriched the abundances of key microorganisms linked to As/Fe/Mn oxidation and GHG mitigation (e.g., Geobacter, Streptomyces, Cupriavidus and Chloroflexus). Our findings document the efficacy of nitrate+biochar@birnessite microsphere treatment as an effective remediation strategy to simultaneously mitigate As(III) pollution and GHG emissions in flooded paddy soils.},
}
@article {pmid40323477,
year = {2025},
author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG},
title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {6},
pages = {195},
pmid = {40323477},
issn = {1559-131X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; },
abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.},
}
@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation &amp; purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}
@article {pmid40323169,
year = {2025},
author = {Zhu, D and Galley, J and Pizzini, J and Musteata, E and Douglas, MV and Chazin, WJ and Skaar, EP and Tabor, JJ and Britton, RA},
title = {Microbial Biosensor for Sensing and Treatment of Intestinal Inflammation.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2504364},
doi = {10.1002/advs.202504364},
pmid = {40323169},
issn = {2198-3844},
support = {//Baylor College of Medicine Seed Funding/ ; //Crohn's and Colitis Foundation Litwin Pioneer Award (RAB)/ ; R01AI123278//National Institutes of Health grants/ ; U19AI157981//National Institutes of Health grants/ ; R01AI155586//National Institutes of Health grants/ ; R01AI164587//National Institutes of Health grants/ ; U19AI174999//National Institutes of Health grants/ ; },
abstract = {Synthetic biology has enabled the development of biosensors to detect intestinal inflammation, yet few target the clinically validated biomarker of intestinal inflammation calprotectin with both diagnostic and therapeutic capabilities. Here, an optimized calprotectin biosensor is presented that leverages a zinc uptake regulator (Zur) controlled promoter coupled with a memory circuit to detect and record intestinal inflammation in vivo. The level of biosensor activation strongly correlates with calprotectin levels in the colon of two independent mouse models of colitis. Coupling of the biosensor with the production of the anti-inflammatory cytokine IL10 allowed for the resolution of chemically induced colitis, demonstrating the ability of the biosensor to sense and respond to disease. This work highlights the utility of developing synthetic organisms for the diagnosis and treatment of intestinal disease using clinically validated biomarkers.},
}
@article {pmid40322835,
year = {2025},
author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C},
title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {5},
pages = {e70082},
doi = {10.1111/aji.70082},
pmid = {40322835},
issn = {1600-0897},
support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; },
abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.<br><br>METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.<br><br>RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-&#x3ba;B, MMP3, I&#x3ba;B&#x3b1;, IL-1&#x3b2;, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.<br><br>CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.},
}
@article {pmid40322711,
year = {2025},
author = {Kulsum, U and Patankar, C and Biswas, D},
title = {MOSMAP: Mosquito metagenome analysis pipeline.},
journal = {Bioinformation},
volume = {21},
number = {2},
pages = {110-112},
pmid = {40322711},
issn = {0973-2063},
abstract = {MosMAP is a bioinformatics pipeline designed for mosquito metagenome analysis. MosMAP automates essential processes like quality control, taxonomic classification, species abundance estimation and visualization by integrating tools such as Trimgalore, Kraken 2, Bracken and Krona into a user-friendly workflow. Each of these tools is integrated to ensure a smooth and efficient workflow from raw data to interpretable results. The pipeline simplifies complex bioinformatics tasks, making them accessible to researchers with limited computational expertise. MosMAP demonstrated high concordance with standard bioinformatics workflows such as Kraken and Bracken in terms of read retention, taxonomic accuracy and abundance estimation when applied to metagenomes of mosquito collected in Bhopal, India. This accessible pipeline promotes the simplification of meta-genomics, supporting research in microbiology, ecology and vector-borne diseases.},
}
@article {pmid40322468,
year = {2025},
author = {Shan, H and Wang, J and Zhang, Q and Ming, Z and Zhang, Y and He, P and Fang, P and Zhang, M and Li, W and Shi, H and Guan, Y and Yang, S},
title = {Pathogen surveillance and risk factors for pulmonary infection in patients with lung cancer: A retrospective single-center study.},
journal = {Open medicine (Warsaw, Poland)},
volume = {20},
number = {1},
pages = {20251180},
pmid = {40322468},
issn = {2391-5463},
abstract = {BACKGROUND: Early and accurate diagnosis of pulmonary infection (PI) is crucial for the timely implementation of appropriate treatment strategies in lung cancer patients.<br><br>METHODS: Metagenomic next-generation sequencing and conventional testing were performed in lung cancer patients with and without PI. The pathogen profiles were analyzed, and risk factors for PI were explored using univariate and multivariate logistic regression models.<br><br>RESULTS: A total of 55 lung cancer patients with PI and 59 non-infected lung cancer patients were included. There were 41 underlying pathogens identified by both methods in lung cancer patients with PI. The coexistence of different pathogen types was common, particularly between fungi and viruses, which was observed in 28.57% of cases. The incidence of Streptococcus pneumoniae and Pneumocystis jirovecii is significantly higher in small-cell lung carcinoma patients compared to that in non-small-cell lung carcinoma patients. Besides, cytomegalovirus, P. jirovecii, and Aspergillus were more likely to be found in advanced-stage patients. Risk factor analysis revealed that Karnofsky Performance Status <90 and chemotherapy were strongly associated with PI in lung cancer patients.<br><br>CONCLUSIONS: This study highlights the complexity of PI in lung cancer patients, emphasizing the need for tailored diagnostic and therapeutic strategies based on cancer type and stage.},
}
@article {pmid40321823,
year = {2025},
author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A},
title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19305},
pmid = {40321823},
issn = {2167-8359},
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; Islands ; *Fungi/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Ecosystem ; *Microbiota ; },
abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.},
}
@article {pmid40321713,
year = {2025},
author = {De Coninck, L and Hadermann, A and Ingletto, L and Colebunders, R and Gamnsi Njamnshi, K and Njamnshi, AK and Mokili, JL and Siewe Fodjo, JN and Matthijnssens, J},
title = {Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf024},
pmid = {40321713},
issn = {2057-1577},
abstract = {Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy-hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies have failed to detect Onchocerca volvulus in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A viral particle-based shotgun sequencing approach was used to detect viral sequences in 55 pools of 10 blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the haematophagous blackfly, which also could be present in their nematode host O. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.},
}
@article {pmid40321599,
year = {2025},
author = {Zhou, Z and Song, Y and Yan, Y and Zheng, Y},
title = {Metagenomic Next-Generation Sequencing Improves the Diagnosis Efficiency of Mixed Periprosthetic Joint Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2165-2174},
pmid = {40321599},
issn = {1178-6973},
abstract = {PURPOSE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) in the diagnosis of mixed periprosthetic joint infections (PJI).<br><br>METHODS: The data pertaining to patients suspected of PJI who underwent arthroplasty at our hospital between January 2020 and June 2024 were analyzed. Patients included in the study were subjected to microbial culture and mNGS analyses to evaluate the efficacy of mNGS in diagnosing mixed PJIs.<br><br>RESULTS: Among the 44 PJI patients included, 20 (45.45%) were culture-positive, and 35 (79.55%) were mNGS-positive. Compared to microbial culture, mNGS demonstrated significantly higher sensitivity, negative predictive value, and accuracy (79.55% vs 45.45%, 55.00% vs 35.14%, and 80.70% vs 57.89%, respectively; all&#xa0;P<0.05). However, the specificity of mNGS was significantly lower than culture (84.62% vs 100.00%, P<0.05). For mixed PJIs, the sensitivity of mNGS was notably higher, albeit with lower specificity and positive predictive value compared to microbial culture (72.23% vs 27.27%, 85.19% vs 100.00%, 66.67% vs 100.00%, respectively; all P<0.05). mNGS enables more sensitive detection of co-pathogens in mixed PJI, accelerating targeted therapy and reducing inappropriate broad-spectrum therapy. While its lower specificity requires clinical integration, it clarifies complex diagnoses and streamlines stewardship for improved outcomes.<br><br>CONCLUSION: mNGS is a promising technique for rapidly and accurately detecting co-pathogens in mixed PJI.},
}
@article {pmid40321269,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Cools Portier, S and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A},
title = {Profiling the human luminal small intestinal microbiome using a novel ingestible medical device.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.18.25326056},
pmid = {40321269},
abstract = {The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MD's effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness, and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct SI metabolic footprint, with bile acids and amino acids being the most abundant classes of metabolites. Host and host/microbe-derived bile acids were particularly abundant in SI samples. The application of a fast culturomics approach to two SI samples enabled species-level characterization, resulting in the identification of 90 bacterial species, including five potential novel species. The present study demonstrates the efficacy of our novel sampling MD in enabling comprehensive SI microbiome analysis through an integrative multi-omics approach, allowing the identification of distinct microbiome signatures between SI and fecal samples.},
}
@article {pmid40320901,
year = {2025},
author = {Gervasoni, KN and Iacia, MVMS and Silva, KO and Franco, LG and Mendes, MEF and Neves, TJDC and Sanches, WS and Oliveira, LB and Saito, EA and Vieira, KCO and Pereira, VC and Nai, GA and Winkelstroter, LK},
title = {Protective Effect of Piperine on Indomethacin-Induced Intestinal Damage.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70097},
doi = {10.1002/mnfr.70097},
pmid = {40320901},
issn = {1613-4133},
abstract = {Nonsteroidal antiinflammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammation and chronic pain. Chronic use of NSAIDs is associated with adverse events and organ damage, especially to the gastric mucosa and small intestine. This study evaluates the protective effect of piperine on indomethacin-induced intestinal damage. Eighteen male Mus musculus mice, aged 6-8 weeks, were used. Intestinal damage was induced with indomethacin (10 mg/mL) and cotreatment with piperine (20 mg/mL), both administered orally. After 14 days, the animals were euthanized. Biochemical serological analysis was performed. Intestinal inflammation was assessed based on macroscopic, histopathological, and metagenomic analyses. Histopathological analysis showed a reduction in small intestine inflammation (p < 0.05) and the disappearance of necrosis in the intestinal wall of the large intestine. Crypt and villus measurements showed increased values in the piperine-treated group (p < 0.05). An approximately six-fold increase in aspartate aminotransferase (AST) was observed in the Indomethacin group (p < 0.05). Regarding the intestinal microbiota, an increase in genus diversity was observed in the piperine-treated group (p < 0.05). There was a 50% reduction in micronucleus formation with the administration of piperine 20 mg/kg (p < 0.05). It was concluded that cotreatment with piperine has great potential in mitigating the side effects caused by NSAIDs.},
}
@article {pmid40320531,
year = {2025},
author = {Vidaur, L and Guridi, A and Leizaola, O and Marin, J and Rello, J and Sarasqueta, C and Sorarrain, A and Marimón, JM},
title = {Respiratory dysbiosis as prognostic biomarker of disease severity for adults with community-acquired pneumonia requiring mechanical ventilation.},
journal = {Pneumonia (Nathan Qld.)},
volume = {17},
number = {1},
pages = {10},
pmid = {40320531},
issn = {2200-6133},
support = {FIS17/01463//Instituto de Salud Carlos III/ ; FIS17/01463//Instituto de Salud Carlos III/ ; },
abstract = {OBJETIVES: To ascertain the role of the lung microbiome in the development of severe pneumonia and its potential as a biomarker for disease progression.<br><br>METHODS: BAL samples from 34 adults with severe community-acquired pneumonia (CAP) (17 viral, 8 viral coinfected with bacteria and 9 bacterial) admitted to the ICU for acute respiratory failure between 2019 and 2021 were collected within the first 48&#xa0;h of admission to the ICU. The microbiome was characterized via the Ion 16S Metagenomics Kit and the Ion Torrent sequencing platform. Clinical factors, including survival, mechanical ventilation duration, blood biomarkers and organ failure in terms of acute respiratory distress syndrome (ARDS), shock or acute renal failure, were correlated with microbiome characteristics.<br><br>RESULTS: The microbiome diversity in patients with viral pneumonia was significantly greater than that in patients with bacterial or coinfected pneumonia: the Shannon diversity index was 3.75 (Q1-Q3: 2.5-4.1) versus 0.4 (Q1-Q3: 0.2-1.3) and 0.48 (Q1-Q3: 0.3-1.1), respectively (p&#x2009;<&#x2009;0.05). The microbiome diversity index was associated with severity-of-illness (APACHE II), independent of the etiology of pneumonia (B coefficient -1.845; p&#x2009;<&#x2009;0.01). Patients with severe viral CAP who developed ARDS had a lower presence of Proteobacteria, and those who were complicated with ventilator-associated pneumonia had a higher prevalence of Acinetobacter at admission. The mortality of patients with bacterial or coinfected pneumonia was 35%. In coinfected patients, the diversity index was associated with the development of shock.<br><br>CONCLUSION: Patients with severe CAP have low respiratory microbiome diversity, indicating that respiratory microbiome diversity is a potential biomarker of disease severity.},
}
@article {pmid40320520,
year = {2025},
author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J},
title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {111},
pmid = {40320520},
issn = {2049-2618},
support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; },
mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil Microbiology ; Droughts ; },
abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.<br><br>RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.<br><br>CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.},
}
@article {pmid40320100,
year = {2025},
author = {Kogoj, R and Bosilj, M and Šturm, AC and Korva, M and Smrdel, KS and Kvas, E and Pirš, M and Lepen, L and Triglav, T},
title = {Bioinformatic challenges in metagenomic next generation sequencing data analysis while unravelling a case of uncommon campylobacteriosis.},
journal = {Journal of biomedical informatics},
volume = {},
number = {},
pages = {104841},
doi = {10.1016/j.jbi.2025.104841},
pmid = {40320100},
issn = {1532-0480},
abstract = {OBJECTIVE: This study aimed to employ advanced bioinformatics and modern sequencing approaches to solve a diagnostic problem of persistent Campylobacter spp. molecular detection yet negative culture results from four consecutive stool samples of a previously healthy patient with newly diagnosed selective IgA deficiency with prolonged diarrhoea METHODS: Metagenomic next-generation sequencing (mNGS) based on short-paired end reads with basic bioinformatic read classification analysis was used at first. Due to confusing results, advanced bioinformatics involving contigs construction and classification, reference genome mappings and reads filtering with BBSplit, additionally coupled with metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding were employed to further elucidate the results. Virulence factors were analysed using the Prokka Genome Annotation tool. Modified classical bacteriology methods were finally used for further clarification.<br><br>RESULTS: Short-pair end reads analysis identified several Campylobacter species in all four samples. After advanced bioinformatic approaches were applied, candidatus C. infans was suspected as the putative pathogen. This result was further supported by metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding. Nevertheless, after modifying the culture conditions based on mNGS results, a mixed culture of candidatus C. infans and C.ureolyticus was obtained. Sequencing of the mixed culture resulted in an 87.48&#x202f;% and 73.47&#x202f;% genome coverage of candidatus C. infans and C. ureolyticus, respectively. In the candidatus C. infans genome more virulence factors hits were found than in the C. ureolyticus genome thus supporting the first as the most probable cause of symptoms.<br><br>CONCLUSION: This study shows the pivotal role and strengths of mNGS in unravelling an unusual case of diarrhoea and demonstrates how mNGS can guide established microbiological methods to improve on current limitations. However, it also emphasises the need for careful interpretation of sequencing data, particularly for closely related bacterial species from clinical samples that are known to support complex microbial communities.},
}
@article {pmid40320026,
year = {2025},
author = {Zheng, Y and Yue, Y and Liu, C and Pang, L and Wang, Y and Yang, Z},
title = {The role of riverbed substrates in N2O and CH4 emission: Insights from metagenomic analysis of epilithic biofilms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121772},
doi = {10.1016/j.envres.2025.121772},
pmid = {40320026},
issn = {1096-0953},
abstract = {Riverbed substrates are critical in N2O and CH4 emission with functional microbes adhering to them. However, the role of substrates remains to be fully understood. This study monitors N2O and CH4 emission and collects epilithic biofilms on riverbed substrates with various diameters and size heterogeneity from 10 sections along a mountain river. Compared with the global range, moderate water-air exchange rates of N2O (-2.34-29.2 μg/m[2]/h) and rapid CH4 emission (-2.58-35.2 mg/m[2]/h) are observed. Based on metagenomic analysis, the abundances of nirS and fmdA genes, which encode catalysts in the denitrification and the hydrogenotrophic methanogenesis process, are found to be significantly higher in the medium diameter group (2-100 mm), implying higher N2O and CH4 emission. Meanwhile, the abundance of nirS and nirK genes, which are key to N2O production, is significantly higher in the low size heterogeneity group, promoting N2O release. In contrast, the abundance of ftr, pta,ackA and ACS genes critical in the methanogenesis processes are significantly lower in the low size heterogeneity group, inhibiting CH4 emission. For N2O production, the nitrification process is found to be dominated by species of Nocardioides and Planctomycetales, denitrification process by species of Tabrizicola and Rhodobacteraceae, and dissimilatory nitrate reduction to ammonium process by Leptospiraceae species. In contrast, CH4 is mainly generated by species of Pirellula and Proteobacteria through hydrogenotrophic, acetoclastic and methylotrophic methanogenesis respectively. A structural equation model indicated that substrate physical properties are equally or even more important as/than the aquatic nutrients concentration for N2O or CH4 emission in mountain rivers.},
}
@article {pmid40319779,
year = {2025},
author = {Zhu, J and Li, X and Wang, Y and Gu, X and Wang, H and Ma, J and Huang, Y},
title = {Organic sulfur-driven denitrification pretreatment for enhancing autotrophic nitrogen removals from thiourea-containing wastewater: performance and microbial mechanisms.},
journal = {Water research},
volume = {282},
number = {},
pages = {123753},
doi = {10.1016/j.watres.2025.123753},
pmid = {40319779},
issn = {1879-2448},
abstract = {Thiourea (CH4N2S) is a widely used industrial reagent and is frequently detected in both sewage and industrial wastewater. However, treating thiourea-containing wastewater remains challenging due to its toxicity, high ammonium concentration, and low C/N ratio. In this study, a novel integrated autotrophic-heterotrophic denitrification (IAHD)- completely autotrophic nitrogen removal over nitrite (CANON) process was developed. The degradation pathway of toxic compounds, nitrogen, and sulfur release and transformation, as well as variations in functional genes were comprehensively examined. The results show that by incorporating an IAHD unit, prior to CANON, toxic thiourea was effectively degraded by the recycled nitrate from CANON. The released sulfur and organic carbon served as electron donors facilitating efficient NO3[-]-N reduction. The optimal thiourea/NO3[-]-N ratio for IAHD operation was determined to be 4:1 (m:m), achieving NO3[-] and thiourea removal efficiencies of 90 % and 99 %, respectively. Additionally, NH4[+]-N and SO4[2-]-S concentrations increased by 199.9 mg/L and 201.9 mg/L, respectively. Approximately 53.3 % of thiourea was converted into high-molecular-weight biological metabolites in the IAHD unit, which were subsequently and completely degraded in the CANON unit, where a robust nitrite-shunt and anammox process occurred. 16S rRNA amplicon sequencing revealed that Thiobacillus (with a relative abundance of 39.9 %) was the dominant genera in the IAHD unit, followed by Arenimonas (10.8 %) and norank_o_1013-28-CG33 (12.4 %), indicating that sulfur autotrophic denitrification was the primary pathway for thiourea degradation. Metagenomic analysis further confirmed that thiourea, acting as an electron donor, stimulated the expression of key functional genes involved in denitrification, sulfur oxidation, dissimilatory nitrate reduction, hydrolytic oxidation, and amino acid synthesis and transport pathways. These processes contributed to the active biological transformation of carbon, nitrogen and sulfur in the IAHD unit. This study demonstrates that implementing a prior autotrophic-heterotrophic denitrification unit effectively degrades toxic thiourea, thereby ensuring the subsequent nitrogen removal performance of CANON. This approach offers a new paradigm for the treatment of thiourea-containing wastewater, promoting a more efficient and low-carbon process.},
}
@article {pmid40319631,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Rehman, KU and Ren, Z and Jiménez, N and Zheng, L and Huang, F and Yu, Z and Yu, C and Zhang, J and Cai, M},
title = {Mitigating the transfer risk of antibiotic resistance genes from fertilized soil to cherry radish during the application of insect fertilizer.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109510},
doi = {10.1016/j.envint.2025.109510},
pmid = {40319631},
issn = {1873-6750},
abstract = {The transfer of antibiotic resistance genes (ARGs) from fertilized soil to vegetables, particularly those consumed raw, causes significant public health risks through the food chain. Black soldier fly larvae can efficiently convert animal manure into organic fertilizer with reduced antibiotic resistance. This study utilized metagenomic sequencing to investigate fields treated with control organic fertilizer (COF), black soldier fly organic fertilizer (BOF), and no fertilizer, with the aim of assessing the transfer risks of ARGs from soil to cherry radish. The results indicated that BOF significantly reduced the richness and abundance of ARGs in both soil and cherry radish compared to COF, reducing 13 ARG subtypes and a 27.6% decrease in ARG abundance in cherry radish. Moreover, a significant positive correlation was observed between mobile genetic elements (MGEs) and virulence factors (VFs) with ARGs, with BOF treatment resulting in a relative abundance reduction of 32.8% and 29.1%, respectively. The complexity of networks involving ARGs with MGEs, VFs, and microbial communities in the BOF treatment was 54.2%, 32.3%, and 32.8% lower, respectively, than the COF treatment. Further analysis of metagenomic-assembled genomes (MAGs) revealed the co-occurrence of ARGs, MGEs, and VFs in cherry radish, indicating the presence of potential pathogenic antibiotic-resistant bacteria (PARB). Notably, the abundance of these PARB in BOF radishes decreased by 45.6% compared to COF. These findings underscore the efficacy of insect fertilizer in mitigating the transfer risks of ARGs to radish, highlighting the significance of sustainable agricultural practices in managing the environmental and health risks associated with ARGs.},
}
@article {pmid40319164,
year = {2025},
author = {Fan, Y and Chen, J and Xu, S and Zhou, H and Shang, Y and Tian, X and Wang, B and Zhao, Y and Shan, G and Zhao, Y and Zhang, P and Chen, X},
title = {Bacillus cereus is a key microbial determinant of intractable otitis media with effusion.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {150},
pmid = {40319164},
issn = {2730-664X},
abstract = {BACKGROUND: Currently, the mechanisms by which otitis media with effusion (OME) progresses to intractable OME is unclear. Since crosstalk between microbiome and host contributes to many diseases, we hypothesized that similar interactions could occur in the middle ear effusion (MEE) samples from patients with OME and influence intractable OME pathogenesis. This study aimed to evaluate the microbial profile of MEE samples and to determine whether there were microbial differences between the MEE microbiota of patients with intractable OME and those with rapidly cured OME.<br><br>METHODS: MEE samples were collected from 46 OME patients, including 20 from the long course group and 26 from the short course group. Metagenomic sequencing was performed on 30 of these samples, allowing the identification of microbial differences associated with varying disease durations. The difference was verified by further experimental validation, including fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR).<br><br>RESULTS: The alpha diversity indices and overall MEE microbial structure show no significant difference between the long course and short course groups, but species such as Bacillus cereus, Nocardiopsis dassonvillei, and Rothia aeria are significantly more prevalent in the MEE of long course OME patients. qPCR analyses and FISH also confirm the difference in the abundance of Bacillus cereus between the two groups.<br><br>CONCLUSIONS: Bacillus cereus plays a role in the persistence of OME infection and serves as a potential biomarker to predict OME prognosis. Further studies are warranted to explore the value of Bacillus cereus detection in informing early intervention.},
}
@article {pmid40297421,
year = {2025},
author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA},
title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40297421},
support = {F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; },
abstract = {OBJECTIVE: The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women, and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology.<br><br>METHODS: Self-collected vaginal swabs and questionnaires on dietary and health practices were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Additionally, medication regimen and disease activity and severity were captured for the RA cohort. Vaginal swabs were subjected to full-length 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, c-reactive protein, and anti-citrullinated protein antibodies (ACPAs).<br><br>RESULTS: Vaginal microbial richness and genera Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal IL-18 and EGF levels were increased in the RA group; IL-18 correlated with multiple microbial features whereas EGF levels were not associated with bacterial composition or other host factors. Within the RA cohort, decreased relative abundance of Streptococcus was associated with joint pathologies, and Lactobacillus gasseri was lower in individuals with serum detection of ACPAs and rheumatoid factor. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines.<br><br>CONCLUSIONS: We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, disease activity and severity, and medication use. This work opens a new avenue in the multidisciplinary approach to RA patient care.},
}
@article {pmid40318372,
year = {2025},
author = {Chu, D and Zhang, H and Wang, Z and Ning, K},
title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179522},
doi = {10.1016/j.scitotenv.2025.179522},
pmid = {40318372},
issn = {1879-1026},
abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.},
}
@article {pmid40318358,
year = {2025},
author = {Karatas, M and Bloemen, M and Swinnen, J and Roukaerts, I and Gucht, SV and Van Ranst, M and Wollants, E and Matthijnssens, J},
title = {Untapped potential of wastewater for animal and potentially zoonotic virus surveillance: Pilot study to detect non-human animal viruses in urban settings.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109500},
doi = {10.1016/j.envint.2025.109500},
pmid = {40318358},
issn = {1873-6750},
abstract = {INTRODUCTION: Wastewater surveillance has become an essential tool for monitoring viral outbreaks and surveillance of human viruses. While PCR-based methods are most frequently used, more advanced techniques, such as shotgun metagenomics in combination with viral capture methods, have been developed. These capture methods significantly improve the ability to detect nearly all (known) viruses at once in complex samples, including wastewater. In this study, we focus on tracking animal specific and zoonotic viruses in city wastewater using metagenomics combined with hybrid-capture approach.<br><br>METHODS: We collected 6 wastewater samples from Leuven and Brussels, situated in the center of Belgium. Automated wastewater samplers collected 50&#xa0;mL samples every 10&#xa0;min resulting in a 24&#xa0;h composite influent wastewater. All samples were processed using the TWIST comprehensive research panel capture, designed to target over 3,000 human and animal viruses species and 15,000 strains. Sequencing was performed on the AVITI sequencing platform, targeting an average of ten million reads per sample. The sequencing data were analyzed using the EsViritu tool.<br><br>RESULTS: Over 2294 viral genomes or segments were recovered from wastewater samples. Of these, 168 were associated with non-human vertebrate animals, including cats, dogs, pigeons, and rats, spanning 51 virus species. We identified near-complete genomes of clinically relevant animal viruses, such as pigeon circovirus, chicken anemia virus, feline bocaparvovirus 2, canine minute virus, rat coronavirus, canine parvovirus, and porcine circovirus. Additionally, we noted the presence of viruses with known cross-species transmission potential, including porcine torovirus, rosavirus, hepatitis E virus, rat hepatitis virus, and cardiovirus.<br><br>CONCLUSION: The results demonstrate the ability to track a wide range of animal viruses in urban wastewater, potentially forming an early warning system for zoonotic diseases, ultimately being a useful tool for One Health based public health approaches.},
}
@article {pmid40318224,
year = {2025},
author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ},
title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf088},
pmid = {40318224},
issn = {1751-7370},
abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.},
}
@article {pmid40316928,
year = {2025},
author = {Zhang, Y and Sun, D and Fang, Y and Feng, Y and Wu, Y and Shen, W and Wu, W and Gao, X and Sun, Y and Ma, X and Gao, F and Zhu, C and Zhou, J and Gu, C},
title = {Uncommon pulmonary manifestation of hepatitis B virus: a case report of secondary organizing pneumonia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {645},
pmid = {40316928},
issn = {1471-2334},
support = {Z-2014-06-2301//China International Medical Exchange Foundation Xiansheng Clinical Research Special Fund Research Project/ ; 2023-SSGJ-002//Key Construction Disciplines of Provincial and Municipal Co construction of Zhejiang/ ; 2021-GFXK-04//Peak Discipline of Jiaxing First Hospital/ ; 2021AD30177//Science and Technology Project of Jiaxing/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Hepatitis B virus/genetics/isolation &amp; purification ; *Hepatitis B/complications/virology/diagnosis ; Lung/pathology/virology ; DNA, Viral/genetics ; Viral Load ; Organizing Pneumonia ; },
abstract = {BACKGROUND: Hepatitis B virus (HBV) primarily affects the liver, but increasingly, it is recognized for its potential extrahepatic manifestations. This case highlights the importance of considering viral infections in the differential diagnosis of pulmonary nodules.<br><br>CASE PRESENTATION: A 63-year-old man presented with a new mixed ground-glass nodule in the left lower lobe during a routine check-up. He had a history of liver resection for hepatocellular carcinoma, with results negative for hepatitis B virus surface antigen. The HBV viral load in the patient's serum was below the detection limit of quantitative PCR (qPCR). Immunohistological analysis of lung biopsy samples indicated chronic inflammation. However, after a course of intravenous antibiotics, the nodule increased in size, prompting further investigation. Therefore, lung biopsy tissue was subjected to metagenomic next-generation sequencing (mNGS), and HBV DNA was detected. The patient was diagnosed with secondary organizing pneumonia associated with HBV. Then he was treated with prednisone acetate and had remission.<br><br>CONCLUSION: This case underscores the potential for HBV to manifest as pulmonary complications, such as secondary organizing pneumonia. Therefore, in the stage of infectious diseases in patients with a history of hepatocellular carcinoma, HBV needs to be the focus of monitoring, so as to clarify the cause of diagnosis and treatment as soon as possible.<br><br>CLINICAL TRIAL: Not applicable.},
}
@article {pmid40316630,
year = {2025},
author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD},
title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15356},
pmid = {40316630},
issn = {2045-2322},
support = {Small grant//Universidad del Rosario/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; },
abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.},
}
@article {pmid40316568,
year = {2025},
author = {Joshi, P and Bhattacharjee, R and Sahu, M and Gajjar, D},
title = {Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15375},
pmid = {40316568},
issn = {2045-2322},
mesh = {*Biofilms/growth &amp; development ; Humans ; *Urinary Catheters/microbiology ; *Candida/physiology/isolation &amp; purification/growth &amp; development ; Urinary Tract Infections/microbiology ; *Bacteria/growth &amp; development/isolation &amp; purification/genetics ; Catheter-Related Infections/microbiology ; Coinfection/microbiology ; Metagenomics ; Pseudomonas aeruginosa ; Escherichia coli ; Klebsiella pneumoniae ; },
abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.},
}
@article {pmid40315933,
year = {2025},
author = {Cheng, Z and Wang, J and Liu, X and Cao, S},
title = {Accelerated sludge granulation of novel complete ammonium and nitrate removal via denitratation anammox over nitrite process at elevated loading rates.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132610},
doi = {10.1016/j.biortech.2025.132610},
pmid = {40315933},
issn = {1873-2976},
abstract = {The Complete Ammonium and Nitrate Removal via Denitratation Anammox Over Nitrite (CANDAN) process was evaluated for rapid sludge granulation in a lab-scale sequencing batch reactor. Over 119 days under increasing nitrogen loading rates (NLRs), the system finally achieved average 89.2 % total nitrogen removal at 1.93 kg N/m[3]/d NLR, with sludge particle sizes increasing from 215.6 μm to 924.5 μm. Higher NLRs significantly increased extracellular polymeric substances, especially hydrophobic proteins, enhancing sludge hydrophobicity and aggregation. Metagenomic analysis identified Candidatus Brocadia and Thauera as predominant and key microbial genera for nitrogen removal. Furthermore, the upregulation of carbon metabolism under heightened NLRs facilitated the synthesis of hydrophobic amino acids, promoting sludge granulation. These findings demonstrate NLR-driven granulation mechanisms, highlight optimizing NLR as key for accelerating granulation, providing insights to improve start-up and operational efficiency of CANDAN systems.},
}
@article {pmid40315837,
year = {2025},
author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD},
title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.010},
pmid = {40315837},
issn = {1934-6069},
abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.},
}
@article {pmid40315739,
year = {2025},
author = {Ma, G and Yang, P and Lu, T and Deng, X and Meng, L and Xie, H and Zhou, J and Xiao, X and Tang, X},
title = {Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.},
journal = {Journal of reproductive immunology},
volume = {169},
number = {},
pages = {104535},
doi = {10.1016/j.jri.2025.104535},
pmid = {40315739},
issn = {1872-7603},
abstract = {AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.<br><br>METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.<br><br>RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.<br><br>CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.},
}
@article {pmid40315479,
year = {2025},
author = {Kharey, G and Palace, V and Whyte, L and Greer, C},
title = {Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2023-0099},
pmid = {40315479},
issn = {1480-3321},
abstract = {A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of 3 environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.},
}
@article {pmid40315414,
year = {2025},
author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ},
title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012268},
doi = {10.1371/journal.pcbi.1012268},
pmid = {40315414},
issn = {1553-7358},
abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.},
}
@article {pmid40315131,
year = {2025},
author = {Donvil, L and Housmans, JAJ and Peeters, E and Vranken, W and Orlando, G},
title = {In-silico identification of archaeal DNA-binding proteins.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf169},
pmid = {40315131},
issn = {1367-4811},
abstract = {MOTIVATION: The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, this data is unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms.<br><br>RESULTS: To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions.<br><br>AVAILABILITY: Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at xenusia.ipynb.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid40314681,
year = {2025},
author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q},
title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.},
journal = {The new microbiologica},
volume = {48},
number = {1},
pages = {46-59},
pmid = {40314681},
issn = {1121-7138},
mesh = {Humans ; *Microbiota ; *Biomedical Research ; Bibliometrics ; Gastrointestinal Microbiome ; },
abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.},
}
@article {pmid40314024,
year = {2025},
author = {Malwe, AS and Longwani, U and Sharma, VK},
title = {XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf037},
pmid = {40314024},
issn = {2631-9268},
mesh = {*Machine Learning ; *Metagenome ; *Xenobiotics/metabolism ; Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; *Bacteria/enzymology/genetics ; Metagenomics/methods ; },
abstract = {Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141 200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38 000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.},
}
@article {pmid40313842,
year = {2025},
author = {Lu, X and Du, X and Zhong, D and Li, R and Cao, J and Huang, S and Wang, Y},
title = {Nanopore Environmental Analysis.},
journal = {JACS Au},
volume = {5},
number = {4},
pages = {1570-1590},
pmid = {40313842},
issn = {2691-3704},
abstract = {As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.},
}
@article {pmid40313750,
year = {2025},
author = {Ndione, MHD and Ndiaye, EH and Dieng, M and Diouf, B and Sankhé, S and Diallo, D and Kane, M and Sene, NM and Mbanne, M and Sy, FA and Diop, SMBS and Doukanda, SFM and Sall, AA and Faye, O and Dia, N and Weaver, SC and Faye, O and Diallo, M and Fall, G and Gaye, A and Diagne, MM},
title = {Mosquito-Based Detection of Endogenous Jaagsiekte Sheep Retrovirus in Senegal: Expanding the Scope of Xenosurveillance.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5951454/v1},
pmid = {40313750},
issn = {2693-5015},
abstract = {Background Mosquitoes are well-known vectors for arthropod-borne viruses, yet their role as passive carriers of non-arthropod-borne viruses remains underexplored. Xenosurveillance, a method that utilizes blood-feeding arthropods to sample host and pathogen genetic material, has emerged as a valuable tool in viral ecology. In this study, we report the first identification of Jaagsiekte Sheep Retrovirus (JSRV)-related sequences in blood-fed mosquitoes collected in Senegal. JSRV, a betaretrovirus responsible for ovine pulmonary adenocarcinoma, is typically found in sheep, but its genetic trace in mosquitoes offers a novel perspective on host-vector contact and surveillance. Our study aimed to investigate whether mosquitoes can serve as sentinels for detecting both pathogens and host-derived markers in complex ecosystems. Methods Mosquitoes were collected between 2016 and 2019 from three ecologically significant regions in Senegal (Louga, Barkedji, and Kedougou). Blood-fed mosquitoes were pooled and subjected to RNA extraction and metagenomic sequencing using Illumina NextSeq550. Sequencing data were analyzed with CZ-ID and BLAST for viral identification. RT-qPCR assays were designed to validate the presence of JSRV-related sequences, targeting conserved regions of the envelope gene and 3' untranslated region. Phylogenetic analysis was conducted using MAFFT and IQ-TREE to compare the detected sequence with global exogenous and endogenous JSRV references. Results A diverse array of viruses across mosquito species, including both arboviruses and non-arthropod-borne viruses. A JSRV-related sequence was detected in a single blood-fed mosquito pool collected in Barkedji (2019). The RT-qPCR assay confirmed JSRV presence, validating the sequencing results. Phylogenetic analysis revealed strong similarity to known endogenous JSRV (enJSRV) sequences integrated in the sheep genome, indicating that the detected material likely originated from host DNA ingested during blood feeding. Discussion This study presents the first report of endogenous retroviral sequences detected in mosquitoes, alongside the identification of actively circulating viruses, highlighting the broader potential of mosquitoes as environmental sentinels. While mosquitoes are not biological vectors for JSRV, their ability to capture both host-derived retroviral material and pathogenic viral genomes through bloodmeals reinforces the value of xenosurveillance for monitoring livestock-vector-environment interactions. These findings contribute to broader efforts in integrated disease surveillance and underscore the utility of combining metagenomics with molecular diagnostics to detect diverse viral signals in high-risk ecological settings.},
}
@article {pmid40313611,
year = {2025},
author = {Ren, X and Sun, H and Cheng, Y and Zhang, Y and Gao, D},
title = {Neurocysticercosis detected by targeted next-generation sequencing of cerebrospinal fluid: a case report.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1504348},
pmid = {40313611},
issn = {1664-2295},
abstract = {The patient, a middle-aged male with a long history of the disease, had experienced recurrent headaches for 26 years and episodic shaking of the right limb with slurred speech for the past month. He was previously diagnosed with cerebral cysticercosis and had shown improvement after anthelmintic treatment. In recent years, he noted a resurgence of headaches. One month prior, he developed right limb shaking and occasional slurred speech. A clinical neurological examination was unremarkable, but cranial MRI and cerebrospinal fluid sequencing confirmed a diagnosis of cerebral cysticercosis. Anthelmintic treatment was administered, resulting in symptom improvement.},
}
@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}
@article {pmid40313600,
year = {2025},
author = {Tang, M and Zhang, Z and Lin, L and Niu, J and Meng, G and Wang, W and Wang, J and Wang, Y},
title = {Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {65-75},
pmid = {40313600},
issn = {2730-5848},
abstract = {UNLABELLED: Although the compositional alterations of gut bacteria in ketogenic diet (KD) have been intensively investigated, the causal relationship between this extreme diet and the microbiota changes is not fully understood. Here, we studied the growth dynamics of intestinal bacteria in KD. We used the CoPTR method to calculate the peak-to-trough ratio (PTR) based on metagenomic sequencing data, serving as an indicator of bacterial growth rates. Notably, Akkermansia muciniphila, a bacterium strongly linked to the therapeutic benefits of KD, exhibited one of the highest growth rates, aligning with its markedly elevated abundance. Our findings also revealed discrepancies in the change patterns of CoPTR values and relative abundances for various bacteria across different diet groups, some of which might be attributed to the exceptionally high or low growth rates of specific species. For some of the species demonstrating obvious differences in growth rates between KD and standard diet, we conducted in vitro culture experiments, supplementing them with diverse nutritional sources to elucidate the underlying mechanisms. The integrative analysis of bacterial abundance and growth dynamics can help deepen our understanding of the gut microbiota changes caused by KD and the therapeutic effects of this special diet.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00228-7.},
}
@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth &amp; development ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.<br><br>METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.<br><br>RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}
@article {pmid40313410,
year = {2025},
author = {Liu, J and Zhou, Y and Feng, J and Cai, C and Zhang, S},
title = {Comparative metagenomic analysis reveals the adaptive evolutionary traits of siboglinid tubeworm symbionts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533506},
pmid = {40313410},
issn = {1664-302X},
abstract = {Tubeworms flourish in marine cold seeps and hydrothermal vents through the establishment of symbiotic relationships with chemosynthetic bacteria. However, the environmental adaptations and evolutionary relationships of tubeworm symbionts across diverse habitats and hosts remain largely unknown. In this study, we characterized the genomes of 26 siboglinid tubeworm symbionts collected from deep-sea hydrothermal vents, cold seeps, and deep-sea mud, including two sequenced in this study and 24 previously published. Phylogenetic analysis classified the 26 symbiont genomes into five distinct clusters at the genus level. The findings highlight the remarkable diversity in symbiont classification, influenced by the habitat and species of tubeworm, with the symbiont genome characteristics of various genera revealing unique evolutionary strategies. Siboglinid symbionts exhibit functional metabolic diversity, encompassing chemical autotrophic capabilities for carbon, nitrogen, and sulfur metabolism, hydrogen oxidation, and a chemoorganotrophic ability to utilize various amino acids, cofactors, and vitamins. Furthermore, the symbiont's homeostatic mechanisms and CRISPR-Cas system are vital adaptations for survival. Overall, this study highlights the metabolic traits of siboglinid symbionts across different genera and enhances our understanding of how different habitats and hosts influence symbiont evolution, offering valuable insights into the strategies that symbionts use to adapt and thrive in extreme environments.},
}
@article {pmid40313389,
year = {2025},
author = {Yu, D and Liu, Y and Cai, H and Huang, W and Wu, H and Yang, P},
title = {Metagenomic investigation of bacterial laccases in a straw-amended soil.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19327},
pmid = {40313389},
issn = {2167-8359},
mesh = {*Laccase/genetics/metabolism ; *Metagenomics ; *Soil Microbiology ; Phylogeny ; *Bacteria/enzymology/genetics ; *Soil/chemistry ; Escherichia coli/genetics ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.<br><br>METHODS: Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.<br><br>RESULTS: A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.<br><br>IMPLICATIONS: These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.},
}
@article {pmid40313234,
year = {2025},
author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N},
title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/19390211.2025.2498127},
pmid = {40313234},
issn = {1939-022X},
abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.},
}
@article {pmid40313154,
year = {2025},
author = {Abiola, C and Gwak, JH and Lee, UJ and Adigun, AO and Rhee, SK},
title = {Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2502002},
doi = {10.71150/jm.2502002},
pmid = {40313154},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; 2021R1A2C3004015//Ministry of Science and ICT/ ; RS-2023-00213601//Ministry of Science and ICT/ ; 2020R1A6A1A06046235//Ministry of Education/ ; //Korea Institute of Marine Science &amp; Technology Promotion/ ; RS-2024-00436293//Ministry of Oceans and Fisheries/ ; },
mesh = {*Soil Microbiology ; Phylogeny ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Ammonia/metabolism ; Oxidation-Reduction ; Soil/chemistry ; Metagenomics ; Filtration ; Nitrites/metabolism ; },
abstract = {Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera "Candidatus Nitrosocosmicus" and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.},
}
@article {pmid40313146,
year = {2025},
author = {Jeong, H and Choe, Y and Nam, J and Ban, YH},
title = {A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2409026},
doi = {10.71150/jm.2409026},
pmid = {40313146},
issn = {1976-3794},
support = {//Ministry of Science and ICT/ ; IITP-2025-RS-2023-00260267//Institute for Information &amp; communications Technology Planning &amp; Evaluation/ ; 202305080001//Kangwon National University/ ; //National Research Foundation of Korea/ ; 2021R1C1C2006260//Ministry of Science and ICT/ ; RS-2023-00301850//Ministry of Education/ ; },
mesh = {*Streptomyces/genetics/metabolism ; *Multigene Family ; *Biosynthetic Pathways/genetics ; *Genome, Bacterial ; Secondary Metabolism/genetics ; Biological Products/metabolism ; *Genomics/methods ; },
abstract = {Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.},
}
@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation &amp; purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.<br><br>MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.<br><br>RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.<br><br>CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}
@article {pmid40312727,
year = {2025},
author = {Wang, L and Wu, Y and Zhao, ZB and Jia, T},
title = {Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {45},
pmid = {40312727},
issn = {2524-6372},
support = {52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.<br><br>RESULTS: In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30&#xa0;cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30&#xa0;cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.<br><br>CONCLUSIONS: Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.},
}
@article {pmid40312673,
year = {2025},
author = {Qin, X and Song, Y and Ding, J and Qin, X and Chen, K and Wang, H},
title = {Symptomatic central nervous system infections in kidney transplant recipients: a 20-years multicenter observational study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {641},
pmid = {40312673},
issn = {1471-2334},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; *Central Nervous System Infections/epidemiology/microbiology/etiology/diagnosis/mortality/cerebrospinal fluid ; Retrospective Studies ; Middle Aged ; Adult ; *Transplant Recipients/statistics &amp; numerical data ; China/epidemiology ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections in kidney transplant recipients (KTRs) remain poorly characterized, with current evidence largely derived from isolated case reports over the past two decades. This multicenter study aims to systematically delineate the epidemiology, clinical profiles, and outcomes of CNS infections in a large KTR cohort.<br><br>METHODS: We conducted a retrospective analysis of 3,602 KTRs across three transplant centers in China (May 2004-July 2024). CNS infections were defined by: 1) neurological symptoms/signs, and 2) microbiological confirmation via cerebrospinal fluid (CSF) analysis, including metagenomic next-generation sequencing (mNGS) and routine microbiologic testing (bacterial and fungal cultures).<br><br>RESULTS: CNS infections were diagnosed in 0.53% of KTRs (19/3602), with symptom onset occurring 2-121&#xa0;months post-transplantation. Etiologies included bacterial (47%, 9/19), viral (32%, 6/19), and fungal (21%, 4/19) pathogens. Notably, 79% of cases (15/19) were exclusively identified by mNGS, whereas conventional cultures failed detection. Presenting symptoms included headache (79%) and altered mental status (42%). Mortality reached 42% (8/19) within 9-22&#xa0;days of diagnosis; among survivors, 73% (8/11) exhibited neurological sequelae.<br><br>CONCLUSIONS: CNS infections in KTRs are rare but characterized by rapid progression and high fatality rate. While the risk of CNS infections persists throughout the post-transplant period, 1-6&#xa0;months after transplantation is a higher-incidence period of CNS infections. KTRs with neurological symptoms (particularly headache and elevated CSF pressure) should undergo CSF mNGS which is critical in diagnosing such infections.},
}
@article {pmid40312516,
year = {2025},
author = {Kim, DD and Swarthout, JM and Worby, CJ and Chieng, B and Mboya, J and Earl, AM and Njenga, SM and Pickering, AJ},
title = {Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40312516},
issn = {2058-5276},
support = {n/a//Tufts University/ ; U19AI110818//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.},
}
@article {pmid40312036,
year = {2025},
author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C},
title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-15},
doi = {10.1163/18762891-bja00075},
pmid = {40312036},
issn = {1876-2891},
abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.},
}
@article {pmid40311978,
year = {2025},
author = {Wang, YX and Dong, BX and Liu, YJ and Tan, YQ and An, YT and Lin, LH and Li, G},
title = {Molecular cloning, characterization, and structural stability analysis of a rare acidic catechol 2,3-dioxygenase from the metagenome of coal-polluted soil.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {143652},
doi = {10.1016/j.ijbiomac.2025.143652},
pmid = {40311978},
issn = {1879-0003},
abstract = {Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous environmental pollutants that pose substantial health hazards, especially in coal-mining areas. This study presented the metagenomic identification and comprehensive characterization of a novel acidic catechol 2,3-dioxygenase, C23O927, derived from a coal-contaminated soil metagenome. Optimal enzymatic activity for C23O927 was observed at pH 4.0 and 55 °C, with remarkable stability across a wide pH spectrum (2.0-10.0) and temperature range (30 °C-60 °C). The enzyme displayed robust tolerance to various organic solvents and salts, and its activity was notably activated by diverse metal ions. Distinct from other catechol 2,3-dioxygenases, C23O927 exhibited oxygen tolerance and maintained robust activity after purification at 4 °C for up to three days. The structural stability of C23O927 is attributed to its unique extended β-sheet structure and increased α-helices. These characteristics help enhance rigidity and reduce the exposure of the hydrophobic core, thereby conferring greater stability on C23O927. The unique properties of C23O927, which include an optimal pH for acidic environments, salt tolerance, resistance to metal ions and organic solvents, and thermal stability, render it a promising candidate for industrial waste management and soil bioremediation.},
}
@article {pmid40311618,
year = {2025},
author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N},
title = {Global genetic structure of human gut microbiome species is related to geographic location and host health.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.014},
pmid = {40311618},
issn = {1097-4172},
abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.},
}
@article {pmid40311598,
year = {2025},
author = {Hong, Y and Cui, J and Xu, G and Li, N and Peng, G},
title = {Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156656},
doi = {10.1016/j.phymed.2025.156656},
pmid = {40311598},
issn = {1618-095X},
abstract = {BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.<br><br>PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.<br><br>METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.<br><br>RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.<br><br>CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.},
}
@article {pmid40311430,
year = {2025},
author = {Chen, Z and Hu, Y and Qiu, G and Liang, D and Cheng, J and Chen, Y and Wang, G and Zhu, X and Xie, J},
title = {Inoculation with Acinetobacter indicus CZH-5 in internal circulation airlift zeolite spheres sequencing batch reactor to augment simultaneous removal of nitrogen, phosphorus, and tetracycline.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138384},
doi = {10.1016/j.jhazmat.2025.138384},
pmid = {40311430},
issn = {1873-3336},
abstract = {Inoculating functional bacterial strains is a cost-effective strategy for enhancing treatment of anaerobic digestion liquids in swine wastewater. This study systematically evaluated inoculation of heterotrophic nitrification aerobic denitrification strain Acinetobacter indicus CZH-5 in an internal circulation airlift zeolite sphere-based sequencing batch reactor (IR) for aerobic removal of nitrogen (N), phosphorus (P), and tetracycline (TEC). Inoculation with CZH-5 promoted secretion of quorum sensing signaling molecules, specifically N-acyl-homoserine lactones (C6-HSL and C10-HSL). These signaling molecules enhance quorum sensing and reinforce cooperation among functional bacteria. Under optimal conditions, average removal efficiencies of total nitrogen, total phosphate, and TEC were 92.8 %, 88.4 %, and 93.1 %, respectively. The removal performance in IR exceeded that of the control by 26 %-71 %. N removal involved complete nitrification-denitrification, while accumulated P was transformed into phosphate monoesters within biofilm. Metagenomic analysis identified Thauera and Acinetobacter as the dominant genera, and Acinetobacter indicus as predominant species. Inoculation enhanced microbial richness and diversity to improve system operational stability. The abundance of functional genes associated with N, P, and TEC transformations significantly increased compared to the control. This study aimed to investigate the characteristics and mechanisms of inoculating a heterotrophic nitrification aerobic denitrification strain into an aerated biofilm system for swine wastewater remediation.},
}
@article {pmid40311350,
year = {2025},
author = {Monge-Olivares, L and Peñalva, G and Pulido, MR and Garrudo, L and Ángel Doval, M and Ballesta, S and Merchante, N and Rasero, P and Cuberos, L and Carpes, G and López-Cerero, L},
title = {Quantitative study of ESBL and carbapenemase producers in wastewater treatment plants in Seville, Spain: a culture-based detection analysis of raw and treated water.},
journal = {Water research},
volume = {281},
number = {},
pages = {123706},
doi = {10.1016/j.watres.2025.123706},
pmid = {40311350},
issn = {1879-2448},
abstract = {Antibiotics can modify populations of multidrug-resistant microorganism (MDRO) in urban wastewater. Our objectives were to quantify the differences in MDR Gram-negative bacteria between influents and effluents of WWTPs of a Spanish city and to evaluate the influence of human antibiotic prescriptions, as well as the persistence of these bacteria after treatment and their genetic relatedness to clinical isolates. The mean count of ESBL producers and carbapenemase producers were 3.77 and 2.74 log 10 CFU/ml, respectively. The reduction achieved by water treatment of ESBL-producing organisms was 1.4-log (96.11 %), whereas a 1.8-log reduction (98.36 %) was obtained regarding carbapenemase producing organisms. Aeromonas spp. predominated among MDROs and blaKPC-2 was the main carbapenemase detected in the influent wastewater samples. Among Escherichia coli and Klebsiella pneumoniae influent isolates, 44 % and 30 %, respectively, belonged to high-risk clones. Regarding Enterobacteriaceae, 10.6 % matched clinical isolates and one strain from an ongoing hospital outbreak was identified among raw samples. New MDROs and persistence of certain strains were detected in effluent samples. Quinolone and third-generation cephalosporin prescriptions, flow rate and population density were associated with higher OXA-48 producer counts. Despite reductions, additional technologies should be implemented in WWTPs receiving hospital discharges. Given the prevalence of environmental species, culture-based and metagenomic approaches should be combined to distinguish between human and sewage sources for antibiotic resistance monitoring. Overall, this study shows that WWTPs with secondary treatment are effective at removing MDRO, and antibiotic stewardship is a potential strategy to reduce the release of MDROs.},
}
@article {pmid40311348,
year = {2025},
author = {Liu, C and Yan, S and Luo, X and Zheng, Y and Zhen, G},
title = {Iron-based materials maintain biofilm equilibrium and function as external capacitors to minimize electron loss under intermittent power supply in MEC-AD methane production.},
journal = {Water research},
volume = {281},
number = {},
pages = {123677},
doi = {10.1016/j.watres.2025.123677},
pmid = {40311348},
issn = {1879-2448},
abstract = {Microbial electrolysis cell-anaerobic digestion (MEC-AD) is a cost-effective approach for methane (CH4) recovery from food waste, but its CH4 conversion efficiency requires improvement. To address this, a MIL-100(Fe)-modified carbon cloth anode was developed to enhance anodic biofilm formation and CH4 bioconversion efficiency. At an applied voltage of 0.8 V, the highest daily CH4 yield reached 141.6 mL/g COD/d, a 61 % increase, and increased further to 227.5 mL/g COD/d under intermittent power supply. By facilitating extracellular electron transfer (EET) in electrogenic bacteria, MIL-100(Fe) regulated biofilm thickness and maintained dynamic biofilm equilibrium. Additionally, as an external capacitor, MIL-100(Fe) functioned as a "temporary storage site" for electrons under intermittent power supply, reducing bioelectron loss. Metagenomic analysis revealed that MIL-100(Fe) significantly enriched Bacteroidia and Methanosarcina, promoting carbohydrate metabolism and CH4 production. Under intermittent power supply, MIL-100(Fe) further enriched Geobacter, enhancing electron transfer efficiency. This study demonstrates that iron-based anode modification effectively enhances CH4 production from food waste by optimizing biofilm structure and metabolic pathways, providing a promising strategy for improving MEC-AD performance.},
}
@article {pmid40310938,
year = {2025},
author = {Ma, WJ and Wang, C and Kothandapani, J and Luzentales-Simpson, M and Menzies, SC and Bescucci, DM and Lange, ME and Fraser, ASC and Gusse, JF and House, KE and Moote, PE and Xing, X and Grondin, JM and Hui, BW and Clarke, ST and Shelton, TG and Haskey, N and Gibson, DL and Martens, EC and Abbott, DW and Inglis, GD and Sly, LM and Brumer, H},
title = {Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadk7633},
doi = {10.1126/science.adk7633},
pmid = {40310938},
issn = {1095-9203},
abstract = {The gut microbiota of mammals possess unique metabolic pathways with untapped therapeutic potential. Using molecular insights into dietary fiber metabolism by the human gut microbiota, we designed a targeted drug delivery system based on bespoke glycoconjugates of a complex plant oligosaccharide called GlycoCaging. GlycoCaging of exemplar anti-inflammatory drugs enabled release of active molecules triggered by unique glycosidases of autochthonous gut bacteria. GlycoCaging ensured drug efficacy was potentiated, and off-target effects were eliminated in murine models of inflammatory bowel disease. Biochemical and metagenomic analyses of gut microbiota of individual humans confirmed the broad applicability of this strategy.},
}
@article {pmid40309222,
year = {2025},
author = {Slosser, T and Wenick, M and Markert, E and Trembath-Reichert, E and Ward, LM},
title = {Novel hot spring Thermoproteota support vertical inheritance of ammonia oxidation and carbon fixation in Nitrososphaeria.},
journal = {Access microbiology},
volume = {7},
number = {4},
pages = {},
pmid = {40309222},
issn = {2516-8290},
abstract = {Aerobic ammonia oxidation is crucial to the nitrogen cycle and is only known to be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] and a single lineage of archaea belonging to the Nitrososphaeria class of Thermoproteota [ammonia-oxidizing Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture only a limited subset of the full diversity of this clade. Here, we describe several genomes of AOA from metagenomic sequencing of a hot spring microbial mat, representing several poorly characterized basal lineages that may be important for understanding the early evolution of archaeal ammonia oxidation. These genomes include a novel genus most closely related to Nitrososphaera as well as novel species belonging to the genera Nitrosotenuis, Nitrososphaera and Nitrosotalea. Furthermore, the distributions and phylogenetic relationships of key metabolic genes support a history of vertical inheritance of ammonia oxidation and carbon fixation from the last common ancestor of crown group AOA.},
}
@article {pmid40309194,
year = {2025},
author = {Tang, CT and Wu, Y and Tao, Q and Zeng, CY and Chen, YX},
title = {Thalidomide mitigates Crohn's disease colitis by modulating gut microbiota, metabolites, and regulatory T cell immunity.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {4},
pages = {101121},
pmid = {40309194},
issn = {2214-0883},
abstract = {Thalidomide (THA) is renowned for its potent anti-inflammatory properties. This study aimed to elucidate its underlying mechanisms in the context of Crohn's disease (CD) development. Mouse colitis models were established by dextran sulfate sodium (DSS) treatment. Fecal microbiota and metabolites were analyzed by metagenomic sequencing and mass spectrometry, respectively. Antibiotic-treated mice served as models for microbiota depletion and transplantation. The expression of forkhead box P3[+] (FOXP3[+]) regulatory T cells (Tregs) was measured by flow cytometry and immunohistochemical assay in colitis model and patient cohort. THA inhibited colitis in DSS-treated mice by altering the gut microbiota profile, with an increased abundance of probiotics Bacteroides fragilis, while pathogenic bacteria were depleted. In addition, THA increased beneficial metabolites bile acids and significantly restored gut barrier function. Transcriptomic profiling revealed that THA inhibited interleukin-17 (IL-17), IL-1β and cell cycle signaling. Fecal microbiota transplantation from THA-treated mice to microbiota-depleted mice partly recapitulated the effects of THA. Specifically, increased level of gut commensal B. fragilis was observed, correlated with elevated levels of the microbial metabolite 3alpha-hydroxy-7-oxo-5beta-cholanic acid (7-ketolithocholic acid, 7-KA) following THA treatment. This microbial metabolite may stable FOXP3 expression by targeting the receptor FMR1 autosomal homolog 1 (FXR1) to inhibit autophagy. An interaction between FOXP3 and FXR1 was identified, with binding regions localized to the FOXP3 domain (aa238-335) and the FXR1 domain (aa82-222), respectively. Conclusively, THA modulates the gut microbiota and metabolite profiles towards a more beneficial composition, enhances gut barrier function, promotes the differentiation of FOXP3[+] Tregs and curbs pro-inflammatory pathways.},
}
@article {pmid40309109,
year = {2025},
author = {Zhang, Z and Sun, J and Wang, D and Lin, T and Yin, Y and Wang, W and Wang, Y and Wang, Z and Fan, L and Jiao, X},
title = {Effects of rotation corn on potato yield, quality, and soil microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1493333},
pmid = {40309109},
issn = {1664-302X},
abstract = {INTRODUCTION: Potato is an important crop that can be used both as grain and vegetable in northern China. However, the continuous cropping system of potato has led to a sharp decline in its yield and quality. As one of the effective strategies to alleviate the continuous cropping obstacle, crop rotation has received extensive attention in agricultural practices. On this basis, we have conducted an in-depth exploration of the effects of the potato-maize rotation system on the structure and diversity of the soil microbial community, aiming to analyze the internal correlation mechanism between the structure of the soil microbial community and the yield and quality of crops.<br><br>METHODS: This study was based on fields that had been under potato monoculture for five years and established six experimental treatments: potato-potato-potato (IR-A), potato-maize-potato (IR-B), potato-maize-maize (IR-C), potato-potato-potato (RF-A), potato-maize-potato (RF-B), and potato-maize-maize (RF-C).<br><br>RESULTS: The results showed that under the IR planting model, IR-B significantly increased potato yield and vitamin C content while reducing reducing sugar content compared to IR-A (p < 0.05). In the RF planting model, RF-B significantly increased potato yield, starch content, and vitamin C content compared to RF-A (p < 0.05). Microbial community structure results indicated that crop rotation significantly enhanced the relative abundance of microorganisms such as Bradyrhizobium, Pseudomonas, Sphingomonas, Purpureocillium, Streptomyces, and Halovivax (p < 0.05). These microorganisms are involved in the cycling of carbon, phosphorus, and other nutrients in the soil, playing an important role in promoting root growth, organic matter decomposition, and alleviating soil salinization. The LEfSe and RDA indicated significant differences in microbial communities between monoculture and crop rotation (p < 0.05), with soil slow-growing rhizobia, Burkholderia, and actinomycetes positively correlated with potato yield and quality. Additionally, KEGG functional annotation of different treatments revealed that K00239, K00626, K01681, and K01915 were involved in three key metabolic pathways related to carbon and nitrogen. A total of 20 significantly enriched pathways were identified (p < 0.05), among which K01681 is involved in the tricarboxylic acid cycle and is a differential gene in the RF-B treatment, suggesting that the efficient expression of K01681 during crop rotation contributes to the material cycling of the soil ecosystem. LEfSe analysis of the bins revealed that under the RF-C treatment, the relative abundance of Hyphomicrobiales was significantly higher than in other treatments (p < 0.05). Hyphomicrobiales are involved in the nitrogen fixation process and play an important role in soil nutrient cycling and plant nutrition. In summary, the potato-maize rotation significantly altered the composition of soil microbial communities (p < 0.05), increasing the relative abundance of beneficial microorganisms. This change helps maintain the health of the soil ecosystem, promotes nutrient cycling, reduces the incidence of diseases, and effectively improves both the yield and quality of potatoes.<br><br>DISCUSSION: The potato-maize rotation significantly altered the composition of soil microbial communities (p < 0.05), increasing the relative abundance of beneficial microorganisms. This change helps maintain the health of the soil ecosystem, promotes nutrient cycling, reduces the incidence of diseases, and effectively improves both the yield and quality of potatoes.},
}
@article {pmid40309103,
year = {2025},
author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F},
title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575405},
pmid = {40309103},
issn = {1664-302X},
abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.<br><br>METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.<br><br>DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.},
}
@article {pmid40308966,
year = {2025},
author = {Li, W and Zhao, M and Wu, W and Chen, G and Hang, Y and Zheng, H and Gao, Z and Liu, J and Zhao, Y},
title = {The application prospect of metagenomic next-generation sequencing technology in diagnosing suspected lower respiratory tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1494638},
pmid = {40308966},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; Aged ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; China ; Sensitivity and Specificity ; Aged, 80 and over ; Young Adult ; Viruses/genetics/isolation &amp; purification/classification ; Bacterial Infections/diagnosis/microbiology ; },
abstract = {OBJECTIVE: Lower respiratory tract infections present substantial diagnostic and therapeutic challenges, negatively impacting individual health. This study aims to utilize metagenomic next-generation sequencing (mNGS) technology to comprehensively explore the spectrum of pathogens, the detection of antibiotic resistance genes, and contributing factors associated with lung infections.<br><br>METHOD: The mNGS data of 217 patients with suspected lung infections attending the Respiratory Department of Nanjing Lishui People's Hospital and Gaochun People's Hospital from September 2022 to September 2023 were retrospectively analyzed. The study assessed the pathogenic spectrum of lung infections and compared the performance of patients with mNGS results from conventional microbiological techniques (CMT).<br><br>RESULTS: The overall positivity rate of mNGS was 95.20%, demonstrating superior sensitivity (97.01% vs. 41.79%) and accuracy (75.56% vs. 56.67%) compared to CMT. Bacterial infections were the most prevalent, accounting for 60.76% of cases. And the most prevalent bacteria, fungus and virus were Mycobacterium tuberculosis (14.41%), Candida albicans (15.72%), and EB virus (14.85%), respectively. The primary resistance genes detected were tetM (17, 8.29%), mel (6, 2.93%), and PC1 beta-lactamase (blaZ) (3, 1.46%). Notably, TEM-183, PDC-5 and PDC-3 were exclusively detected in the Chronic Obstructive Pulmonary Disease (COPD) group. The multivariate binary logistic regression analysis revealed that there was no significant association between gender, presence of hypertension, or COPD with the type of infection in patients (p=0.679, p=0.229, p=0.345). However, the immune status was found to be statistically significant (p=0.009).<br><br>CONCLUSION: With the guidance of mNGS, patients with suspected respiratory tract infections can rapidly and accurately establish a pathogenic basis for their conditions. mNGS effectively identify mixed infections, enrich the pathogen spectrum of lung infections, and provide a large and reliable information base for the clinical realization of targeted medication.},
}
@article {pmid40308204,
year = {2025},
author = {Karalius, MC and Ramachandran, PS and Wapniarski, A and Wang, M and Zia, M and Hills, NK and Wintermark, M and Grose, C and Dowling, MM and Wilson, J and Lee, S and Chung, M and Barry, M and Xu, H and DeRisi, JL and Wilson, MR and Fullerton, HJ and , },
title = {Infection in Childhood Arterial Ischemic Stroke: Metagenomic Next-Generation Sequencing Results of the VIPS II Study.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STROKEAHA.124.050548},
pmid = {40308204},
issn = {1524-4628},
abstract = {BACKGROUND: Acute respiratory infection transiently increases risk for childhood arterial ischemic stroke (AIS). We hypothesize that this paradox of a common exposure linked to a rare outcome could be explained by either (1) the infection hypothesis: unusual or multiple pathogens or (2) the host response hypothesis: heterogeneity in the inflammatory response to infection. We leverage metagenomic next-generation sequencing (mNGS), a comprehensive microbial detection tool, to test the first hypothesis.<br><br>METHODS: The VIPS II study (Vascular Effects of Infection in Pediatric Stroke II) prospectively enrolled children with AIS at 22 international sites over 5 years (December 2016 to January 2022). Sites measured prestroke clinical infection via standardized parental interviews and chart abstraction. To assess more broadly the background spectrum of pathogens, a central research laboratory performed mNGS on plasma and oropharyngeal swabs collected within 72 hours of stroke. mNGS was also performed on biological samples from stroke-free children (June 2017 to January 2022), both without (well) and with (ill) documentation of clinical infection.<br><br>RESULTS: VIPS II enrolled 205 patients with AIS, 95 stroke-free well children, and 47 stroke-free ill children. Clinical infection, most commonly upper respiratory tract infection, was detected in 81 of 205 (40%) of patients. Both plasma and oropharyngeal swab mNGS data were available for 190 of 205 patients with AIS, 91 of 95 stroke-free well children, and 27 of 47 stroke-free ill children. mNGS detected viruses in 27 of 190 (14%) patients with AIS, 9 of 91 stroke-free well children (10%), and 9 of 27 (33%) stroke-free ill children. Most were common upper respiratory viruses. Coinfections were rare. Similar viruses were found in patients with AIS and stroke-free children.<br><br>CONCLUSIONS: mNGS detected a variety of common childhood viruses in both patients with AIS and stroke-free children, suggesting that the type of infection does not explain AIS susceptibility. Rather, the alternative hypothesis regarding an unusual host immune response to common infections in the pathogenicity of AIS should be further explored.},
}
@article {pmid40307949,
year = {2025},
author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ},
title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {108},
pmid = {40307949},
issn = {2049-2618},
support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.<br><br>RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.<br><br>CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.},
}
@article {pmid40307838,
year = {2025},
author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C},
title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {170},
pmid = {40307838},
issn = {1466-609X},
support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Female ; Intensive Care Units/organization &amp; administration/statistics &amp; numerical data ; Prospective Studies ; *Health Personnel/statistics &amp; numerical data ; China ; Adult ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?<br><br>DESIGN: Prospective, multicentre, cross-sectional study.<br><br>SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.<br><br>PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.<br><br>MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.<br><br>RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change&#x2009;=&#x2009;1.22, 95% CI: 1.12-1.34, p <&#x2009;0.001). The &#x3b2;-diversity of ARG between the two groups differed significantly (p =&#x2009;0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall&#x2009;=&#x2009;0.96, p for nonlinear&#x2009;=&#x2009;0.84).<br><br>CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.<br><br>TRIAL REGISTRATION: NCT06228248.},
}
@article {pmid40307822,
year = {2025},
author = {Huo, Y and Wu, C and Ma, D},
title = {Application of metagenomic next-generation sequencing in the diagnosis and treatment of acute pneumonia caused by Tropheryma whipplei.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {207},
pmid = {40307822},
issn = {1471-2466},
mesh = {Humans ; Male ; Female ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; Aged ; *Tropheryma/genetics/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; Adult ; Cilastatin, Imipenem Drug Combination/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Acute Disease ; Tomography, X-Ray Computed ; *Whipple Disease/drug therapy/diagnosis/microbiology ; Imipenem/therapeutic use ; },
abstract = {OBJECTIVE: The treatment plan and process for acute pneumonia caused by Tropheryma whipplei have not been clearly defined. The study aimed to conduct a retrospective analysis of the treatment for patients with acute pneumonia, caused by Tropheryma whipplei, diagnosed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF).<br><br>METHODS: All patients underwent routine blood examinations and chest CT scans. Electronic fiberoptic bronchoscopy was performed to collect BALF samples from the lesion subsegments. The BALF samples were subjected to mNGS analysis. During hospitalization, all patients were treated with imipenem-cilastatin combined with compound sulfamethoxazole (SMZ-TMP) tablets for anti-infection, and they took SMZ-TMP orally for 3&#xa0;months after discharge and followed up.<br><br>RESULTS: We identified 7 cases where Tropheryma whipplei was the primary pathogen, with 3 of these cases having it as the sole detected pathogen. The clinical manifestations of acute Tropheryma whipplei pneumonia are atypical. Chest CT scans revealed that 3 cases had exudative lesions in both lungs, 4 cases had unilateral pulmonary exudative lesions, 3 cases had bilateral pulmonary nodules, 2 cases had interstitial changes, and 3 cases had pleural effusion. Following treatment, all follow-up cases showed no recurrence.<br><br>CONCLUSIONS: The mNGS examination of bronchoalveolar lavage fluid can significantly improve the early diagnosis of acute pneumonia caused by Tropheryma whipplei. The treatment involving imipenem-cilastatin combined with SMZ-TMP, followed by oral SMZ-TMP for three months, is effective.},
}
@article {pmid40307239,
year = {2025},
author = {Langwig, MV and Koester, F and Martin, C and Zhou, Z and Joye, SB and Reysenbach, AL and Anantharaman, K},
title = {Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4076},
pmid = {40307239},
issn = {2041-1723},
support = {DBI-2047598//National Science Foundation (NSF)/ ; OCE-2049478//National Science Foundation (NSF)/ ; },
mesh = {*Hydrothermal Vents/virology/microbiology ; *Viruses/genetics/classification/isolation &amp; purification ; *Ecosystem ; Metagenome ; Genome, Viral ; Pacific Ocean ; Bacteriophages/genetics/classification ; Phylogeny ; Seawater/virology ; Gammaproteobacteria/virology ; Microbiota ; Virome ; },
abstract = {Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.},
}
@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}
@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}
@article {pmid40306604,
year = {2025},
author = {Lee, SH and Han, C and Shin, C},
title = {IUPHAR Review: Microbiota-Gut-Brain Axis and its role in Neuropsychiatric Disorders.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107749},
doi = {10.1016/j.phrs.2025.107749},
pmid = {40306604},
issn = {1096-1186},
abstract = {The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.},
}
@article {pmid40305950,
year = {2025},
author = {An, S and Li, J and Du, J and Feng, L and Zhang, L and Zhang, X and Zhuang, Z and Zhao, Z and Yang, G},
title = {Coupled nitrogen and phosphorus cycles mediated by coordinated variations of functional microbes in industrial recirculating aquaculture system.},
journal = {Water research},
volume = {280},
number = {},
pages = {123726},
doi = {10.1016/j.watres.2025.123726},
pmid = {40305950},
issn = {1879-2448},
abstract = {Industrial Recirculating Aquaculture Systems (IRAS) represent a sustainable and efficient approach to aquaculture, offering significant benefits in water conservation and environmental management. A comprehensive understanding of nitrogen (N) and phosphorus (P) cycling is essential for optimizing system design and operational strategies, enabling the maintenance of a balanced ecosystem within IRAS. Here, water microbial communities in the shrimp aquaculture pond (AP) and nitrification tank (NT) of the IRAS were investigated using a metagenomics-based approach to explore the mechanisms of N and P coupling cycles. Results showed that (1) N and P cycling genes were more abundant in AP water than in NT, with higher potentials for degrading organic N and P compounds, nitrate reduction, denitrification, and phosphate uptake in AP; and their hosts (functional bacteria) were identified as Marivivens for nitrate reduction, Polaribacter and Erythobacter for organophosphorus hydrolysis, and Fluviibacter and Sediminibacterium for phosphate uptake; (2) the coupling of N and P cycles was observed through the abundance of functional genes, likely mediated by coordinated variations in host composition, with nitrite content as a key factor influencing this variation; several bacterial species possessing both N and P cycling genes were identified, primarily engaged in the degradation of organic N and P compounds, denitrification, and phosphate uptake. This study highlights the coupling of N and P cycling in IRAS and the important role of functional bacteria in maintaining water quality. The results also have important implications for the management and improvement of IRAS for more effective aquaculture activities.},
}
@article {pmid40305569,
year = {2025},
author = {Hernandez-Valencia, JC and Gómez, GF and Correa, MM},
title = {Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320593},
doi = {10.1371/journal.pone.0320593},
pmid = {40305569},
issn = {1932-6203},
mesh = {Animals ; *Anopheles/virology ; Colombia ; *Virome/genetics ; *Metagenomics/methods ; *Mosquito Vectors/virology ; Phylogeny ; Malaria/transmission ; Metagenome ; },
abstract = {Anopheles darlingi is a main malaria vector in the neotropical region, but its viral component is not well studied, especially in the neotropics. This work aimed to analyze the virome in Anopheles darlingi from malaria endemic regions of Colombia. Specimens were collected from the Bajo Cauca, Chocoan Pacific and northwestern Amazonas regions and analyzed using an RNA-Seq approach. Results revealed a variety of RNA viral sequences with homology to those of Insect-Specific Viruses belonging to Rhabdoviridae, Partitiviridae, Metaviridae, Tymoviridae, Phasmaviridae, Totiviridae, Ortervirales and Riboviria. Despite geographical and ecological differences among regions, the An. darlingi viral composition remains consistent in different areas, with a core group of viral operational taxonomic units-vOTUs shared by the populations. Furthermore, diversity analysis uncovered greater dissimilarities in viral sequence among mosquitoes from geographically distant regions, particularly evident between populations located at both sides of the Andes Mountain range. This study provides the first characterization of the metavirome in An. darlingi from Colombia and lays the foundation for future research on the complex interactions among viruses, hosts, and microbiota; it also opens a new line of investigation on the viruses in Anopheles populations of Colombia.},
}
@article {pmid40305442,
year = {2025},
author = {Cayrou, C and Silver, K and Owen, L and Dunlop, J and Laird, K},
title = {Domestic laundering of healthcare textiles: Disinfection efficacy and risks of antibiotic resistance transmission.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321467},
doi = {10.1371/journal.pone.0321467},
pmid = {40305442},
issn = {1932-6203},
mesh = {*Disinfection/methods ; *Textiles/microbiology ; Humans ; *Laundering/methods ; Microbial Sensitivity Tests ; Detergents/pharmacology ; *Cross Infection/prevention &amp; control/microbiology ; *Drug Resistance, Microbial ; Staphylococcus aureus/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; United Kingdom ; Microbiota/drug effects ; Decontamination/methods ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Enterococcus faecium/drug effects ; },
abstract = {Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are a major public health concern, with the evidence base for the potential role of textiles as fomites in microbial transmission growing. In the UK, domestic laundering machines (DLMs) are commonly used to clean healthcare worker uniforms, raising concerns about their effectiveness in microbial decontamination and role in AMR development. This study aimed to evaluate DLMs' ability to decontaminate microorganisms and their potential impact on AMR. The performance of six DLMs was assessed using Enterococcus faecium bioindicators under various wash cycles and detergent conditions. Shotgun metagenomics was used to analyse the microbiome and resistome of DLMs. The minimum inhibitory concentrations of domestic detergents were determined for Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, and detergent tolerance and antibiotic cross-resistance were assessed. Results showed only 50% (3/6) of DLMs achieved sufficient decontamination (≥5 log10 CFU reduction) at 60°C during full-length cycles, with rapid cycles performing inconsistently. Microbiome analysis revealed the presence of potentially pathogenic bacteria (e.g., Mycobacterium sp. Pseudomonas sp. and Acinetobacter sp.) and antibiotic resistance genes, including efflux pumps and target modification genes. Detergent tolerance assays showed increased bacterial tolerance to detergents, with cross-resistance to antibiotics observed in S. aureus and K. pneumoniae, including carbapenem and β-lactam groups. Whole genome sequencing identified mutations in genes encoding efflux pumps in S. aureus (MrgA) and K. pneumoniae (AcrB) after detergent exposure, which could impact efflux pump function. Findings suggest domestic laundering of healthcare uniforms may be insufficient for decontamination, posing risks for HAI transmission and AMR. Revising laundering guidelines to ensure effective DLM performance, detergent efficacy, and considering alternatives like onsite/industrial laundering are crucial to enhancing patient safety and controlling AMR in healthcare settings.},
}
@article {pmid40304791,
year = {2025},
author = {Bu, Y and Zhang, X and Xiong, Z and Li, K and Zhang, S and Lin, M and Zhao, G and Zheng, N and Wang, J and Zhao, S},
title = {Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {107},
pmid = {40304791},
issn = {1432-0614},
support = {2022YFD1301000//National Key R&amp;D Program of China/ ; CAAS-ZDRW202308//the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Fermentation/drug effects ; *Isoflavones/pharmacology/administration &amp; dosage/metabolism ; *Trifolium/chemistry ; Genistein/pharmacology/administration &amp; dosage ; *Bacteria/classification/genetics/drug effects/metabolism/isolation &amp; purification ; Female ; Ammonia/metabolism ; Urease/metabolism ; Urea/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Metagenomics ; },
abstract = {Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH3-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.},
}
@article {pmid40304704,
year = {2025},
author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J},
title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12494},
pmid = {40304704},
issn = {2041-1014},
support = {DE029612//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE028252//NIH-NIDCR/ ; },
abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.},
}
@article {pmid40304525,
year = {2025},
author = {Fernández-Quintela, A and Laveriano-Santos, EP and Portolés, T and Gual-Grau, A and Sancho, JV and Portillo, MP},
title = {Changes in Liver Metabolome Induced by Pterostilbene and Resveratrol in a Rat Model of Liver Steatosis.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70078},
doi = {10.1002/mnfr.70078},
pmid = {40304525},
issn = {1613-4133},
support = {AGL-2015-65719-R//Ministerio de Econom&#xed;a y Competitividad/ ; //Fondo Europeo de Desarrollo Regional (FEDER)/ ; CB12/03/30007//Instituto de Salud Carlos III (CIBERobn)/ ; IT1482-22//Government of the Basque Country/ ; },
abstract = {To gain more light on the effects of resveratrol and pterostilbene in the hepatic metabolic modifications in an in vivo model of diet-induced hepatic steatosis, and to explore their relationships with gut microbiota by untargeted metabolomics and metagenomics. Rats were divided into five groups receiving either a standard diet or a high-fat high-fructose (HFHF) diet supplemented or not with pterostilbene (15 or 30 mg/kg body weight/day; PT15 or PT30 groups, respectively) or resveratrol (30 mg/kg body weight/day; RSV30 group). Supplementation with the stilbenes reduced the hepatic steatosis induced by the HFHF diet. After the metabolomics study, 27 differentially expressed metabolites showed variable importance in projection scores > 1 and could be considered as potential biomarkers. Therefore, based on the pathway enrichment analysis, "riboflavin metabolism" and "nicotinate and nicotinamide metabolism" revealed significant enrichment. Further, riboflavin showed positive correlations to Eubacterium and Faecalibacterium, and negative correlations to Lactobacillus and Oscillospira genera. Nicotinamide mononucleotide was only positively correlated to the Ralstonia genus. The untargeted metabolomics approach showed that the actions of resveratrol or pterostilbene on the prevention of liver steatosis are mediated by specific mechanisms of action. Particularly, pterostilbene, but not resveratrol, is suggested to significantly enrich riboflavin or nicotinate and nicotinamide metabolic pathways.},
}
@article {pmid40304520,
year = {2025},
author = {Flörl, L and Meyer, A and Bokulich, NA},
title = {Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0052425},
doi = {10.1128/aem.00524-25},
pmid = {40304520},
issn = {1098-5336},
abstract = {Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.},
}
@article {pmid40303946,
year = {2024},
author = {Dakal, TC and Xu, C and Kumar, A},
title = {Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification.},
journal = {Frontiers in medical technology},
volume = {6},
number = {},
pages = {1434799},
pmid = {40303946},
issn = {2673-3129},
abstract = {The microbiome of the gut is a complex ecosystem that contains a wide variety of microbial species and functional capabilities. The microbiome has a significant impact on health and disease by affecting endocrinology, physiology, and neurology. It can change the progression of certain diseases and enhance treatment responses and tolerance. The gut microbiota plays a pivotal role in human health, influencing a wide range of physiological processes. Recent advances in computational tools and artificial intelligence (AI) have revolutionized the study of gut microbiota, enabling the identification of biomarkers that are critical for diagnosing and treating various diseases. This review hunts through the cutting-edge computational methodologies that integrate multi-omics data-such as metagenomics, metaproteomics, and metabolomics-providing a comprehensive understanding of the gut microbiome's composition and function. Additionally, machine learning (ML) approaches, including deep learning and network-based methods, are explored for their ability to uncover complex patterns within microbiome data, offering unprecedented insights into microbial interactions and their link to host health. By highlighting the synergy between traditional bioinformatics tools and advanced AI techniques, this review underscores the potential of these approaches in enhancing biomarker discovery and developing personalized therapeutic strategies. The convergence of computational advancements and microbiome research marks a significant step forward in precision medicine, paving the way for novel diagnostics and treatments tailored to individual microbiome profiles. Investigators have the ability to discover connections between the composition of microorganisms, the expression of genes, and the profiles of metabolites. Individual reactions to medicines that target gut microbes can be predicted by models driven by artificial intelligence. It is possible to obtain personalized and precision medicine by first gaining an understanding of the impact that the gut microbiota has on the development of disease. The application of machine learning allows for the customization of treatments to the specific microbial environment of an individual.},
}
@article {pmid40303154,
year = {2024},
author = {Albert, E and Kis, IE and Kiss, K and K-Jánosi, K and de Oliveira Costa, M and Tolnai, G and Biksi, I},
title = {Abortion and Lethal Septicaemia in Sows Caused by a Non-ST194 Streptococcus equi subsp. zooepidemicus.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {4008946},
pmid = {40303154},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Streptococcal Infections/veterinary/microbiology/epidemiology/mortality ; Female ; *Abortion, Veterinary/microbiology/epidemiology ; *Swine Diseases/microbiology/epidemiology/mortality ; Pregnancy ; *Sepsis/veterinary/microbiology/epidemiology ; Disease Outbreaks/veterinary ; Hungary/epidemiology ; Streptococcus ; },
abstract = {Outbreaks of zoonotic Streptococcus equi subsp. zooepidemicus (SEZ) have caused severe epidemics in the pig sector since the 1970s in Southeastern Asia, China, and more recently North America. Cases of high mortality caused by peracute septicaemia were all attributed to strains of a highly virulent clonal lineage belonging to the sequence type (ST) 194. In Europe, only two outbreaks have been reported with similar features, caused by other sequence types. In August 2023, a febrile disease followed by abortion and subsequent death was observed among sows kept in a small-scale organic pig farm in West Hungary. Symptoms, pathological lesions, and microbiological findings were suggestive of septicaemia from bacterial origin caused by SEZ. According to the results of the routine laboratory testing, no other relevant infectious agents were involved. Whole-genome sequence analysis assigned the examined strains to ST138, unrelated to any of the European isolates. It also revealed a few common SEZ virulence genes, compared to the highly virulent ST194 strains. A sudden weather change and subsequent extremely high average daily temperature before the outbreak could be identified as the only predisposing factor. The immediate antibiotic treatment and applied biosecurity measures might have helped to restrict and terminate the outbreak. To our knowledge, this is the first report on abortion and lethal septicaemia in sows from Central and Eastern Europe. The results call attention to the potential of non-ST194 SEZ strains to cause outbreaks in pig farms.},
}
@article {pmid40303144,
year = {2024},
author = {Meng, X and Sun, J and Yao, M and Sun, Y and Xu, H and Liu, C and Chen, H and Guo, J and Nie, X and He, L and Zhao, Z and Li, N and Wang, Z and Wang, J},
title = {Isolation and Identification of Severe Fever with Thrombocytopenia Syndrome Virus from Farmed Mink in Shandong, China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {9604673},
pmid = {40303144},
issn = {1865-1682},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) virus, recently named Bandavirus dabieense, belongs to the genus Bandavirus of family Phenuiviridae, and it causes SFTS in humans with clinical symptoms including fever, thrombocytopenia, gastrointestinal symptoms, and leukocytopenia. However, there are few reports on the pathogenesis of SFTSV in animals. This study first isolated the SFTSV strain SD22-2 from sick-farmed mink. Viral metagenomics was used to detect SFTSV nucleotide in the clinical specimens obtained from symptomatic minks. Then, we isolated the virus using Vero and DH82 cells, and Real-Time Quantitative PCR (RT-qPCR), indirect immunofluorescence assay, transmission electron microscopy, and Western blotting identified it. Meanwhile, phylogenetic analysis based on partial L, M, and S segment sequences indicated that the mink-origin SFTSV strain SD22-2 belonged to genotype D and was genetically close to the HB2016-003 strain isolated from humans. Taken together, we isolated and identified an SFTSV from farmed mink that may be the reservoir hosts of SFTSV. We should pay more attention to farmed minks and biosecurity practices, and active surveillance at fur farms must be reviewed and enhanced.},
}
@article {pmid40303140,
year = {2024},
author = {Song, Y and Zuo, O and Zhang, G and Hu, J and Tian, Z and Guan, G and Luo, J and Yin, H and Shang, Y and Du, J},
title = {Emergence of Lumpy Skin Disease Virus Infection in Yaks, Cattle-Yaks, and Cattle on the Qinghai-Xizang Plateau of China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {2383886},
pmid = {40303140},
issn = {1865-1682},
mesh = {Animals ; Cattle ; *Lumpy Skin Disease/epidemiology/virology ; *Lumpy skin disease virus/genetics/isolation &amp; purification/classification ; China/epidemiology ; Phylogeny ; Tibet/epidemiology ; *Cattle Diseases/epidemiology/virology ; Genome, Viral ; },
abstract = {Lumpy skin disease (LSD) is a viral disease caused by lumpy skin disease virus (LSDV), which mainly infects cattle and can cause huge economic losses. In May 2023, yaks, cattle-yaks, and cattle in Tibet (Xizang), China, developed fever, skin nodules, and severe discharges and were suspected to be cases of LSD. Samples from these animals were analyzed using molecular biology and serological methods. The RPO30, P32, and GPCR genes were amplified by PCR and sequenced, and the whole genome of the virus was determined using viral metagenomics technology. Sequencing results showed that it was indeed an LSDV infection, and enzyme-linked immunosorbent assay results confirmed the presence of LSDV antibodies. The whole genome phylogenetic tree shows that LSDV/CHINA/Tibet/2023 is different from the previous epidemic strains in China, but clusters with India 2022 strain. This is the first report of LSD in yaks, cattle-yaks, and cattle on the highest altitude plateau in the world.},
}
@article {pmid40303134,
year = {2024},
author = {Mulder, KP and Pasmans, F and van Nieuwerburgh, F and Terriere, N and Kelly, M and Bregman, S and Verbrugghe, E and Martel, A},
title = {High Prevalence of a Novel Circovirus in the European Hedgehog (Erinaceus europaeus), a Common Species in Decline.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {4670252},
pmid = {40303134},
issn = {1865-1682},
mesh = {Animals ; *Hedgehogs/virology ; *Circovirus/isolation &amp; purification/genetics/classification ; *Circoviridae Infections/veterinary/epidemiology/virology ; Phylogeny ; Europe/epidemiology ; Prevalence ; },
abstract = {Hedgehog (Erinaceus europaeus) declines in western Europe have been associated with the emergence of Hedgehog diphtheric disease (HDD), with a probable multifactorial, yet unidentified etiology. We used metagenomic sequencing of cell-free DNA (cfDNA) in hedgehog blood to identify possible causes of HDD. We detected a novel circovirus species in the European hedgehog, providing the first record of a circovirus within the mammalian order Eulipotyphla. The novel circovirus genome exhibits the characteristic circovirus structure, including a functional replicase (REP) and capsid (CAP) gene. Phylogenetic analysis placed all four detected genomes in a monophyletic clade, most closely related to sequences isolated from dogs. Subsequent PCR-based screening of 188 hedgehog liver samples demonstrated a high prevalence (61%) of this circovirus in hedgehogs brought to wildlife rescue centers, however, without any significant association with HDD. Since circoviruses are well known to interfere with host immunity across mammalian and avian taxa, the high level of circovirus detection in hedgehogs warrants further research into the role of this novel virus in hedgehog health.},
}
@article {pmid40303123,
year = {2024},
author = {Wang, K and Liu, S and Liang, X and Hu, W and Wen, Z and Wang, J and Wang, X and An, F and Chen, Z and Yan, H and Yan, H and Wang, L and Zhang, X and Yu, J and Wei, WK and Hua, Y},
title = {Identification and Genetic Analysis of Species D Rotaviruses in Pangolin Samples.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {1773821},
pmid = {40303123},
issn = {1865-1682},
mesh = {Animals ; *Rotavirus/genetics/isolation &amp; purification/classification ; Phylogeny ; *Pangolins/virology ; *Rotavirus Infections/veterinary/virology ; Genome, Viral ; },
abstract = {Pangolins have been found to carry severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related coronaviruses. In light of this discovery, interest has been piqued in viromes of these heavily trafficked wild animals. In this study, we performed viral metagenomic sequencing to explore viromes of both confiscated dead pangolins and captive healthy pangolins. Sequence reads of vertebrate-associated viruses in Herpesviridae, Retroviridae, Iridoviridae, Reoviridae, Arenaviridae, and Flaviviridae were detected in confiscated dead pangolins. A novel rotavirus (RV) (Reoviridae), showing a high degree of genetic similarity to the RV species D (RVD) that was previously unreported in mammals, was further confirmed by using reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing. Three out of 18 samples from the confiscated dead pangolins were positive for genomic sequences of the novel RV. Importantly, sequence alignments and phylogenetic analyses demonstrated that these RV strains genetically belonged to the RVD. Nevertheless, these novel RVD strains were divergent from known RVD strains that have been found only in Avian. They formed a separate genetic cluster. Five serial passages were attempted to isolate the RV, but no live virus was obtained. In addition, fecal samples were collected from healthy pangolins (n = 41) in our institution and screened for RVs by viral metagenomic sequencing and RT-PCR. In these fecal samples, neither species D nor previously identified species A RVs were detected. This study reported RVDs in pangolin samples for the first time to our knowledge. Identifiability disagreements between wild and captive pangolins highlight the need for further exploration into pangolin viruses to better understand their emergence and transmission potential.},
}
@article {pmid40303119,
year = {2024},
author = {Lovy, J and Iwanowicz, LR and Welch, TJ and Allam, B and Getchell, RG and Geraci-Yee, S and Good, C and Snyder, J and Raines, CD and Das, N},
title = {Seasonal Mortality of Wild Atlantic Menhaden (Brevoortia tyrannus) Is Caused by a Virulent Clone of Vibrio (Listonella) anguillarum; Implications for Biosecurity along the Atlantic Coastal United States.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {8816604},
pmid = {40303119},
issn = {1865-1682},
mesh = {Animals ; *Fish Diseases/microbiology/mortality/epidemiology ; *Vibrio/pathogenicity/genetics/isolation &amp; purification ; Seasons ; *Vibrio Infections/veterinary/mortality/microbiology/epidemiology ; Fishes ; New Jersey/epidemiology ; Atlantic Ocean/epidemiology ; New York/epidemiology ; Virulence ; },
abstract = {Atlantic menhaden are a highly migratory marine species in the Eastern United States that suffer from seasonal chronic mortality. Affected fish show neurologic signs referred to as spinning disease, including circling at the surface and erratic corkscrew swimming before death. We investigated three similar menhaden mortality events consistent with spinning disease in coastal New Jersey and New York between 2020 and 2021 to understand the cause. A unique strain of Vibrio (Listonella) anguillarum (serogroup O3) was detected regularly in high loads, particularly in the brains of moribund fish, by both metagenomics and bacterial isolation. The most common histopathological changes in moribund fish were hemorrhagic meningitis, encephalitis, pyknosis, and karyorrhexis of hematopoietic tissues in the kidney and spleen. Whole genome sequencing of isolates from moribund fish representing a wide spatial and temporal range showed that they were nearly identical clones, suggesting it to be a pathogenic strain circulating in the population. Though V. anguillarum is believed to be the main pathogen associated with spinning disease and mortality, Yersinia ruckeri (serotype O1) was isolated from smaller numbers of fish. Considering the highly migratory nature of Atlantic menhaden throughout the eastern United States and their use as bait for other fisheries, these findings identify potential biosecurity challenges that should be considered in Atlantic salmon aquaculture, fisheries, and emerging marine aquaculture in the region.},
}
@article {pmid40303091,
year = {2024},
author = {Wang, YM and Deng, LS and Huang, BZ and Li, HY and Duan, JQ and Yan, YX and Lai, SY and Ai, YR and Zhou, YC and Qing, Y and Xu, ZW and Zhu, L},
title = {Whole Genome Characterization and Pathogenicity of a SC2020-1-Like PRRSV-1 Strain Emerging in Southwest China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {5627927},
pmid = {40303091},
issn = {1865-1682},
mesh = {Animals ; *Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/classification ; Swine ; *Porcine Reproductive and Respiratory Syndrome/virology/epidemiology/pathology ; China/epidemiology ; *Genome, Viral ; Phylogeny ; Virulence ; },
abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV), encompassing PRRSV-1 and PRRSV-2, significantly impacts the global pig industry by causing reproductive disorders and respiratory difficulties. In this paper, we isolated a novel PRRSV-1 strain, named SCPJ2023, from weaned piglets in Sichuan. Utilizing primary macrophages, we isolated SCPJ2023 and performed complete genome sequencing through metagenomic analysis. Phylogenetic analysis classified SCPJ2023 as pan-European subtype 1. SCPJ2023 showed a 95.3% similarity to SC2020-1. Amino acid analysis identified differences in Nsp2, GP3, and GP4 between SCPJ2023 and other representative strains. In vivo challenge experiments demonstrated that SCPJ2023 induced clinical symptoms in piglets, including coughing, fever, reduced appetite, and depression. Pathological examinations revealed hemorrhage and congestion, increased inflammatory cells, thickening of the alveolar wall, and collapse of the alveolar cavity in SCPJ2023-infected piglets. Altogether, our study identified a novel pathogenic isolate of PRRSV-1, expanding the newly named SC2020-1-like subgroup by identifying additional strains beyond the initial SC2020-1 isolate.},
}
@article {pmid40303019,
year = {2024},
author = {Stadler, J and Lillie-Jaschniski, K and Zwickl, S and Zoels, S and Theuns, S and Ritzmann, M and Vereecke, N},
title = {Cross-Correlation between Biosecurity Measures and the Detection of Viral and Bacterial Agents on German Farms with Respiratory Disease.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {6205899},
pmid = {40303019},
issn = {1865-1682},
mesh = {Animals ; Germany/epidemiology ; Swine ; *Swine Diseases/microbiology/epidemiology/virology/prevention &amp; control ; *Biosecurity ; Farms ; Animal Husbandry ; *Bacterial Infections/veterinary/epidemiology/microbiology ; Bacteria/isolation &amp; purification/classification ; Porcine respiratory and reproductive syndrome virus/isolation &amp; purification ; Porcine Reproductive and Respiratory Syndrome/epidemiology/virology/microbiology ; },
abstract = {Effective porcine health management relies majorly on diagnostic tests, vaccination, treatment strategies, and a proper biosecurity management plan. However, understanding the link between circulating microbes and biosecurity measures on a pig farm is not evident. Substantial progress has been made in recent years with the availability of new diagnostic tools (e.g., sequencing-based diagnostics) and extensive biosecurity management questionnaires. However, the interpretation and correlation of these results are hampered by the abundance of gained (meta)data. Therefore, we aimed to cross-correlate viral and bacterial pathogens with respiratory tropism detected by third-generation nanopore metagenomic sequencing with biosecurity measures assessed by Biocheck.UGent™. The study was conducted on 25 sow farms with attached nurseries in Germany with known respiratory distress. The biosecurity level of the study farms complied with the European averages. Interestingly, the farms with the highest biosecurity score showed the lowest overall prevalence of porcine reproductive and respiratory syndrome virus (PRRSV) and Actinobacillus sp.; the circulation of well-studied pathogenic viruses, such as PRRSV, was correlated with overall lower biosecurity scores, a higher number of stillborn piglets, and cocirculation of porcine parvovirus type 7. Moreover, potential risk factors for lesser-known agents (e.g., porcine hemagglutinating and encephalomyelitis virus, porcine respiratory coronavirus, and porcine polyomavirus) could also be addressed. For the bacterial pathogen Glaesserella sp., a correlation with increased clinical signs was observed, whereas Lactobacillus sp. and Moraxella sp. are putative biomarkers for pig farms with better biosecurity scores. In conclusion, in-depth cross-correlation of (meta)data from new diagnostic platforms with biosecurity measures on pig farms may contribute to a better understanding of new actions in adapting biosecurity measures. This will not only contribute to improved animal welfare and economic productivity but also helping to address (new) zoonotic disease threats and potential treatments.},
}
@article {pmid40302920,
year = {2025},
author = {Gao, Z and Jiang, Y and Chen, M and Wang, W and Liu, Q and Ma, J},
title = {Enhancing fever of unknown origin diagnosis: machine learning approaches to predict metagenomic next-generation sequencing positivity.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1550933},
pmid = {40302920},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Fever of Unknown Origin/diagnosis/etiology ; Female ; Male ; Middle Aged ; Algorithms ; Adult ; Aged ; },
abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) can potentially detect various pathogenic microorganisms without bias to improve the diagnostic rate of fever of unknown origin (FUO), but there are no effective methods to predict mNGS-positive results. This study aimed to develop an interpretable machine learning algorithm for the effective prediction of mNGS results in patients with FUO.<br><br>METHODS: A clinical dataset from a large medical institution was used to develop and compare the performance of several predictive models, namely eXtreme Gradient Boosting (XGBoost), Light Gradient-Boosting Machine (LightGBM), and Random Forest, and the Shapley additive explanation (SHAP) method was employed to interpret and analyze the results.<br><br>RESULTS: The mNGS-positive rate among 284 patients with FUO reached 64.1%. Overall, the LightGBM-based model exhibited the best comprehensive predictive performance, with areas under the curve of 0.84 and 0.93 for the training and validation sets, respectively. Using the SHAP method, the five most important factors for predicting mNGS-positive results were albumin, procalcitonin, blood culture, disease type, and sample type.<br><br>CONCLUSION: The validated LightGBM-based predictive model could have practical clinical value in enhancing the application of mNGS in the etiological diagnosis of FUO, representing a powerful tool to optimize the timing of mNGS.},
}
@article {pmid40302838,
year = {2025},
author = {Pallen, MJ and Ponsero, AJ and Telatin, A and Moss, CJ and Baker, D and Heavens, D and Davidson, GL},
title = {Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.},
journal = {Access microbiology},
volume = {7},
number = {4},
pages = {},
pmid = {40302838},
issn = {2516-8290},
abstract = {Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.},
}
@article {pmid40302016,
year = {2025},
author = {Zhou, H and Tang, L and Fenton, KA and Song, X},
title = {Exploring and Evaluating Microbiome Resilience in the Gut.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf046},
pmid = {40302016},
issn = {1574-6941},
abstract = {The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.},
}
@article {pmid40301729,
year = {2025},
author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S},
title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {39},
pmid = {40301729},
issn = {2730-7182},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.<br><br>RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200&#xa0;m, with a slight increase observed above 1400&#xa0;m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.<br><br>CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.},
}
@article {pmid40301728,
year = {2025},
author = {Munoz Briones, J and Brubaker, DK},
title = {A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {115},
pmid = {40301728},
issn = {1471-2105},
support = {2120200//Directorate for Biological Sciences/ ; R01HD110367//National Institute of Child Health and Human Development/ ; },
mesh = {Humans ; *Microbiota ; *Metabolomics/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; *Computational Biology/methods ; Principal Component Analysis ; Crohn Disease/microbiology ; Multiomics ; },
abstract = {BACKGROUND: The number and size of multi-omics datasets with paired measurements of the host and microbiome is rapidly increasing with the advance of sequencing technologies. As it becomes routine to generate these datasets, computational methods to aid in their interpretation become increasingly important. Here, we present a framework for integration of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE integrates multi-omics data using single-omic latent variables (LV) organized in a structured meta-model to determine the combinations of features most predictive of a phenotype or condition.<br><br>RESULTS: We developed a supervised version of LIVE leveraging sparse Partial Least Squares Discriminant Analysis (sPLS-DA) LVs, and an unsupervised version leveraging sparse Principal Component Analysis (sPCA) principal components which both can incorporate covariate awarness. LIVE performance was tested on publicly available metagenomic and metabolomics data set from Crohn's Disease (CD) and Ulcerative Colitis (UC) status patients in the PRISM and LLDeep cohorts, and benchmarked against existing gut microbiome multi-omics approaches and vaginal microbiome datasests, achieving consistent and comparable performances. In addition to these benchmarking efforts, we present a detailed analysis and interpretation of both versions of LIVE using the PRISM and LLDeep cohorts. LIVE reduced the number of feature interactions from the original datasets for CD and UC from millions to less than 20,000 while conditioning the disease-predictive power of gut microbes, metabolites, enzymes, on clinical variables.<br><br>CONCLUSIONS: LIVE makes a distinct, complementary contribution to current methods to integrate microbiome data and offers key advantages to existing approaches in the interpretable integration of multi-omics data with clinical variables to predict to disease outcomes and identify microbiome mechanisms of disease.},
}
@article {pmid40301726,
year = {2025},
author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J},
title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {258},
pmid = {40301726},
issn = {1471-2180},
support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; },
mesh = {Humans ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Culture Media/chemistry ; *Biodiversity ; *Bacteriological Techniques/methods ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.},
}
@article {pmid40300742,
year = {2025},
author = {Wang, B and Huang, T and Zhu, L and Hu, J and Ma, S and Sun, Q and Chen, K},
title = {Effect of cyanobacterial bloom proliferation on antibiotic resistance genes in the sediments of a eutrophic lake.},
journal = {Environmental research},
volume = {278},
number = {},
pages = {121717},
doi = {10.1016/j.envres.2025.121717},
pmid = {40300742},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) represent an emerging pollutant of increasing concern. In this study, we analyzed the composition and spatiotemporal variation of ARGs in the sediments of eutrophic Chaohu Lake, China, using a metagenomic method. A total of 22 ARGs and 199 ARGs subtypes were detected, with the most prevalent subtypes being multidrug (57.720 %) and rifamycin (21.781 %). A higher abundance of ARGs in Chaohu Lake was observed (p < 0.05) during winter and spring owing to multiple factors, including variations in seasonal inputs and hydraulic conditions, occurrence of cyanobacterial blooms, and changes in ARGs host bacterial communities. Spatially, a higher abundance of multidrug was observed in sediments near the Nanfei River outlet, which flows through urban areas; whereas higher levels of bacitracin were observed in sediments near the Zhao River outlet, which flows through agricultural areas. Cyanobacterial blooms and declines change the sediment physicochemical properties, endogenous phosphorus contents, microbial communities, and seasonal ARGs distribution. Correlation and collinearity analyses indicated that ARGs were transferred horizontally via mobile genetic elements (MGEs). High-risk ARGs in Chaohu Lake were observed at a very low proportion, although certain ARGs presented health risks in the western lake during spring. In this study, we highlight the interactions between cyanobacterial blooms and variations in ARGs in Chaohu Lake and provide novel insights into ARGs dynamics in eutrophic freshwater ecosystems.},
}
@article {pmid39796227,
year = {2025},
author = {Lu, Y and Li, M and Gao, Z and Ma, H and Chong, Y and Hong, J and Wu, J and Wu, D and Xi, D and Deng, W},
title = {Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
pmid = {39796227},
issn = {1422-0067},
support = {32160771//National Nature Science Foundation of China/ ; 32302707//National Nature Science Foundation of China/ ; 202101BD070001-006//Yunnan Provincial Agricultural Union Foundation/ ; 202202AE090005//Major Science and Technology Projects in Yunnan Province/ ; 202301AU070117//Yunnan Province Basic Research Program Project/ ; XDYC-CYCX-2022-0029//"Xingdian Talent" Industry Innovation Talent Program in Yunnan Province/ ; },
mesh = {Humans ; *Whole Genome Sequencing/methods ; *Genetics, Population/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Software ; *Genome, Human ; Genetic Variation ; *Metagenomics/methods ; Machine Learning ; },
abstract = {With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics. The goal is to examine the application and progress of resequencing technologies in this field and to consider future developments, including deep learning models and machine learning algorithms, which promise to enhance analytical methodologies and drive further advancements in population genomics.},
}
@article {pmid40303081,
year = {2024},
author = {Yuan, Y and Li, L and Liu, Z and Yang, X and Wang, W and Xu, W and Liu, N and Sui, L and Zhao, Y and Liu, Q and Wang, Z},
title = {First Report and Genetic Characterization of Border Disease Virus in Sheep from Hulunbuir, Northeastern China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {9924724},
pmid = {40303081},
issn = {1865-1682},
mesh = {Animals ; Sheep ; China/epidemiology ; Phylogeny ; *Border disease virus/genetics/isolation &amp; purification/classification ; *Border Disease/epidemiology/virology ; *Sheep Diseases/virology/epidemiology ; Genome, Viral ; },
abstract = {Border disease virus (BDV), a member of the Pestivirus genus within the Flaviviridae family, is known to inflict significant economic losses on livestock farms due to its association with reproductive disorders and persistent infections in sheep and goats. However, comprehensive epidemiological investigations of BDV in China are scarce. This study examined BDV infection in sheep from Hulunbuir, Inner Mongolia, northeastern China, utilizing metagenomic sequencing and polymerase chain reaction (PCR) assay. Among the 96 serum samples analyzed, only one tested positive for BDV nucleotide sequence, yielding a prevalence rate of 1.0%. A total of 11,985 nt long genome sequences was amplified, which showed nucleotide identities ranging from 76.6% to 87.2% and amino acid identities ranging from 85.2% to 93.2% with other BDV strains worldwide. Phylogenetic analysis unequivocally placed the viral strain within genotype BDV-3, showing a close genetic affinity with strain JSLS12-01 identified in Jiangsu province, China. Furthermore, selection pressure analyses suggested that purifying selection predominantly influenced the evolutionary dynamics of BDV genomes. This study marks the inaugural detection of BDV in sheep within Inner Mongolia, northeastern China, thereby enhancing our understanding of the extensive genetic diversity and geographical distribution of BDV strains across the country. These findings hold relevance for the livestock industry and disease surveillance efforts, offering valuable insights into the prevalence and genetic characteristics of BDV in this region.},
}
@article {pmid40303833,
year = {2023},
author = {Wang, Y and Gu, C and Han, Q and Fu, S and Wang, J and Zhuang, J and Guo, G and Liu, J and Yu, X and Qu, G and Shen, Z},
title = {A Novel Pathogen of an Emerging Infectious Disease (Large Kidney Disease) in Farmed Blue Foxes.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {6629054},
pmid = {40303833},
issn = {1865-1682},
mesh = {Animals ; *Foxes/virology ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; *Retroviridae Infections/veterinary/virology/epidemiology ; *Kidney Diseases/veterinary/virology/epidemiology ; China/epidemiology ; Phylogeny ; },
abstract = {An emerging infectious disease (EID) in foxes called "large kidney disease", characterized by enlarged kidneys, has been breaking out in fox farms in China, although its pathogenesis has not yet been elucidated. Here, we performed viral metagenomics sequencing on diseased fox tissue samples that identified a virus with 82.6% homology to the xenotropic murine leukemia virus-related virus (XMRV) PreXMRV-1 provirus strain (GenBank accession number NC_007815.2) in sick fox tissue. It was named PreXMRV-20, and its genome was verified by reverse transcription-polymerase chain reaction (PCR) and PCR product sequencing. Nonenveloped and polygonal virus-like particles consistent with the shape and size of XMRV were observed by negative staining electron microscopy. Administered subcutaneously, PreXMRV-20 infected weaned foxes, leading to growth retardation. The discovery of the PreXMRV-20 strain (the first isolation of an XMRV homolog in blue foxes) identifies a potential public health issue in blue fox breeding since XMRV has been confirmed to be a zoonotic virus.},
}
@article {pmid40303754,
year = {2023},
author = {Righi, C and Curini, V and Torresi, C and Cammà, C and Pirani, S and Di Lollo, V and Gobbi, P and Giammarioli, M and Viola, G and Pela, M and Feliziani, F and Petrini, S},
title = {Molecular Detection and Genetic Characterization of Bovine Kobuvirus (BKV) in Diarrhoeic Calves in a Central Italy Herd.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {6637801},
pmid = {40303754},
issn = {1865-1682},
mesh = {Animals ; Cattle ; Italy/epidemiology ; *Cattle Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Kobuvirus/genetics/isolation &amp; purification ; *Picornaviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; *Polyomavirus Infections/veterinary/virology/epidemiology ; *Tumor Virus Infections/veterinary/virology/epidemiology ; },
abstract = {Bovine kobuvirus (BKV) is an infectious agent associated with neonatal calf diarrhoea (NCD), causing important economic losses to dairy and beef cattle herds worldwide. Here, we present the detection rate and characterize the genome of BKV isolated from diarrhoeic calves from a Central Italy herd. From January to December 2021, we collected blood samples and nasal and rectal swabs from 66 calves with severe NCD between 3 and 20 days of age. After virological (bovine coronavirus, bovine viral diarrhoea virus, and bovine rotavirus), bacteriological (Escherichia coli spp. and Salmonella spp.), and parasitological (Cryptosporidium spp., Eimeria spp., and Giardia duodenalis) investigations, we detected BKV using the metagenomic analysis. This result was confirmed using a specific polymerase chain reaction assay that revealed the number of BKV-positive nasal (24.2%) and rectal swabs (31.8%). The prevalence of BKV was higher than that of BCoV. Coinfection with BKV and BCoV was detected in 7.5% of the rectal swabs, highlighting the involvement of another infectious agent in NCD. Using next generation sequencing (NGS) approach, it was possible to obtain the complete sequence of the BKV genome from other two rectal swabs previously analysed by real-time PCR. This is the first report describing the whole genome sequence (WGS) of BKV from Italy. The Italian BKV genomes showed the highest nucleotide sequence identity with BKV KY407744.1, identified in Egypt in 2014. The sequence encoding VP1 best matched that of BKV KY024562, identified in Scotland in 2013. Considering the small number of BKV WGSs available in public databases, further studies are urgently required to assess the whole genome constellation of circulating BKV strains. Furthermore, pathogenicity studies should be conducted by inoculating calves with either only BKV or a combination with other enteric pathogens for understanding the probable role of BKV in NCD.},
}
@article {pmid40303817,
year = {2023},
author = {Li, C and Qiu, M and Li, S and Sun, Z and Huang, Z and Qi, W and Qiu, Y and Li, J and Feng, B and Zhao, D and Lin, H and Zheng, W and Yu, X and Tian, K and Fan, K and Zhu, J and Chen, N},
title = {Metagenomic and Pathogenic Assessments Identify a Pathogenic Porcine Reproductive and Respiratory Syndrome Virus 1 with New Deletions from Adult Slaughter Pig in 2022.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {1975039},
pmid = {40303817},
issn = {1865-1682},
mesh = {Animals ; *Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/isolation &amp; purification ; Swine ; *Porcine Reproductive and Respiratory Syndrome/virology/epidemiology ; China/epidemiology ; Phylogeny ; Metagenomics ; Genome, Viral ; Sequence Deletion ; },
abstract = {Since we first reported porcine reproductive and respiratory syndrome virus 1 (PRRSV1) wild type strains in mainland China in 2011, PRRSV1 infection has been detected in more than 20 provinces in China. During the routine investigation of PRRSV1 epidemiology in 2022, we isolated a novel PRRSV1 strain (SD1291) from an adult slaughter pig in Linyi, Shandong Province. The SD1291 could only be isolated with primary alveolar macrophages (PAMs), not with Marc-145 cells. In addition, the 2022 SD1291 isolate has higher in vitro replication efficacy than the 2014 PRRSV1 HLJB1 isolate in PAMs. Due to high genetic variation, the complete genome of SD1291 was determined by metagenomic sequencing, which showed that SD1291 shares the highest genome similarity (88.12%) with the PRRSV1 HeB47 isolate. Sequence alignment results identified a four-amino-acid deletion in nsp2 and a five-amino-acid deletion in the GP3 and GP4 overlap region of SD1291. A complete-genome-based phylogenetic tree showed that SD1291 is grouped with BJEU06-1-like PRRSV1 isolates. A piglets' challenge study showed that SD1291 can cause high fever (the highest is 41°C), reduced weight gain, mild lung consolidation, and interstitial pneumonia indicating that SD1291 is a pathogenic PRRSV1 isolate. Overall, this study first identified a novel pathogenic PRRSV1 isolate from an adult slaughter pig in China. Our findings also suggested that new PRRSV1 variants could escape the current PRRSV vaccination system and circulate in adult swine herds, which deserve more attention.},
}
@article {pmid40303779,
year = {2023},
author = {Nelsen, A and Knudsen, D and Hause, BM},
title = {Identification of a Novel Astrovirus Associated with Bovine Respiratory Disease.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {8512021},
pmid = {40303779},
issn = {1865-1682},
mesh = {Animals ; Cattle ; *Cattle Diseases/virology ; *Astroviridae Infections/veterinary/virology ; Phylogeny ; *Astroviridae/isolation &amp; purification/genetics/classification ; *Respiratory Tract Infections/veterinary/virology ; },
abstract = {Astroviruses (AstVs) cause gastrointestinal disease in mammals and avians. Emerging evidence suggests that some AstVs have extraintestinal tissue tropism, with AstVs detected in the liver, kidney, central nervous system, and the respiratory tract variably associated with disease. In cattle, AstV infection has been linked to gastroenteric or neurologic disease. Here, metagenomic sequencing of a lung from a bovine with respiratory disease identified a novel AstV with a predicted capsid-encoding ORF2 amino acid sequence with 66% identity to caprine astrovirus (CAstV G2.1). A quantitative reverse transcription PCR (qRT-PCR) targeting ORF2 found four out of 49 (8%) lungs and one out of 48 (2%) enteric samples obtained from bovine diagnostic submissions positive for the novel bovine astrovirus (BAstV). In two strongly qRT-PCR-positive lung samples, intense novel BAstV nucleic acid signals were mainly localized in the cytoplasm of alveolar macrophages and mononuclear cells using RNAscope® in situ hybridization (ISH). Genetic analysis of two novel BAstV genomes determined from qRT-PCR positive samples found high similarity for ORF1ab nucleotide sequence (92.1% and 93.9%) to BAstV strain BSRI-1, while ORF2 nucleotide sequence was most similar to CAstV G2.1 (74.6% and 77.6%). Phylogenetic analysis of the novel BAstV sequences found a close genetic relationship to the single BAstV (BSRI-1) previously identified from a bovine respiratory sample as well as bovine and caprine AstVs identified from various tissues. Further research is needed to determine the clinical significance of BAstV in respiratory diseases.},
}
@article {pmid40300608,
year = {2025},
author = {Wirbel, J and Andermann, TM and Brooks, EF and Evans, L and Groth, A and Dvorak, M and Chakraborty, M and Palushaj, B and Reynolds, GZM and Porter, IE and Al Malki, M and Rezvani, A and Gooptu, M and Elmariah, H and Runaas, L and Fei, T and Martens, MJ and Bolaños-Meade, J and Hamadani, M and Holtan, S and Jenq, R and Peled, JU and Horowitz, MM and Poston, KL and Saber, W and Kean, LS and Perales, MA and Bhatt, AS},
title = {Accurate prediction of absolute prokaryotic abundance from DNA concentration.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101030},
doi = {10.1016/j.crmeth.2025.101030},
pmid = {40300608},
issn = {2667-2375},
abstract = {Quantification of the absolute microbial abundance in a human stool sample is crucial for a comprehensive understanding of the microbial ecosystem, but this information is lost upon metagenomic sequencing. While several methods exist to measure absolute microbial abundance, they are technically challenging and costly, presenting an opportunity for machine learning. Here, we observe a strong correlation between DNA concentration and the absolute number of 16S ribosomal RNA copies as measured by digital droplet PCR in clinical stool samples from individuals undergoing hematopoietic cell transplantation (BMT CTN 1801). Based on this correlation and additional measurements, we trained an accurate yet simple machine learning model for the prediction of absolute prokaryotic load, which showed exceptional prediction accuracy on an external cohort that includes people living with Parkinson's disease and healthy controls. We propose that, with further validation, this model has the potential to enable accurate absolute abundance estimation based on readily available sample measurements.},
}
@article {pmid40300605,
year = {2025},
author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH},
title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.03.073},
pmid = {40300605},
issn = {1879-0445},
abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.},
}
@article {pmid40300566,
year = {2025},
author = {Mahdi, ES and Komijani, M and Alaghmand, A},
title = {Metagenomics study suggests the role of vitamins and gut microbiome in autism spectrum disorder.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-20},
doi = {10.1159/000545483},
pmid = {40300566},
issn = {1421-9867},
abstract = {INTRODUCTION: Autism is a neurological disability that often appears after the age of three in children, also known as an Autism Spectrum Disorder (ASD). Several studies have examined the influence of some environmental factors, and many parameters related to the behavior of autistic patients have been measured in order to find ways to reduce ASD. This study investigates the relationship between ASD and serum levels of vitamin D3, B12, folic acid, and the gut microbiome.<br><br>METHODS: The serum levels of vitamin D3, B12, and folic acid in ASD patients were measured by the ELISA method and compared to healthy groups. DNA was extracted from stool samples of ASD patients and the control group, and then the gut microbiome was investigated via a metagenomics approach. Metagenomics sequencing was performed to analyze the 16S rRNA gene sequencing for phylum and sub phylum level microbiome.<br><br>RESULT: The result showed no significant change in the VitD3 and folate levels of ASD patients compared to the control group (p=0.157 and p=0.0505, respectively). There was a significant difference in the VitB12 level between control healthy individuals and ASD patients, in which the serum VitB12 concentration was significantly lower than the control group (p=0.0001). Our results regarding gut metagenomics showed that the abundance of the Actinobacteria by the phylum level were significantly higher in the ASD patients compared to the control group (p=0.0013). The abundance of the Firmicutes by the phylum level were significantly lower in the ASD patients compared to the control group (p=0.0016).The abundance of Bifidobacteriaceae, and Ruminococcaceae by the family level were significantly higher in the ASD patients compared to the control group (p=0.0004. and p=0.0489, respectively).Our results indicated less species richness in the ASD patients compared to the control group.<br><br>CONCLUSION: Patients with ASD have lower serum levels of vitamin B12 and different gut microbiome compared to healthy controls. Low vitamin B12 levels and altered gut microbiome are significantly associated with ASD in this study. However, further research is needed to determine whether these factors could serve as predictors of severe outcomes in ASD.},
}
@article {pmid40300499,
year = {2025},
author = {Hayes, A and Zhang, L and Feil, E and Kasprzyk-Hordern, B and Snape, J and Gaze, WH and Murray, AK},
title = {Antimicrobial effects, and selection for AMR by non-antibiotic drugs in a wastewater bacterial community.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109490},
doi = {10.1016/j.envint.2025.109490},
pmid = {40300499},
issn = {1873-6750},
abstract = {Antimicrobial resistance (AMR) is a major threat to human, animal, and crop health. AMR can be directly selected for by antibiotics, and indirectly co-selected for by biocides and metals, at environmentally relevant concentrations. Some evidence suggests that non-antibiotic drugs (NADs) can co-select for AMR, but previous work focused on exposing single model bacterial species to predominately high concentrations of NADs. There is a significant knowledge gap in understanding a range of NAD concentrations, (including lower µg/L concentrations found in the environment) on mixed bacterial communities containing a diverse mobile resistome. Here, we determined the antimicrobial effect and selective potential of diclofenac, metformin, and 17-β-estradiol, NADs that are commonly found environmental pollutants, in a complex bacterial community using a combination of culture based, metagenome, and metratranscriptome approaches. We found that diclofenac, metformin, and 17-β-estradiol at 50 µg/L, 26 µg/L, and 24 µg/L respectively, significantly reduced growth of a bacterial community although only 17-β-estradiol selected for an AMR marker using qPCR (from 7 µg/L to 5400 µg/L). Whole metagenome sequencing indicated that there was no clear selection by NADs for antibiotic resistance genes, or effects on community composition. Additionally, increases in relative abundance of some specific metal resistance genes (such as arsB) were observed after exposure to diclofenac, metformin, and 17-β-estradiol. These results indicate that environmentally relevant concentrations of NADs are likely to affect community growth, function, and potentially selection for specific metal resistance genes.},
}
@article {pmid40300492,
year = {2025},
author = {Huang, Y and Zong, S and Xu, D and He, J and Zhang, Y and Qian, M and Li, Y and Guo, B and Han, J and Qu, D},
title = {Metagenomic analysis reveals differences in antibiotic resistance and transmission risks across various poultry farming models.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179519},
doi = {10.1016/j.scitotenv.2025.179519},
pmid = {40300492},
issn = {1879-1026},
abstract = {As living standards in rural areas continue to improve, farmers are increasingly seeking to diversify their farming models beyond monoculture farming. However, the differences in bacterial resistance and the associated transmission risks between monoculture poultry farming and integrated poultry farming remain poorly understood. This study utilizes metagenomic methods to examine the distribution and transmission of antibiotic resistance across three types of farms in Zhejiang Province, as well as to investigate the horizontal transmission mechanisms of plasmid-mediated blaNDM within these agricultural systems. An analysis of 26 environmental samples and 12 saliva samples from six poultry farms with different models has revealed that integrated poultry farms exhibit a more complex microbial composition and more severe resistance compared to monoculture farms. Furthermore, a blaNDM positive plasmid pndm-CD with complex conjugation transfer region was found in the integrated farms. The insertion sequence (IS) ISCR1 present in the upstream of blaNDM has the potential to promote its spread, while the downstream complex structure IS26-blaCTX-M-IS2-qnrB-TinR-ΔISKrA14 enhances the resistance of the host to β-lactam antibiotics, and improves the competition potential of the host bacteria in the anti-antibiotic environment. This research offers the first metagenomic analysis of the differences in bacterial resistance and transmission risks between various poultry farming models. These results offer a solid theoretical basis for managing the spread of antibiotic resistance in mixed chicken and duck farming operations. Additionally, they are significant for ensuring the health of agricultural workers and the hygiene safety of the poultry meat supply chain.},
}
@article {pmid40300291,
year = {2025},
author = {Mei, J and Sheng, F and Zhang, C and Chen, X},
title = {Imaging monitoring of Balamuthia granulomatous amoebic encephalitis.},
journal = {Clinical neurology and neurosurgery},
volume = {254},
number = {},
pages = {108917},
doi = {10.1016/j.clineuro.2025.108917},
pmid = {40300291},
issn = {1872-6968},
abstract = {Balamuthia granulomatous amoebic encephalitis (GAE) is a rare and highly lethal infectious disease affecting the central nervous system, caused by the Balamuthia amoeba. This article reports the case of a child with normal immune function and no apparent epidemiological risk factors. In the initial stages, routine blood tests, cerebrospinal fluid cell tests, biochemical tests, and metagenomic next-generation sequencing (mNGS) were all normal. Surgical removal of the abscess and subsequent pathological diagnosis revealed a chronic granuloma. mNGS analysis of the brain abscess fluid identified Balamuthia mandrillaris (BM), leading to the diagnosis of Balamuthia GAE, after which antiparasitic treatment was initiated. This case underscores the importance of sustained imaging surveillance in suspected cases of Balamuthia GAE.},
}
@article {pmid40299688,
year = {2025},
author = {Chen, Y and Nian, F and Chen, J and Jiang, Q and Yuan, T and Feng, H and Shen, X and Dong, L},
title = {Metagenomic Microbial Signatures for Noninvasive Detection of Pancreatic Cancer.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13041000},
pmid = {40299688},
issn = {2227-9059},
support = {82173122, 81972234, 82273027//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with poor early detection rates owing to the limited sensitivity and specificity of the current biomarker CA19-9. Gut microbiota dysbiosis plays a key role in PDAC pathogenesis. This study aimed to evaluate the noninvasive approach we developed, combining metagenome-derived microbial signatures with CA19-9, to improve PDAC detection. Methods: This study included 50 treatment-naïve patients with PDAC and their matched controls. Fecal samples were analyzed using shotgun metagenomic sequencing. Machine learning algorithms were used to develop and validate a diagnostic panel integrating microbial signatures and CA19-9 levels. Subgroup analyses were used to confirm the robustness of the microbial markers. Results: The combined models at both species and genus levels effectively distinguished patients with PDAC from healthy individuals, and their strong diagnostic efficacy and accuracy were demonstrated through rigorous validation. Conclusions: In conclusion, the combination of gut microbiome profiling and CA19-9 improves PDAC detection accuracy compared to the use of CA19-9 alone, showing promise for early and noninvasive diagnosis.},
}
@article {pmid40299456,
year = {2025},
author = {Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Kozhakhmetova, S and Morenko, M and Duisebayeva, A and Poddighe, D and Kushugulova, A and Kozhakhmetov, S},
title = {Alterations in Gut Microbiota of Infants Born to Mothers with Obesity.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13040838},
pmid = {40299456},
issn = {2227-9059},
support = {Grant No. AP19575153 "Metagenomic predictors of childhood obesity, cross-talk with maternal mi-croflora", Grant No. AP23489538 and Grant No. BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; Grant No. 20122022CRP1602//Nazarbayev University under Collaborative Research Program/ ; },
abstract = {Background: The impact of maternal obesity on offspring health remains a major and pressing issue. We investigated its impact on the development of the infant gut microbiome during the first six months of life, examining the taxonomic composition, metabolic pathways, and antibiotic resistance genes. Methods: Twenty-four mother-infant pairs were divided into maternally obese (OB, BMI > 36) and normal weight (BM) groups. Shotgun metagenomic sequencing was performed on stool samples collected at birth and at 1, 3, and 6 months. A total of 12 maternal samples and 23 infant samples (n = 35) in the obese group and 12 maternal samples and 30 infant samples (n = 42) in the control group were sequenced. The analysis included taxonomic profiling (MetaPhlAn 4), metabolic pathway analysis (HUMAnN 3), and antibiotic resistance gene screening (CARD/ABRicate). Results: The OB group showed reduced alpha diversity in the first month (p ≤ 0.01) and an increased Firmicutes/Bacteroidetes ratio, peaking at 3 months (p ≤ 0.001). The metabolic profiling revealed enhanced carbohydrate breakdown (p ≤ 0.001) in the BM group and lipid biosynthesis (p ≤ 0.0001) in the OB group pathways. Strong correlations emerged between Lactobacillales and fatty acid biosynthesis (r = 0.7, p ≤ 0.0001) and between Firmicutes and lincosamide (r = 0.8, p ≤ 0.0001). Conclusions: The infants of obese mothers had significantly altered development of the infant gut microbiome, affecting both composition and metabolic potential. These changes may have long-term health consequences and suggest potential therapeutic targets for intervention.},
}
@article {pmid40299453,
year = {2025},
author = {Qin, L and Chen, Y and Luan, S and Yin, X and Pan, J and Wang, L and Yao, Y and Zhou, C and Bao, R and Shen, J and Miao, Q and Hu, B},
title = {Lung Microenvironment Among Patients with Nontuberculous Mycobacterial Pulmonary Disease by Metagenomic Sequencing Technique.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13040818},
pmid = {40299453},
issn = {2227-9059},
support = {NSFC82072325//National Natural Science Foundation of China/ ; },
abstract = {Background: Nontuberculous mycobacterial pulmonary disease (NTM-PD) is an increasingly prevalent chronic infection, where the host immune status plays a crucial role in disease susceptibility and progression. The complex pulmonary microenvironment, characterized by diverse microbial communities and host immune interactions, exhibits distinct features that may be fundamentally altered by the patient's underlying immune state. Methods: A total of 111 sputum specimens and 64 bronchoalveolar lavage fluid (BALF) specimens were collected from 143 patients diagnosed with NTM-PD under different immune states. Metagenomic sequencing was performed on these specimens to characterize and compare the pulmonary microenvironmental features among NTM-PD patients with a distinct immune status through comprehensive bioinformatic analyses. Results: The immunosuppressed group exhibited a lower α-diversity in sputum specimens (p < 0.05). Principal Coordinates Analysis (PCoA) of β-diversity for sputum and BALF specimens revealed significant differences between the groups (p < 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis identified species enriched in the immunosuppressed group. A co-occurrence network analysis indicated that the immunosuppressed group had more structured and actively connected networks compared to the control group. The Mantel test confirmed that the abundance of these species enriched was associated with clinical immune-inflammation-related indicators in patients. Conclusions: Our study reveals the pulmonary microenvironment in immunosuppressed patients with NTM-PD. Further work is required to explore the two-way relationship between micro-organisms and immune and inflammatory responses, with the influence on patient outcomes.},
}
@article {pmid40298885,
year = {2025},
author = {Liu, Y and Wu, R and Wu, J and Li, J and Zhang, Q and Wang, S and Sheng, G},
title = {Improving the shock resistance of anaerobic digestion under demand-oriented biogas production mode by using converter steel slag powder.},
journal = {Waste management &amp; research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {},
number = {},
pages = {734242X251333692},
doi = {10.1177/0734242X251333692},
pmid = {40298885},
issn = {1096-3669},
abstract = {Introducing flexible biogas production (FB) can result in instantaneous high-shock loads for anaerobic digestion system, posing risks to the system's stable operation. Steel slag, a typical metallurgical solid waste, has been demonstrated to enhance the buffering capacity of digestion systems, thereby increasing methane production and achieving 'waste treatment using waste'. However, its efficacy under high-shock loads in FB is uncertain. Pulse feeding experiments simulating FB were conducted to analyse the system's impact resistance with steel slag addition and investigate its enhancement mechanisms. The addition of steel slag improved the methane production rate under various shock conditions, with a particularly notable enhancement under concentration shock. This scenario also saw a significant increase in the generation of soluble chemical oxygen demand and its utilization by microorganisms. This can be attributed to the enrichment of hydrolytic bacterial phyla (Firmicutes) and genera (Gelria), with functional gene analysis revealing an increase in genes associated with Fe(III) reduction and CO2-to-methane pathways. The study results indicate that the role of steel slag as an alkaline, iron-rich material enhances system alkalinity, reduces inhibition from H2 partial pressure and boosts hydrogenotrophic methanogen activity, making it suitable as an exogenous enhancer for demand-oriented anaerobic digestion.},
}
@article {pmid40298543,
year = {2025},
author = {Bisaccia, M and Berini, F and Marinelli, F and Binda, E},
title = {Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/antibiotics14040394},
pmid = {40298543},
issn = {2079-6382},
support = {PNRA16_00105//Italian Ministry of Education, University and Research/ ; CMPT228810//Consorzio Interuniversitario per le Biotecnologie &amp; Italian Ministry of Education, University and Research/ ; IBFM NBFC CN00000033//National Biodiversity Future Center/ ; PNRA22_0000040//Italian Ministry of Education, University and Research/ ; },
abstract = {The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.},
}
@article {pmid40298441,
year = {2025},
author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N},
title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mbio.00705-25},
pmid = {40298441},
issn = {2150-7511},
abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.},
}
@article {pmid40298422,
year = {2025},
author = {Koester, F and Myers, KS and Donohue, TJ and Noguera, DR},
title = {Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017925},
doi = {10.1128/mra.00179-25},
pmid = {40298422},
issn = {2576-098X},
abstract = {To advance the knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from four anaerobic bioreactors fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. This analysis produced 42 unique metagenome-assembled genomes (MAGs) that represent distinct taxa.},
}
@article {pmid40298412,
year = {2025},
author = {Majernik, SN and Beaver, L and Bradley, PH},
title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085724},
doi = {10.1128/msphere.00857-24},
pmid = {40298412},
issn = {2379-5042},
abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.},
}
@article {pmid40298386,
year = {2025},
author = {Chen, Z and Zhang, Z and Nie, BN and Huang, W and Zhu, Y and Zhang, L and Xu, M and Wang, M and Yuan, C and Liu, N and Wang, X and Tian, J and Ba, Q and Wang, Z},
title = {Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118824},
doi = {10.1128/msystems.01188-24},
pmid = {40298386},
issn = {2379-5077},
abstract = {UNLABELLED: The human gut microbiome's role in colorectal cancer (CRC) pathogenesis has gained increasing recognition. This study aimed to delineate the microbiome characteristics that distinguish CRC patients from healthy individuals, while also evaluating the influence of aging, through a comprehensive metagenomic approach. The study analyzed a cohort of 80 CRC patients and 80 matched healthy controls, dividing participants into a normal and a CRC group, further categorized by age into young, middle-aged, and old-aged subgroups. Extensive metagenomic sequencing of fecal samples allowed for the exploration of both the structural and functional profiles of the microbiome, with findings validated in an independent cohort to ensure robustness. Our results highlight notable differences in microbiome composition between CRC patients and healthy individuals, which exhibit age-dependent variations. Specifically, a higher prevalence of pathogenic bacteria, such as Bacteroides vulgatus, known to drive inflammation and carcinogenesis, was observed in CRC patients, alongside a reduction in beneficial microbes, including Lactobacillus. Functionally, the CRC-associated microbiome showed an increase in pathways related to DNA repair, cell cycle regulation, and metabolic activities, such as the Citrate cycle and Galactose metabolism, underscoring distinct microbial alterations in CRC patients that could influence disease onset and progression. These insights lay a foundation for future research into microbiome-based diagnostics and treatments for CRC.<br><br>IMPORTANCE: This study underscores the critical role of the gut microbiome in colorectal cancer (CRC) pathogenesis, particularly in the context of aging. By identifying age-specific microbial biomarkers and functional pathways associated with CRC, our findings provide novel insights into how microbiome composition and metabolic activities influence disease progression. These discoveries pave the way for developing personalized microbiome-based diagnostic tools and therapeutic strategies, potentially improving CRC prevention and treatment outcomes across different age groups. Understanding these microbial dynamics could also inform interventions targeting gut microbiota to mitigate CRC risk and progression.},
}
@article {pmid40298367,
year = {2025},
author = {Zhou, Z and Ma, Y and Zhang, D and Ji, R and Wang, Y and Zhao, J and Ma, C and Zhu, H and Shen, H and Jiang, X and Niu, Y and Lu, J and Zhang, B and Tu, L and Zhang, H and Ma, X and Chen, P},
title = {Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0027625},
doi = {10.1128/msystems.00276-25},
pmid = {40298367},
issn = {2379-5077},
abstract = {Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.},
}
@article {pmid40298267,
year = {2025},
author = {Cheung, S and Zhou, NA and Ruhanya, V and J Jesser, K and Nezomba, I and Musvibe, J and Manyisa, B and Nyandoro, G and Chibukira, P and Mukaratirwa, A and Muserere, ST and Masunda, K and Ong, A and Meschke, JS},
title = {Characterization of enteric pathogens in Harare, Zimbabwe using environmental surveillance and metagenomics.},
journal = {Journal of water and health},
volume = {23},
number = {4},
pages = {477-492},
pmid = {40298267},
issn = {1477-8920},
mesh = {Zimbabwe ; *Metagenomics ; *Environmental Monitoring/methods ; *Wastewater/microbiology ; Humans ; *Bacteria/isolation &amp; purification/genetics/classification ; Drug Resistance, Bacterial ; Sewage/microbiology ; },
abstract = {High diarrheal disease burden remains an urgent concern in low- and middle-income countries, greatly affecting children under the age of 5 years and those living with HIV and AIDS. Treatment of infectious diseases has also become increasingly difficult with the rapid rise of antimicrobial resistance (AMR). Environmental surveillance of wastewater can supplement gaps in clinical surveillance as residents on a sewage system contribute to the wastewater, providing simple, composite samples that can improve understanding about both pathogens and AMR in the community. This study evaluated the effectiveness of environmental surveillance with shotgun metagenomics as a tool to characterize a broad range of enteric pathogens, antibiotic resistance genes, and virulence factor genes (VFGs) in wastewater from six neighborhoods in Harare, Zimbabwe. Alpha and beta diversity of the microbial community were similar between high-income and low-income suburbs. Enteric pathogens of high AMR and clinical concern, including Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica, were detected in all samples. The top VFGs were encoded for delivery, adherence, and motility, functions important in toxin secretion, colonization, and immune modulation. The findings provide a foundation for future studies to explore environmental surveillance and shotgun metagenomics as a public health monitoring tool for enteric diseases.},
}
@article {pmid40297733,
year = {2025},
author = {Nguyen, DS and Tran, DM},
title = {Endophytic bacteriome data of Litchi chinensis established by metagenomic 16S rRNA gene sequencing.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111544},
pmid = {40297733},
issn = {2352-3409},
abstract = {This work reported the diversity profiling and predicted metabolic function of the endophytic bacteriome of lychee (Litchi chinensis S.) cultivated in Dak Lak Province of Vietnam for the first time. Roots of lychee were collected from three different fields in Krong Ana District in Dak Lak. 16S rRNA primers were used to sequence the metagenomic library. Kraken 2 was used to analyze the taxonomic distribution, while the MetaCyc database was used to predict the metabolic function. We identified 10 phyla, 14 classes, 27 orders, 30 families, and 27 genera of the endophytic bacteria from the sample. Actinomycetota was the most predominant phylum (84.49%), and biosynthesis was the bacteriome's primary function (75.42%). Data provided insight into the taxonomic distribution and metabolic function of lychee endophytic bacteria and might be helpful for the next steps concerning sustainable lychee cultivation using endophytic bacteria.},
}
@article {pmid40297591,
year = {2025},
author = {Pei, X and Liu, L and Han, Y},
title = {Advances in human microbiome and prostate cancer research.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576679},
pmid = {40297591},
issn = {1664-3224},
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.},
}
@article {pmid40297587,
year = {2025},
author = {Dora, D and Revisnyei, P and Pasic, A and Galffy, G and Dulka, E and Mihucz, A and Roskó, B and Szincsak, S and Iliuk, A and Weiss, GJ and Lohinai, Z},
title = {Host and bacterial urine proteomics might predict treatment outcomes for immunotherapy in advanced non-small cell lung cancer patients.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1543817},
pmid = {40297587},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology ; Male ; Female ; *Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology ; Middle Aged ; *Proteomics/methods ; Aged ; Immunotherapy/methods ; Treatment Outcome ; *Proteome ; Biomarkers, Tumor/urine ; Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {INTRODUCTION: Urine samples are non-invasive approaches to study potential circulating biomarkers from the host organism. Specific proteins cross the bloodstream through the intestinal barrier and may also derive from gut microbiota. In this study, we aimed to evaluate the predictive role of the host and bacterial urine extracellular vesicle (EV) proteomes in patients with non-small cell lung cancer (NSCLC) treated with anti-PD1 immunotherapy.<br><br>METHODS: We analyzed the urine EV proteome of 33 advanced-stage NSCLC patients treated with anti-PD1 immunotherapy with LC-MS/MS, stratifying patients according to long (>6 months) and short (&#x2264;6 months) progression-free survival (PFS). Gut microbial communities on a subcohort of 23 patients were also analyzed with shotgun metagenomics. Internal validation was performed using the Random Forest (RF) machine learning (ML) algorithm. RF was validated with a non-linear Bayesian ML model. Gene enrichment, and pathway analysis of host urine proteins were analyzed using the Reactome and Gene Ontology databases.<br><br>RESULTS: We identified human (n=3513), bacterial (n=2647), fungal (n=19), and viral (n=4) proteins. 186 human proteins showed differential abundance (p<0.05) according to PFS groups, 101 being significantly more abundant in patients with short PFS and n=85 in patients with long PFS. We found several pathways that were significantly enriched in patients with short PFS (vs long PFS). Multivariate Cox regression showed that human urine proteins MPP5, IGKV6-21, NT5E, and KRT27 were strongly associated with long PFS, and LMAN2, NUTF2, NID1, TNC, IGF1, BCR, GPHN, and PPBP showed the strongest association with short PFS. We revealed that an increased bacterial/host protein ratio in the urine is more frequent in patients with long PFS. Increased abundance of E. coli and E. faecalis proteins in the urine positively correlates with their gut metagenomic abundance. RF ML model supported the reliability in predicting PFS for critical human urine proteins (AUC=0.89), accuracy (95%) and Bacterial proteins (AUC=0.74).<br><br>CONCLUSION: To our knowledge, this is the first study to depict the predictive role of the host and bacterial urine proteome in anti-PD1-treated advanced NSCLC.},
}
@article {pmid40297511,
year = {2025},
author = {Valle, C and Parry, RH and Coutard, B and Colmant, AMG},
title = {Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf023},
pmid = {40297511},
issn = {2057-1577},
abstract = {Jingmenviruses are a distinct group of flavi-like viruses characterized by a genome consisting of four to five segments. Here, we report the discovery of three novel putative jingmenviruses, identified by mining publicly available metagenomics data from mosquito and arachnid samples. Strikingly, these novel jingmenvirus sequences contain up to six genomic segments, with pairs of homologous segments coding for putative structural proteins. Following this discovery, we found an additional homologous segment for two other jingmenvirus genomes, which had gone unnoticed in the initial publications. The presence of a single version of the segments coding for non-structural proteins suggests that we have indeed identified jingmenviruses with infectious units that contain up to six segments. We compared these novel jingmenvirus sequences to published sequences, in particular the segments with multiple open reading frames (ORFs), and we propose that the putative translation initiation mechanisms involved for these segments are ribosomal frameshift resulting in the fusion of ORFs and leaky scanning for overlapping ORFs. These putative mechanisms, conserved for all jingmenvirus sequences analysed, including in homologous segments, require biological confirmation. We also generated structural models of two putative structural proteins in the duplicated segments, and the corresponding alignments enabled us to confirm or identify the homologous relationship between sequences that shared limited nucleotide or amino acid identity. Altogether, these results highlight the fluid nature of jingmenviruses, which is a hallmark of multipartite viruses. Different combinations of segments packaged in different virus particles could facilitate the acquisition or loss of genomic segments and a segment duplication following genomic drift. Our data therefore contribute to the evidence of the multipartite nature of jingmenviruses and the evolutionary role this organization may play.},
}
@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}
@article {pmid40297464,
year = {2025},
author = {Zhang, Y and Ding, G and Gao, Y and Li, Y and Zhou, P and Wu, L and Zhou, M and Wang, J and Tang, J},
title = {Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19384},
pmid = {40297464},
issn = {2167-8359},
mesh = {*Lakes/microbiology/chemistry ; China ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Chaohu Lake (CL) is one of the most polluted areas in China due to its high content of antibiotics. However, the distribution and influencing factors of antibiotic resistance genes (ARGs) in this lake are still controversial.<br><br>METHODS: To solve this problem, we used metagenomic sequencing to investigate the distribution and in-fluencing factors of ARGs in CL.<br><br>RESULTS: Our findings revealed the existence of nine kinds of ARGs, including 45 specific genes. The most abundant types were multidrug, bacitracin, polymyxin, macrolide lincosamide streptogramin, and aminoglycoside. Multiple microorganisms were undeniable ARG reservoirs, although they were not dominant species in the microbiota. Our results also showed that both the microbiota and physiochemical factors played important roles in shaping the distributions of ARGs in CL. Specifically, the levels of PO4-P (0.5927) and total phosphorus (0.4971) had a greater impact than total nitrogen (0.0515), NO3-N (0.0352), NO2-N (-0.1975), and NH3-N (-0.0952).<br><br>CONCLUSIONS: These findings provide valuable insights into the distribution and influencing factors of ARGs in lakes.},
}
@article {pmid40296452,
year = {2025},
author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA},
title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202500002},
doi = {10.1002/pmic.202500002},
pmid = {40296452},
issn = {1615-9861},
support = {C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; },
abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.},
}
@article {pmid40296156,
year = {2025},
author = {Fan, Y and Wang, D and Yang, JX and Ning, D and He, Z and Zhang, P and Rocha, AM and Xiao, N and Michael, JP and Walker, KF and Joyner, DC and Pan, C and Adams, MWW and Fields, MW and Alm, EJ and Stahl, DA and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J},
title = {Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {106},
pmid = {40296156},
issn = {2049-2618},
support = {DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; },
mesh = {*Groundwater/microbiology/chemistry ; Phylogeny ; *Microbiota/genetics ; Tennessee ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Nitrates/analysis ; Water Pollutants, Chemical/analysis ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; },
abstract = {BACKGROUND: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).<br><br>RESULTS: Both taxonomic and phylogenetic &#x3b1;-diversities were reduced in the most impacted wells, while the decline in functional &#x3b1;-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional &#x3b2;-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.<br><br>CONCLUSIONS: Overall, we demonstrated that despite a reduced taxonomic &#x3b1;-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.},
}
@article {pmid40295870,
year = {2024},
author = {Bell, MG and Parry, RH and Lee, TSE and Habarugira, G and McMahon, IE and Thompson, MA and Modhiran, N and Watterson, D and Batovska, J and Lynch, SE and Hall, RA and Harrison, JJ and Hobson-Peters, J},
title = {Synthetic recovery of Yada Yada virus expands insect-specific alphavirus knowledge and facilitates production of chimeric viruses.},
journal = {Npj viruses},
volume = {2},
number = {1},
pages = {45},
pmid = {40295870},
issn = {2948-1767},
support = {AQIRF067-2020-CV//Advance Queensland/ ; },
abstract = {Few insect-specific alphaviruses (ISA) have been discovered, with even fewer culturable to facilitate full characterisation. Here, we report the recovery of an infectious clone of Yada Yada virus (YYV)-a virus previously only detected by metagenomic sequencing of mosquito homogenates. Using the infectious clone, we confirmed the inability of YYV to replicate in vertebrate cells in vitro, with replication limited to only Aedes mosquito-derived cell lines. We further produced and characterised the first monoclonal antibodies (mAbs) to ISAs. Through successful replacement of the structural proteins of YYV with those of other ISAs, Eilat virus, Agua Salud (ASALV), Taï Forest (TALV) and Mwinilunga alphaviruses (MWAV), we established that a replication block for in vitro culture of TALV and MWAV in mosquito cells does not exist at virus entry. Unexpectedly, ASALV structural proteins were recognised by cross-reactive mAbs made to chikungunya (CHIKV) and Ross River viruses (RRV), suggesting a potential antigenic link between ASALV and pathogenic alphaviruses. The YYV genetic backbone was also investigated to generate chimeras displaying the structural proteins of various pathogenic vertebrate-infecting alphaviruses including CHIKV, RRV, Barmah Forest, Sindbis and Mayaro viruses. These chimeras retained the antigenic properties of the parental viruses and did not replicate in vertebrate cells, demonstrating the potential of the YYV platform for vaccine and diagnostic antigen production.},
}
@article {pmid40295861,
year = {2025},
author = {Minch, B and Moniruzzaman, M},
title = {Expansion of the genomic and functional diversity of global ocean giant viruses.},
journal = {Npj viruses},
volume = {3},
number = {1},
pages = {32},
pmid = {40295861},
issn = {2948-1767},
abstract = {Giant viruses (GVs) play crucial roles in the global ocean microbial food web and biogeochemistry. Recent metagenomic advances have uncovered >1800 new GV genomes from the world's oceans. While this rapid increase in genomic information is impressive, it is nowhere close to the extensive genomic information available for other marine entities-e.g., prokaryotes and their "virome". We present 230 new high-quality GV genomes (genomes with 4 or more marker genes) and 398 partial genomes from nine global ocean datasets. Notably, we identified numerous GV genomes from the Baltic Sea, offering insights into their phylogenomics, metabolic potential, and environmental drivers in one of the largest brackish water ecosystems. We discovered new GV functions and identified a significant functional divide between the Imitervirales and Algavirales orders. Additionally, we evaluated factors affecting GV abundance through a case study on the Baltic Sea dataset. Our study significantly expands the marine GV genomic and functional diversity, broadening our understanding of their roles in the food web and biogeochemistry.},
}
@article {pmid40295121,
year = {2025},
author = {Scheffer, G and Rattray, J and Evans, P and Shi, W and Bhatnagar, S and Hubert, CRJ},
title = {Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf041},
pmid = {40295121},
issn = {1574-6941},
abstract = {Nitrate addition for mitigating sulfide production in oilfield systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and re-use associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.},
}
@article {pmid40295679,
year = {2024},
author = {Ha, AD and Aylward, FO},
title = {Automated classification of giant virus genomes using a random forest model built on trademark protein families.},
journal = {Npj viruses},
volume = {2},
number = {1},
pages = {9},
pmid = {40295679},
issn = {2948-1767},
support = {1R35GM147290-01/NH/NIH HHS/United States ; CAREER-2141862//National Science Foundation/ ; },
abstract = {Viruses of the phylum Nucleocytoviricota, often referred to as "giant viruses," are prevalent in various environments around the globe and play significant roles in shaping eukaryotic diversity and activities in global ecosystems. Given the extensive phylogenetic diversity within this viral group and the highly complex composition of their genomes, taxonomic classification of giant viruses, particularly incomplete metagenome-assembled genomes (MAGs) can present a considerable challenge. Here we developed TIGTOG (Taxonomic Information of Giant viruses using Trademark Orthologous Groups), a machine learning-based approach to predict the taxonomic classification of novel giant virus MAGs based on profiles of protein family content. We applied a random forest algorithm to a training set of 1531 quality-checked, phylogenetically diverse Nucleocytoviricota genomes using pre-selected sets of giant virus orthologous groups (GVOGs). The classification models were predictive of viral taxonomic assignments with a cross-validation accuracy of 99.6% at the order level and 97.3% at the family level. We found that no individual GVOGs or genome features significantly influenced the algorithm's performance or the models' predictions, indicating that classification predictions were based on a comprehensive genomic signature, which reduced the necessity of a fixed set of marker genes for taxonomic assigning purposes. Our classification models were validated with an independent test set of 823 giant virus genomes with varied genomic completeness and taxonomy and demonstrated an accuracy of 98.6% and 95.9% at the order and family level, respectively. Our results indicate that protein family profiles can be used to accurately classify large DNA viruses at different taxonomic levels and provide a fast and accurate method for the classification of giant viruses. This approach could easily be adapted to other viral groups.},
}
@article {pmid40294792,
year = {2025},
author = {Xiao, H and Zhou, J and Jia, H},
title = {Letter to the Editor Regarding "Clinical Application Value of Metagenomic Next-Generation Sequencing at Perioperative Period in Patients with Central Nervous System Infections in Neurosurgical Intensive Care Unit".},
journal = {World neurosurgery},
volume = {},
number = {},
pages = {124017},
doi = {10.1016/j.wneu.2025.124017},
pmid = {40294792},
issn = {1878-8769},
}
@article {pmid40294775,
year = {2025},
author = {Liu, Z and Yang, S and Xie, S and Cao, D and Xi, W and Xiao, Y and Xu, X and Wang, Z and Li, L and Hu, J and Wang, X},
title = {Enhancing the detection sensitivity of mNGS in Bronchoalveolar Lavage fluid through cell Counting: An empirical study.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {120311},
doi = {10.1016/j.cca.2025.120311},
pmid = {40294775},
issn = {1873-3492},
abstract = {OBJECTIVES: Lower respiratory tract infections pose significant clinical challenges due to their high morbidity and mortality rates. While metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool, its sensitivity is often compromised by host DNA contamination that overwhelms microbial signals. Selective host DNA depletion through cell lysis effectively reduces host DNA; however, it has an impact on microorganisms with relatively thin cell walls, and samples with low host content may introduce more environment or reagent-derived microbial contamination, interfering the detection results. Methods for determining host DNA depletion based on sample type, sample characteristics or using Spike-in controls to monitor sensitivity do not fully consider the potential limitations of host depletion technology on microbial detection, nor do they evaluate the possible significant impact on detection efficiency. This study aimed to develop a pre-analytical method for accurate host DNA content assessment.<br><br>METHODS: We established a cell-counting-based method for precise cellular content measurement in clinical BALF samples. The protocol involved: (1) evaluating the linearity and robustness of cell-counting dyes in BALF samples with varying characteristics, (2) assessing the correlation between cell counts and extracted nucleic acid mass, (3) investigating cellular counting thresholds for host depletion in clinical BALF analysis, and (4) implementing the optimized cell-counting method in clinical mNGS testing to guide selective-lysis treatment.<br><br>RESULTS: Acridine orange/propidium iodide (AO/PI) staining demonstrated superior performance compared to trypan blue and DAPI, particularly in turbid and bloody BALF samples. Implementing a host depletion threshold at 1&#x202f;&#xd7;&#x202f;10^6 cell counts significantly improves pathogen detection rates in high host background samples, while effectively preserving the detection sensitivity for pathogens in moderate and low host background samples.<br><br>CONCLUSIONS: Our findings demonstrate that cell counting serves as a reliable pre-analytical tool for determining optimal selective-lysis treatment in BALF mNGS testing, enhancing diagnostic accuracy while preserving pathogen integrity.},
}
@article {pmid40294758,
year = {2025},
author = {Thangadural, T and Dobretsov, S and Aeby, G},
title = {Exploring Bacterial Diversity in Acropora pharaonis: Implications for Coral Health and Growth Anomalies.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107616},
doi = {10.1016/j.micpath.2025.107616},
pmid = {40294758},
issn = {1096-1208},
abstract = {Coral growth anomalies (GA) affect many coral genera across the world, yet the etiology of GAs remains unknown, with limited knowledge of associated bacteria. In this study, we investigated bacterial associations between the growth anomalies (GAs) and healthy (H) portions of coral colonies in Acropora faraonis for two seasons to understand microbial dynamics. Additionally, we examined bacteria in water (W), which could be affecting coral bacterial communities. We found that alpha diversity remained consistent between healthy and GA coral tissues, but their relative abundances differed significantly. Notably, differential analysis revealed the abundance of Endozoicomonas spp., differed significantly between GA and H tissue, although it remains the dominant genus in both GA and H tissue. The high relative abundance of Endozoicomonas spp. in both GA and healthy tissue underscores its potential role in maintaining coral health. Structural modifications in GAs, such as changes in polyp sizes or densities, could be responsible for these differences in bacterial abundance. Similarly, microbial community composition remained consistent between seasons but differed in abundance again. We found differences between microbial communities of GAs and water, but no significant differences were observed between GAs and H, and no previously established bacterial pathogens were detected in GA tissue. These findings describe bacterial community patterns in GAs, but their potential role in its pathogenesis remains unknown. Further metagenomic and meta-transcriptomic analyses are needed to understand potential bacterial involvement in GAs. Additionally, investigating viruses and fungi in GA tissue is recommended to gain deeper insights into GA pathogenesis.},
}
@article {pmid40294754,
year = {2025},
author = {Devi, A and Singh, V and Raj, A and Saratale, GD and Ferreira, LFR and Mulla, SI and Bharagava, RN},
title = {Optimization of lipid production in Tetradesmus dimorphus using response surface methodology using tannery wastewater for biodiesel production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132585},
doi = {10.1016/j.biortech.2025.132585},
pmid = {40294754},
issn = {1873-2976},
abstract = {The management of industrial wastewaters and generation of sustainable energy resources are the two major challenges concerned with the global population and depleting fossil fuels. Tannery wastewater (TWW) is a major source of environmental pollution and human health hazardous if released without adequate treatment. The microalgal treatment of TWW among other approaches seems to be beneficial and effective as microalgae use TWW as nutrient source offering wastewater treatment while producing large biomass for biofuel production. Biomass and lipid content are the adequate criteria for higher biodiesel yield. In present study, Tetradesmus dimorphus was grown in TWW with an objective to treat TWW along with the generation of large biomass for biodiesel production and Response Surface Methodology (RSM) was used to optimize the biodiesel production taking into count the parameters such as wastewater concentrations, pH and photoperiod. Results showed that highest biomass and lipid content produced were 1.63 ± 0.02 g/L and 487 ± 11 mg/L, respectively with 213.80 ± 7 mg/L of biodiesel production. Gas Chromatography-Flame Ionization Detection (GC-FID) analysis of biodiesel obtained from Tetradesmus dimorphus lipids showed that it was made up of more than 40 % Methyl decanoate (C11:0) and Methyl erucate (C22:1). The interrelationships between selected parameters like STTWW concentrations, pH and photoperiods reflected the positive impact on lipid productivity as 3D contour depicted the maximum yield at 80 % wastewater concentration, pH 8 and 14 h of photoperiod. Study showed that microalgal treatment of TWW among the other approaches seems beneficial and effective to harness wastewater nutrients while producing valuable biomass for biodiesel production.},
}
@article {pmid40294646,
year = {2025},
author = {Wang, C and Zhang, H and Liu, J},
title = {The diagnostic efficacy of metagenomic next-generation sequencing in spontaneous bacterial peritonitis: System review and meta-analysis.},
journal = {Gastroenterologia y hepatologia},
volume = {},
number = {},
pages = {502456},
doi = {10.1016/j.gastrohep.2025.502456},
pmid = {40294646},
issn = {0210-5705},
abstract = {OBJECTIVE: The objective of this research is to assess the accuracy and reliability of metagenomic next-generation sequencing (mNGS) in identifying pathogens in spontaneous bacterial peritonitis (SBP) patients and its impact on antibiotic treatment decisions.<br><br>METHODS: Electronic databases were searched up to July 31, 2023. Studies reporting mNGS diagnostic sensitivity and specificity in SBP were included. Random or fixed-effects models were used. Heterogeneity was assessed using chi-squared test and I&#xb2; statistics.<br><br>RESULTS: Out of 75 identified studies, four studies with a total of 420 SBP patients were included. The pooled sensitivity for mNGS in ascites was 94% (95% CI: 86-97%), and specificity was 81% (95% CI: 71-89%). The AUC was calculated to be 0.95 (95% CI: 0.92-0.96), indicating high diagnostic accuracy. The most common pathogens identified by mNGS were Gram-positive bacteria (36%), followed by Gram-negative bacteria (29%), viruses (22%), and fungi (11%).<br><br>CONCLUSION: mNGS shows high diagnostic accuracy in detecting pathogens in SBP patients, offering significant value in optimizing antimicrobial therapy. Its ability to identify a broad spectrum of pathogens makes it a promising tool in clinical management of SBP.},
}
@article {pmid40294554,
year = {2025},
author = {Zeng, H and Yang, H and Fu, Z and Ma, L and Lu, L and Zeng, T and Xiao, Y and Lyu, W},
title = {Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105206},
doi = {10.1016/j.psj.2025.105206},
pmid = {40294554},
issn = {1525-3171},
abstract = {The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems.},
}
@article {pmid40293591,
year = {2025},
author = {Orlova, EA and Sinkov, VV and Ogarkov, OB and Suzdalnitsky, AE and Kondratov, IG and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI},
title = {Metagenomic Analysis of Caseum of Tuberculosis Foci.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {40293591},
issn = {1573-8221},
abstract = {The microbiota of the deep lung regions significantly differs from that of the upper respiratory tract by much lower biomass and dynamic diversity. In our previous studies we found that the biodiversity of the satellite microbiota of tuberculosis foci is sharply reduced in comparison with intact lung tissues. These findings allowed us to classify microbial communities in the caseous necrosis of tuberculomas into two types: (i) mycobacterial caseoma (tuberculoma), where 70% or more of the genomes correspond to Mycobacterium tuberculosis, and (ii) a polymicrobial community, where the concentration of M. tuberculosis varies from 0 to 10%. Using shotgun metagenomic sequencing, 14 tuberculomas from 13 patients were analyzed on a NextSeq 550 platform (Illumina). Taxonomic classification of short reads was performed using Kraken 2. The results show that, on average, 99.95% of the short reads belonged to human DNA or were unclassified. However, the classified reads related to bacterial genomes confirmed the concept that in many cases, tuberculomas contained polymicrobial communities that either replaced or supplemented the original mycobacterial microbiota of the caseous material.},
}
@article {pmid40293286,
year = {2025},
author = {Elsakhawy, OK and Roozitalab, A and Abouelkhair, MA},
title = {Genome sequence of a bovine respiratory syncytial virus strain from a cow in Tennessee.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0007225},
doi = {10.1128/mra.00072-25},
pmid = {40293286},
issn = {2576-098X},
abstract = {We report the genome sequence of a bovine respiratory syncytial virus strain (hereafter referred to as BRSV_23), identified in a cow in Tennessee. This genome sequence updates the currently circulating BRSV field strains in the United States, providing insights into viral evolution and epidemiology to improve diagnostics and control strategies.},
}
@article {pmid40293266,
year = {2025},
author = {Wilson, A and Gias, E and Little, A and Jauregui, R and Low, YS and Pulford, D and Steyn, A and Sylvester, K and Green, D and O'Keefe, J and McCulley, M},
title = {Genome sequence of a divergent strain of canine distemper virus detected in New Zealand fur seals.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0015125},
doi = {10.1128/mra.00151-25},
pmid = {40293266},
issn = {2576-098X},
abstract = {We report the draft genome sequence of a strain of canine distemper virus detected in New Zealand fur seals (Arctocephalus forsteri). A high-quality draft consensus genome was produced through a combination of long- and short-read metagenomic sequencing approaches. Phylogenetic analysis confirms that the virus is a divergent strain of canine distemper virus.},
}
@article {pmid40293263,
year = {2025},
author = {Dias, D and Nascimento, B and Cruz, A and Silva, S and Reis, L and Silva, F and Silva, L and Silva, S and Vieira, D and Brandão, R and Junior, J and Santos, A and Reis, H and Neto, J},
title = {Coding-complete genome sequence of a divergent member of the genus Gordisvirus detected in Sabethes (Peytonulus) undosus Coquillet mosquitoes (Diptera: Culicidae) from Brazil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0127524},
doi = {10.1128/mra.01275-24},
pmid = {40293263},
issn = {2576-098X},
abstract = {We report the complete genome sequence of a divergent member of the genus Gordisvirus (family Xinmoviridae, order Mononegavirales), obtained through metagenomic sequencing of Sabethes (Peytonulus) undosus Coquillett mosquitoes in the Brazilian Amazon. Phylogenetic analyses confirmed its classification. The genome comprises 12,150 nucleotides and encodes five open-reading frames.},
}
@article {pmid40291804,
year = {2025},
author = {Wu, Y and Mo, J and Wang, Q and Li, J and Wei, J and Zhang, N and Dong, Y and Zhu, X and Lu, T and Huang, S},
title = {Microbiome and metabolome explain the high-fat diet-induced diabetes development and diabetes resistance in Guizhou mini-pigs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1555069},
pmid = {40291804},
issn = {1664-302X},
abstract = {Type 2 diabetes mellitus (T2DM) is an obesity-related disease claiming substantial global mortality annually. Current animal models of T2DM remain limited, with low success rates in establishing porcine models of high-fat diet (HFD)-induced T2DM. Our experimental design employed 35 Guizhou mini-pigs to develop a T2DM model via HFD induction, aiming to identify microbial and metabolic signatures associated with disease pathogenesis and resistance. At month 10, five individuals from the control (CTR), T2DM (DM), and T2DM resistant (anti-DM) groups were slaughtered, samples were collected, and relevant indices were measured. Metagenomics, metabolomics, and 16S rRNA sequencing were performed to identify microbes and metabolites linked to T2DM progression and resistance. Key findings demonstrated anti-DM group parameters-including metabolic indices (fasting blood glucose, insulin levels, HbA1c, IVGTT), histopathology (HE-stained pancreatic/hepatic tissues), microbial profiles (structural, compositional, functional), and metabolomic signatures-occupied intermediate positions between CTR and DM groups. Network analyses revealed: (1) Lactobacillus, L. amylovorus, fingolimod, polyoxyethylene sorbitan monooleate, thiamine, and atrazine in HFD-associated networks; (2) Limosilactobacillus reuteri, N-oleoyl-L-serine, tolbutamide, tetradecanoyl carnitine, 3'-sulfogalactosylceramide, and guggulsterone in T2DM resistance networks; (3) Ruminococcaceae NK4A214 group, diethyl phthalate, zingerone, enalapril, 5-hydroxytryptophol, 2'-deoxyinosine, icariin, and emetine in T2DM progression networks. These results further clarify the role of the gut microbiota and serum metabolites in the development of T2DM in the Guizhou mini-pig model.},
}
@article {pmid40291803,
year = {2025},
author = {Yang, M and Cai, Y and Bai, T and Han, X and Zeng, R and Liu, D and Liu, T and Liu, R and Ma, C and Yu, L},
title = {Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1512694},
pmid = {40291803},
issn = {1664-302X},
abstract = {INTRODUCTION: Tobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of the rhizosphere microbiome in tobacco plants infected with Fusarium root rot remain poorly understood.<br><br>METHODS: In this study, we analyzed the differences in the compositions and functions of the bacterial and fungal communities in the rhizosphere and root endosphere of healthy tobacco plants and tobacco with Fusarium root rot using amplicon sequencing and metagenomic sequencing.<br><br>RESULTS AND DISCUSSION: Our results showed that Fusarium root rot disrupted the stability of bacteria-fungi interkingdom networks and reduced the network complexity. Compared to healthy tobacco plants, the Chao1 index of bacterial communities in the rhizosphere soil of diseased plants increased by 4.09% (P < 0.05), while the Shannon and Chao1 indices of fungal communities decreased by 13.87 and 8.17%, respectively (P < 0.05). In the root tissues of diseased plants, the Shannon index of bacterial and fungal communities decreased by 17.71-27.05% (P < 0.05). Additionally, we observed that the rhizosphere microbial community of diseased tobacco plants shifted toward a pathological combination, with a significant increase in the relative abundance of harmful microbes such as Alternaria, Fusarium, and Filobasidium (89.46-921.29%) and a notable decrease in the relative abundance of beneficial microbes such as Lysobacter, Streptomyces, Mortierella, and Penicillium (48.48-81.56%). Metagenomic analysis further revealed that the tobacco rhizosphere microbial communities of diseased plants played a significant role in basic biological metabolism, energy production and conversion, signal transduction, and N metabolism, but their functions involved in C metabolism were significantly weakened. Our findings provide new insights into the changes in and interactions within the rhizosphere and root endosphere microbiomes of tobacco plants under the stress of Fusarium soil-borne fungal pathogens, while laying the foundation for the exploration, development, and utilization of beneficial microbial resources in healthy tobacco plants in the future.},
}
@article {pmid40291800,
year = {2025},
author = {Huang, YY and Zhu, D and Yang, LQ and Ortúzar, M and Yang, ZF and Lv, ZH and Xie, KQ and Jiang, HC and Li, WJ and Yin, YR},
title = {Characterization, thermostable mechanism, and molecular docking of a novel glucose-tolerant β-glucosidase/β-galactosidase from the GH1 family isolated from Rehai hot spring.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1559242},
pmid = {40291800},
issn = {1664-302X},
abstract = {INTRODUCTION: As a renewable alternative to fossil fuels, second-generation bioethanol production relies heavily on efficient lignocellulose conversion, with β-glucosidase playing a critical role.<br><br>METHODS: This study focused on the &#x3b2;-glucosidase gene y50bg4 discovered in the Tengchong Rehai metagenome. The recombinant enzyme Y50Bg4 was obtained through PCR amplification, cloning, and expression. It was subsequently separated and purified using a Ni-NTA affinity chromatography column, and its enzymatic properties were analyzed.<br><br>RESULTS: Enzymatic characterization revealed that Y50Bg4 efficiently hydrolyzes substrates like cellobiose, pNPGlc, and lactose. Y50Bg4 achieved optimal activity at 60&#xb0;C and pH 6.0, maintaining 100% stability after 2&#x202f;h of incubation at 60&#xb0;C. The residual activity remained above 60% after 24&#x202f;h of incubation across a pH range of 4.0 to 10.0. Kinetic constants analysis showed K m values of 4.69&#x202f;mg/mL for cellobiose and 0.53&#x202f;mM for pNPGlc, with V max values of 39.71&#x202f;&#x3bc;mol/min/mg and 20.39&#x202f;&#x3bc;mol/min/mg, respectively. Furthermore, the enzyme exhibits exceptional glucose tolerance, with Y50Bg4 retaining over 80% of its activity even at a glucose concentration of 3,000&#x202f;mM. In practical applications, Y50Bg4 can work synergistically to degrade corn straw when combined with commercial cellulase. When Y50Bg4 (0.05&#x202f;mg/mL) was added to the commercial cellulase reaction system, the glucose yield from corn straw increased by 11.6% after a reaction period of 24&#x202f;h at 50&#xb0;C. The results indicate that Y50Bg4 exhibits the activities of both &#x3b2;-glucosidase and &#x3b2;-galactosidase. Molecular docking and kinetic simulations revealed that Y50Bg4 has a higher affinity for cellobiose than for lactose and identified structural regions (residues 325-350 and 390-410) that contribute to its thermal stability.<br><br>DISCUSSION: These findings highlight the potential of Y50Bg4 for industrial applications in bioethanol production and cellulose hydrolysis. In summary, Y50Bg4, with its exceptional enzymatic properties, presents significant application value and market potential in industrial sectors such as bioethanol production and cellulose hydrolysis.},
}
@article {pmid40290900,
year = {2025},
author = {Kodio, A and Coulibaly, D and Doumbo, S and Konaté, S and Koné, AK and Dama, S and Niangaly, A and Tall, ML and Konaté, AM and L'Ollivier, C and Levasseur, A and Bittar, F and Djimdé, A and Doumbo, OK and Raoult, D and Thera, MA and Ranque, S},
title = {Gut microbiota influences Plasmodium falciparum malaria susceptibility.},
journal = {New microbes and new infections},
volume = {65},
number = {},
pages = {101586},
pmid = {40290900},
issn = {2052-2975},
abstract = {BACKGROUND: The gut microbiota has recently been associated with malaria susceptibility/resistance in animal models and humans. This study aimed to assess its influence on malaria attack and Plasmodium parasitemia in children living in a malaria-endemic area of Mali.<br><br>METHODS: Healthy children were enrolled in a 16-month cohort study in Bandiagara. Their gut bacteria and fungi community structures were characterized via 16S and ITS metabarcoding at enrolment. Clinicians monitored malaria attacks. Asymptomatic Plasmodium carriage was assessed by real-time polymerase chain reaction.<br><br>RESULTS: Of the 300 children, 107 (36&#xa0;%) had at least one malaria attack, and 82 (27&#xa0;%) had at least one episode of asymptomatic Plasmodium parasitemia. The gut bacterial community structure, but not the fungal community, was associated with susceptibility/resistance to both malaria attacks and asymptomatic P. falciparum parasitemia. Higher gut bacteria richness was independently associated with susceptibility to both asymptomatic parasitemia episodes and malaria attacks. 17 bacteria, and 7 fungi were associated with susceptibility to malaria attacks, and 8 bacteria, and 3 fungi were associated with resistance. 15 bacteria and 13 fungi were associated with susceptibility to asymptomatic Plasmodium parasitemia episodes, and 19 bacteria and 3 fungi were associated with resistance.<br><br>CONCLUSION: Further studies are needed to confirm these findings, which point the way to strategies aimed at reducing the risk of malaria by modulating gut microbiota components in at-risk populations.},
}
@article {pmid40290560,
year = {2025},
author = {Hosszu-Fellous, K and Cordey, S and Masouridi-Levrat, S and Simonetta, F and Laubscher, F and Combescure, C and Mamez, AC and Giannotti, F and Morin, S and Docquier, M and Pradier, A and Royston, L and Chalandon, Y and Neofytos, D and Kaiser, L},
title = {Blood Virome After Allogeneic Hematopoietic Stem Cell Transplantation.},
journal = {Open forum infectious diseases},
volume = {12},
number = {4},
pages = {ofaf213},
pmid = {40290560},
issn = {2328-8957},
abstract = {BACKGROUND: Haploidentical allogeneic hematopoietic cell transplant recipients (allo-HCTr) receiving posttransplant cyclophosphamide (haplo-PTCy) are at higher risk for infectious complications, including viral infections.<br><br>METHODS: We performed a retrospective, single-center, propensity-score matched-pair study including adult haplo-PTCy and allo-HCTr from human leukocyte antigen (HLA)-matched donors, undergoing transplantation in our institution between 2016 and 2022. For each patient, 4 blood samples (day [D] 0, D30, D90, and D180 posttransplantation) were extracted from the biobank and tested with metagenomic next-generation sequencing (mNGS) to describe the blood virome and identify viral RNA/DNA signatures potentially unrecognized by routinely available tests. Routine and symptom-driven polymerase chain reaction (PCR) test results performed during the study period were reviewed.<br><br>RESULTS: Twenty-five matched pairs of haplo-PTCy and HLA-matched allo-HCTr were included in the analysis. Plasma mNGS detected a total of 155 and 190 different viral RNA/DNA signatures in haplo-PTCy and HLA-matched allo-HCTr, respectively between D0 and D180. The number of viral signatures was significantly lower in the haplo-PTCy group compared to HLA-matched allo-HCTr at D90 (-1.0 [95% confidence interval {CI},
-1.7 to -.3]; P = .01) and during the period between D30 and D180 (-1.9 [95% CI, -3.3 to -.5]; P = .01). Certain viral species (Anelloviridae, Epstein-Barr virus) were more prevalent in HLA-matched patients. Symptom-driven PCR tests showed higher infection rates of usual viral pathogens in haplo-PTCy versus HLA-matched allo-HCTr (P = .02).<br><br>CONCLUSIONS: Frequently deployed, targeted PCR tests showed increased viral infection prevalence in haplo-PTCy patients. Conversely, mNGS testing applied at specific timepoints revealed a lower number of commensal viruses in this patient group. More studies on routine use of mNGS are needed to further assess its clinical relevance and value.},
}
@article {pmid40290406,
year = {2025},
author = {Zhu, H and Guo, Y and Chen, H and Ni, L and Zhu, B and Qu, T},
title = {A Case of Pulmonary Infection Caused by Rhodococcus equi in an AIDS Patient and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2021-2027},
pmid = {40290406},
issn = {1178-6973},
abstract = {Rhodococcus equi is a rare opportunistic Gram-positive bacterium that primarily affects immunocompromised individuals, particularly those with human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). The infection often presents as a multisystem, disseminated disease with rapid progression and high mortality if not promptly diagnosed and treated. We report the case of a 34-year-old male AIDS patient who developed pulmonary infection due to Rhodococcus equi. Cultures from bronchoalveolar lavage fluid, metagenomic next-generation sequencing (mNGS), and bronchoscopic brushing all indicated infection with Rhodococcus equi. Following combined anti-infective treatment, the pulmonary infection was controlled, and his condition improved. Clinicians should be alert to the possibility of Rhodococcus equi infection in AIDS patients, emphasizing early diagnosis and targeted therapy to improve patient outcomes.},
}
@article {pmid40290137,
year = {2025},
author = {Kong, F and Wang, S and Zhang, Y and Li, C and Dai, D and Wang, Y and Cao, Z and Yang, H and Shengli Li, and Wei Wang, },
title = {Alanine Derived from Ruminococcus_E bovis Alleviates Energy Metabolic Disorders during the Peripartum Period by Providing Glucogenic Precursors.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0682},
pmid = {40290137},
issn = {2639-5274},
abstract = {Peripartum dairy cows commonly experience energy metabolism disorders, which lead to passive culling of postpartum cows and a decrease in milk quality. By using ketosis peripartum dairy cows as a model, this study aims to elucidate the metabolic mechanism of peripartum cows and provide a novel way for managing energy metabolic disorders. From a cohort of 211 cows, we integrated multi-omics data (metagenomics, metabolomics, and transcriptomics) to identify key microbes and then utilized an in vitro rumen fermentation simulation system and ketogenic hepatic cells to validate the potential mechanisms and the effects of postbiotics derived from key microbes. Postpartum cows with metabolic disorders compensate for glucose deficiency through mobilizing muscle proteins, which leads to marked decreases in milk protein content. Concurrently, these cows experience rumen microbiota disturbance, with marked decreases in the concentrations of volatile fatty acids and microbial protein, and the deficiency of alanine (Ala) in microbial protein is correlated with the metabolic disorder phenotype. Metagenomic binning and in vitro fermentation assays reveal that Ruminococcus_E bovis (MAG 189) is enriched in amino acid biosynthesis functions and responsible for Ala synthesis. Furthermore, transcriptomic and metabolomic analyses of the liver in metabolic disorder cows also show impaired amino acid metabolism. Supplementation with Ala can alleviate ketogenesis in liver cell models by activating the gluconeogenesis pathway. This study reveals that Ruminococcus_E bovis is associated with host energy metabolism homeostasis by supplying glucogenic precursors to the liver and suggests the use of Ala as a method for the treatment of energy metabolism disorders in peripartum cows.},
}
@article {pmid40289407,
year = {2025},
author = {Aho, VTE and Clerbaux, LA and Kupczok, A and Tillett, B and Garg, N and Henderickx, JGE},
title = {A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202500019},
doi = {10.1002/pmic.202500019},
pmid = {40289407},
issn = {1615-9861},
abstract = {Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling the function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies of the microbiome, complementing genome-resolved metagenomics, metatranscriptomics, and metabolomics. The potential advancements from metaproteomics and multiomics research touch a breadth of disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, and medicine, and could lead to both fundamental and applied discoveries. However, there are significant roadblocks to widespread adoption of metaproteomics among microbiome researchers. In this Viewpoint article, we highlight the pivotal role of metaproteomics in microbiome research by showcasing its advantages, exploring opportunities to overcome challenges, and paving the way for its broader adoption as a mainstream technique. We hope that the recommendations provided in this Viewpoint article will inspire new, beneficial collaborations between proteomics experts, algorithm and infrastructure developers, biochemists, cell biologists, and microbiologists, enabling the construction of a knowledge base of microbiome function that can have an immediate and direct impact on host health and the environment.},
}
@article {pmid40289251,
year = {2025},
author = {Slager, J and Simpson, HL and Gacesa, R and Chen, L and Tan, IL and Gelderloos, J and Maatman, A and Wijmenga, C and Zhernakova, A and Fu, J and Weersma, RK and Gonera, G and Jonkers, IH and Withoff, S},
title = {High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489071},
doi = {10.1080/19490976.2025.2489071},
pmid = {40289251},
issn = {1949-0984},
mesh = {Humans ; *Celiac Disease/microbiology/diet therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Middle Aged ; Adult ; Netherlands ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Aged ; },
abstract = {BACKGROUND: Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterized by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution.<br><br>METHODS: To address these limitations, we analyzed fecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analyzed in tCeD patients and controls.<br><br>RESULTS: Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients.<br><br>CONCLUSION: Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome's role in intestinal health and disease.},
}
@article {pmid40289223,
year = {2025},
author = {Salma Santhosh, S and Meena, S and Baskar, M and Karthikeyan, S and Vanniarajan, C and Ramesh, T},
title = {Transformative strategies for saline soil restoration: Harnessing halotolerant microorganisms and advanced technologies.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {5},
pages = {140},
pmid = {40289223},
issn = {1573-0972},
support = {UGCES-22-OB-TAM-F-SJSGC-16232//University Grants Commission (UGC) - Savitribai Jyotirao Phule Fellowship for Single Girl Child (SJSGC)/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; Salinity ; Biodegradation, Environmental ; Salt Tolerance ; *Bacteria/metabolism/genetics ; Gene Editing ; },
abstract = {Soil salinity is a critical global challenge that severely impairs crop productivity and soil health by disrupting water uptake, nutrient acquisition, and ionic balance in plants, thereby posing a significant threat to food security. This review underscores innovative strategies to mitigate salinity stress, focusing on the pivotal role of halotolerant microorganisms and their synergistic interactions with plants. Halotolerant microorganisms enhance plant resilience through diverse mechanisms under salinity, including exopolysaccharide production, sodium sequestration, and phytohormone regulation. It improves ionic balance, nutrient uptake, and root development, facilitated by osmoregulatory and genetic adaptations. In this discussion, we explored emerging technologies, including genome editing (e.g., CRISPR-Cas9), synthetic biology, and advanced omics-based tools such as metagenomics and metatranscriptomics. These cutting-edge approaches offer profound insights into microbial diversity and their functional adaptations to saline environments. By leveraging these technologies, it is possible to design targeted bioremediation strategies through the customization of microbial functionalities to address specific environmental challenges effectively. Advanced methodologies, such as microbial volatile organic compounds (mVOCs), nanotechnology, and stress-tolerant microbial consortia, significantly enhance plant stress tolerance and facilitate soil restoration. Moreover, integrating digital technologies, including machine learning and artificial intelligence (AI), optimizes bioremediation processes by providing precise, scalable, and adaptable solutions tailored to diverse agricultural ecosystems. The synergistic application of halotolerant microbe-mediated approaches with advanced biotechnological and digital innovations presents a transformative strategy for saline soil restoration. Future research should focus on harmonizing these technologies and methodologies to maximize plant-microbe interactions and establish resilient, sustainable agricultural systems.},
}
@article {pmid40289152,
year = {2025},
author = {Jarrige, D and Tardy, V and Loux, V and Rué, O and Chabbi, A and Terrat, S and Maron, PA},
title = {Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14723},
pmid = {40289152},
issn = {2045-2322},
support = {ANR-20-PAMR-0004//Agence Nationale de la Recherche/ ; },
mesh = {*Soil Microbiology ; *Triticum ; *Metagenomics/methods ; *Microbiota/genetics ; *Grassland ; Bacteria/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; High-Throughput Nucleotide Sequencing ; },
abstract = {Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions. Metagenomics allows studying taxa that are often overlooked in microbiota studies, such as protists or viruses. Here, we employed metagenomics to characterise microbial successions after wheat straw input in a 4-month in-situ field study. We compared microbial successions patterns with those obtained by high throughput amplicon sequencing on the same soil samples to validate metagenomics as a tool for the fine analysis of microbial population dynamics in situ. Taxonomic patterns were concordant between the two methodologies but metagenomics allowed studying all the microbial groups simultaneously. Notably, our results evidenced that each domain displayed a specific dynamic pattern after wheat straw amendment. For instance, viral sequences multiplied in the early phase of straw decomposition, in parallel to copiotrophic bacteria, suggesting a "kill-the-winner" pattern that, to our knowledge, had not been observed before in soil. Altogether, our results highlighted that both inter and intra-domain trophic interactions were impacted by wheat amendment and these patterns depended on the land use history. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.},
}
@article {pmid40289138,
year = {2025},
author = {Weathers, SP and Li, X and Zhu, H and Damania, AV and Knafl, M and McKinley, B and Lin, H and Harrison, RA and Majd, NK and O'Brien, BJ and Penas-Prado, M and Loghin, M and Kamiya-Matsuoka, C and Yung, WKA and Solis Soto, LM and Maru, DM and Wistuba, I and Parra Cuentas, ER and Hernandez, S and Futreal, A and Wargo, JA and Schulze, K and Darbonne, WC and Ajami, NJ and Woodman, SE and de Groot, JF},
title = {Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3950},
pmid = {40289138},
issn = {2041-1723},
mesh = {Humans ; *Glioblastoma/genetics/immunology/mortality/therapy/drug therapy ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Female ; Middle Aged ; *Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy ; Temozolomide/therapeutic use/administration &amp; dosage ; Antibodies, Monoclonal, Humanized/therapeutic use/administration &amp; dosage ; Mutation ; Aged ; Adult ; *B7-H1 Antigen/antagonists &amp; inhibitors ; Tumor Microenvironment ; Prospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use ; Treatment Outcome ; },
abstract = {This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.},
}
@article {pmid40289100,
year = {2025},
author = {Mok, K and Tomtong, P and Ogawa, T and Nagai, K and Torrungruang, P and Charoensiddhi, S and Nakayama, J and Wanikorn, B and Nitisinprasert, S and Vongsangnak, W and Nakphaichit, M},
title = {Synbiotic-driven modulation of the gut microbiota and metabolic functions related to obesity: insights from a human gastrointestinal model.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {250},
pmid = {40289100},
issn = {1471-2180},
support = {FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; },
mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Obesity/microbiology/metabolism ; *Gastrointestinal Tract/microbiology/metabolism ; Feces/microbiology ; Limosilactobacillus reuteri/growth &amp; development ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Microbial Viability ; Adult ; Male ; *Gastrointestinal Microbiome ; Female ; },
abstract = {Synbiotic interventions have gained increasing attention for modulating gut microbiota and metabolic functions in obesity-related disorders. This study evaluated the effects of Limosilactobacillus reuteri KUB-AC5 (10[8] CFU) and Wolffia globosa powder (6 g/day) using an in vitro continuous human gastrointestinal model. Fecal samples from obese donors were used to simulate the ascending and descending colon, with microbial viability, diversity, and metabolite production assessed over 14 days via culture-dependent and culture-independent methods. Synbiotic supplementation increased anaerobic bacterial counts by 2.6 log CFU/mL in the ascending colon and 2.2 log CFU/mL in the descending colon, with notable increases in lactic acid bacteria and reductions in Enterobacteriaceae. Metagenomic analysis revealed an increasing trend in microbial diversity and evenness after 7 days of treatment, though the changes were not statistically significant. PERMANOVA analysis confirmed significant shift in microbial community composition between stabilization, treatment, and washout periods (p < 0.05). Additionally, butyrate levels significantly increased (p < 0.05), while p-cresol, a deleterious metabolite, significantly decreased (p < 0.05). Bile acid composition was modulated, with increased tertiary bile acid 3-oxo-LCA and enhanced bile acid deconjugation, suggesting improved lipid metabolism and potential weight management benefits. These findings highlight the potential of synbiotic supplementation to enhance beneficial bacterial populations, improve microbial diversity, and support metabolic health in obesity management.},
}
@article {pmid40289092,
year = {2025},
author = {Qiu, J and Hu, P and Li, F and Huang, Y and Yang, Y and Sun, F and Wu, P and Lai, Y and Wang, Y and He, X and Dong, Y and Zhang, P and Zhang, S and Wu, N and Wang, T and Yang, S and Li, S and Yuan, J and Liu, X and Liu, G and Hu, Y and Wu, JHY and Chen, D and Pan, A and Pan, XF},
title = {Circulating linoleic acid and its interplay with gut microbiota during pregnancy for gestational diabetes mellitus.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {245},
pmid = {40289092},
issn = {1741-7015},
support = {2022YFC2702905//National Key R&amp;D Program of China/ ; 82325043//the National Science Fund for Distinguished Young Scholars/ ; 82473646//Natural Science Foundation of China/ ; 2024NSFSC0578//Sichuan Provincial Natural Science Foundation/ ; YJ202346//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Circulating linoleic acid (LA) levels have been reported to be associated with various metabolic outcomes. However, the role of LA and its interplay with gut microbiota in gestational diabetes mellitus (GDM) remains unclear. This study aimed to investigate the longitudinal association between circulating LA levels during pregnancy and the risk of GDM, and the potential role of gut microbiota.<br><br>METHODS: A nested case-control study was conducted within the ongoing Tongji-Huaxi-Shuangliu Birth Cohort in Chengdu, China. Blood and fecal samples were collected during early and middle pregnancy from 807 participants. GDM was diagnosed in middle pregnancy using the International Association of Diabetes and Pregnancy Study Groups criteria. Plasma LA levels were measured using gas chromatography-mass spectrometry, and gut microbiota was analyzed through 16S rRNA gene sequencing and shotgun metagenomic sequencing. A two-sample Mendelian randomization study was conducted using data from the IEU OpenGWAS database and the FinnGen consortium.<br><br>RESULTS: Elevated plasma LA levels were associated with a lower risk of GDM in both early (P for trend&#x2009;=&#x2009;0.002) and middle pregnancy (P for trend&#x2009;=&#x2009;0.02). Consistently, Mendelian randomization analysis revealed that each unit increase in LA was associated with a 16% reduction in GDM risk (odds ratio: 0.84, 95% confidence interval: 0.72, 0.95). In early pregnancy, higher plasma LA levels were correlated with higher adiponectin&#xa0;levels (P&#x2009;<&#x2009;0.001) and lower levels of triglycerides (P&#x2009;<&#x2009;0.001), HbA1c (P&#x2009;=&#x2009;0.04), and C-peptide (P&#x2009;=&#x2009;0.04). The LA-accociated microbiota mediated the relationship between LA and C-peptide (P&#x2009;=&#x2009;0.01). Additionally, the inverse association between LA and GDM was modified by Bilophila&#xa0;(P for interaction&#x2009;=&#x2009;0.03), with a stronger association observed in participants with lower Bilophila levels in early pregnancy. Metagenomic analyses further showed that&#xa0;the LA-associated pathway (D-galacturonate degradation I) and its key enzyme (EC 4.2.1.7) were associated with metabolic traits.<br><br>CONCLUSIONS: Our study provides evidence for an inverse causal association between plasma LA levels during pregnancy and GDM risk, which is both mediated and modified by gut microbiota.},
}
@article {pmid40289075,
year = {2025},
author = {Wu, J and Xiang, Y and Li, F and Liu, X and Dang, N and Guo, J},
title = {Phialophora americana infection in a patient with a compound heterozygous CARD9 mutation.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {613},
pmid = {40289075},
issn = {1471-2334},
support = {2022M710852//China Postdoctoral Science Foundation/ ; 82102420//National Natural Science Foundation of China/ ; ZR2024QH034//Natural Science Foundation of Shandong Province/ ; },
abstract = {Phaeohyphomycosis caused by Phialophora americana is relatively rare in clinical practice. Deficiency in the human caspase recruitment domain-containing protein 9 (CARD9) is associated with infections caused by Phialophora americana. In this case, the patient has had a decade-long history of recurrent tinea corporis and recently presented with an invasive, deep subcutaneous infection in the right axilla caused by Phialophora americana. Metagenomic next-generation sequencing (mNGS) confirmed that the pathogen infecting the patient was Phialophora americana. Whole exome sequencing (WES) revealed that the patient had compound heterozygous CARD9 gene mutations, with a c.952-1G > A mutation in intron 6 and a c.184 + 5G > T mutation in intron 2. The expression of the CARD9 protein and the levels of cytokines, including IL-17 and IFN-γ, were observed to be decreased in the patient. After an ineffective treatment with amphotericin B, voriconazole was administered for antifungal therapy and yielded satisfactory results. Following discharge, the patient continued oral voriconazole for ongoing antifungal treatment. One month after discharge, the patient returned to the hospital for a follow-up examination, during which it was observed that the symptoms had been successfully resolved. The novel compound heterozygous mutations may lead to CARD9 deficiency, which in turn results in susceptibility to Phialophora americana infection.},
}
@article {pmid40288855,
year = {2025},
author = {Prisacar, M and Leichert, LI},
title = {Functional metaproteomics for enzyme discovery.},
journal = {Methods in enzymology},
volume = {714},
number = {},
pages = {61-82},
doi = {10.1016/bs.mie.2025.01.029},
pmid = {40288855},
issn = {1557-7988},
abstract = {Discovery of microbial biocatalysts traditionally relied on activity screening of isolated bacterial strains. However, since most microorganisms cannot be cultivated in the lab, such an approach leaves the majority of the microbial enzyme diversity untapped. Metagenomic approaches, in which the DNA from a microbial community is directly isolated and then used either for the creation of an expression library or for sequencing and metagenome annotation have alleviated this shortcoming to an extent, but have their own limitations: the generation of large expression libraries is time-consuming and their screening is costly, while metagenome annotation can infer biocatalytic function only from prior knowledge. We have thus developed a functional metaproteomic approach, which combines the immediacy of traditional activity screening with the comprehensiveness of a meta-omics approach. Briefly, the whole metaproteome of an environmental sample is separated on a 2-D gel, biocatalytically active proteins are visualized in-gel through zymography, and those candidate biocatalysts are then identified through mass spectrometry, searching against a metagenome-derived database obtained from the very same environmental sample. Here we explain the process in detail, with a focus on esterases, and give guidelines on how to develop a functional metaproteomic workflow for enzyme discovery.},
}
@article {pmid40288854,
year = {2025},
author = {Lorente-Arévalo, &#xc1; and Gimeno-Pérez, M and Ortega, C and Finnigan, J and Charnock, S and Hidalgo, A},
title = {Ultrahigh-throughput screening assay for PET-degrading enzymes.},
journal = {Methods in enzymology},
volume = {714},
number = {},
pages = {489-503},
doi = {10.1016/bs.mie.2025.01.021},
pmid = {40288854},
issn = {1557-7988},
abstract = {In recent years, several PET-degrading enzymes have been identified from both known microorganisms and metagenomic sources in response to the growing environmental issue of polyethylene terephthalate (PET) accumulation. Despite this progress, there is a limited number of (ultra)high-throughput screening methods for assessing PET-hydrolyzing activity without relying on surrogate substrates. This method utilizes the coupled activity of ketoreductases (KREDs) and diaphorase to produce a fluorescent compound (resorufin) in the presence of PET degradation products, offering a more direct and efficient screening approach. A metagenomic KRED was coupled with the diaphorase from Clostridium kluyveri to enable the detection of the hydrolysis of PET degradation products catalyzed by the Bacillus subtilis BS2 esterase. The coupled reaction was established in water-in-oil microdroplets, encapsulating a single E. coli cell per droplet, demonstrating its potential for use in the ultrahigh-throughput screening of metagenomic libraries or randomized libraries for directed evolution campaigns.},
}
@article {pmid40288852,
year = {2025},
author = {Ashcroft, E and Poma, M and Tischler, D and Munoz-Munoz, J},
title = {Mining metagenomes from extremophiles as a resource for novel glycoside hydrolases for industrial applications.},
journal = {Methods in enzymology},
volume = {714},
number = {},
pages = {45-60},
doi = {10.1016/bs.mie.2025.02.008},
pmid = {40288852},
issn = {1557-7988},
abstract = {The exploration of metagenomes from extremophiles has emerged as a promising approach for discovering novel glycoside hydrolases (GHs) with potential industrial applications. Extremophiles, which thrive in harsh conditions such as high salinity, extreme temperatures, and acidic or alkaline environments, produce enzymes naturally adapted to function under these conditions. This unique adaptability makes them highly desirable for industrial processes requiring robust and efficient biocatalysts. These biocatalysts reduce reliance on harsh chemicals and energy-intensive processes, contributing to greener industrial operations. This review underscores the power of metagenomics in bypassing the need to culture large libraries of extremophiles in the lab. High-throughput sequencing and bioinformatics enable the identification of novel GH-encoding genes directly from environmental DNA. While metagenomic mining has yielded promising results, challenges such as the expression of extremophile-derived genes in mesophilic hosts, low activity yields, and scalability remain. Advances in synthetic biology and protein engineering could address these bottlenecks, enabling more efficient utilization of GHs. Additionally, integrating machine learning for predictive functional annotation may accelerate the identification of high-value candidates.},
}
@article {pmid40288735,
year = {2025},
author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J},
title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121693},
doi = {10.1016/j.envres.2025.121693},
pmid = {40288735},
issn = {1096-0953},
abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.},
}
@article {pmid40288632,
year = {2025},
author = {Gao, Y and Cheng, Z and Huang, B and Mao, Y and Hu, J and Wang, S and Wang, Z and Wang, M and Huang, S and Han, M},
title = {Deciphering the profiles and hosts of antibiotic resistance genes and evaluating the risk assessment of general and non-general hospital wastewater by metagenomic sequencing.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126313},
doi = {10.1016/j.envpol.2025.126313},
pmid = {40288632},
issn = {1873-6424},
abstract = {Hospital wastewater (HWW) is a substantial environmental reservoir of antibiotic resistance genes (ARGs) and poses risks to public health and aquatic ecosystems. However, research on the diversity, transmission mechanisms, pathogenic hosts, and risks of ARGs in different HWW types is limited. This study involved the collection of HWW samples from 15 hospitals in Hefei, China, which were subsequently categorized as general hospitals (GHs) and non-general hospitals (NGHs). A 280.28-Gbp sequencing dataset was generated using a metagenomic sequencing strategy and analyzed using metagenomic assembly and binning approaches to highlight these issues in GHs and NGHs. Results showed significant differences between GHs and NGHs in ARG distribution, microbial community composition, and hosts of ARGs. Potential pathogens such as Rhodocyclaceae bacterium ICHIAU1 and Acidovorax caeni were more abundant in GHs. Furthermore, plasmid-mediated ARGs (45.21%) were more prevalent than chromosome-mediated ARGs (25.74%) in HWW, with a significantly higher proportion of plasmid-mediated ARGs in GHs compared to NGHs. The co-occurrence of ARGs and mobile genetic elements was more frequent in GHs. Additionally, the antibiotic resistome risk index was higher in GHs (38.73 ± 12.84) than NGHs (22.53 ± 11.80), indicating a greater risk of ARG transmission in GHs. This pioneering study provides valuable insights into the transmission mechanisms and hosts of ARGs in hospital settings, emphasizing the increased risk of ARG transmission in GHs.},
}
@article {pmid40288628,
year = {2025},
author = {Zhou, S and Li, Y and Yang, S and Lin, L and Deng, T and Gan, C and An, W and Xu, M},
title = {The role of electroactive biofilms in enhanced para-chlorophenol transformation collaborated with biosynthetic palladium nanoparticles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126312},
doi = {10.1016/j.envpol.2025.126312},
pmid = {40288628},
issn = {1873-6424},
abstract = {Bioremediation is a cost-effective strategy for decomposition of chlorinated organic contaminants, but its application is often hindered by the generation of toxic chlorinated byproducts. Though the design of functional biofilms, incorporating microbially-inspired catalytic materials, has emerged as a promising solution for tackling the byproducts issues, the microbial mechanisms driving these processes remain inadequately understood. This study demonstrates a hybrid electroactive biofilm (EAB)-palladium nanoparticles (Pd NPs) system that effectively separates the dechlorination and mineralization of para-chlorophenol (4-CP), and most importantly, it provides new insights into the microbial and genetic roles of EABs in this process. Under an applied potential of -0.6 V, Pd NPs via palladate reduction were biogenically synthesized and deposited on the cytomembranes within the biofilm, achieving an 82% decrease in 4-CP concentration within 48 hours. The ultra-performance liquid chromatogram and mass spectrum confirmed that 4-CP was initially dechlorinated to phenol by the biogenic Pd NPs before undergoing further degradation by the biofilm, effectively preventing toxic chlorinated byproducts. The Dechloromonas, Pseudomonas, and Geobacter were identified as predominant genera in the system and the metagenomics analysis noted increased relative abundance of ring-cleavage genes like pcaG, dmpB/xylE, and catA. Importantly, the abundance of dmpB/xylE was primarily associated with Dechloromonas and Pseudomonas, further highlighted that the dmpB/xylE-pathway was important for rapid 4-CP decomposition in the system. This study advances the understanding of EAB-Pd NPs synergy, showcasing an innovative and sustainable approach for the efficient removal of halogenated pollutants.},
}
@article {pmid40288249,
year = {2025},
author = {Wang, K and Ding, W and Yang, X and Lü, W and Ren, H and Jiang, X},
title = {The components and aromaticity of dissolved organic matter derived from aquatic plants determine the CO2 and CH4 emission potential.},
journal = {Water research},
volume = {281},
number = {},
pages = {123685},
doi = {10.1016/j.watres.2025.123685},
pmid = {40288249},
issn = {1879-2448},
abstract = {Lakes are integral to the carbon cycle through the processing of dissolved organic matter (DOM). However, the specific contributions of various aquatic plants to carbon emissions during their decomposition remain inadequately understood. In this study, decomposition experiments were performed on three aquatic plants-algae, Phragmites australis (PA), and Potamogeton crispus L. (PC)-using advanced techniques, including FT-ICR-MS and metagenomics, to investigate the mechanisms of carbon dioxide (CO2) and methane (CH4) emissions. The results indicate that algae exhibit a substantial potential for CO2 emissions, with emissions reaching up to 2193 μmol·g[-1]. Conversely, PA contributes the highest CH4 emissions, reaching up to 2397 μmol·g[-1]. Factors such as the protein-like content and aromaticity of DOM molecules significantly influence emission levels. DOM with lower aromaticity undergoes easier decomposition in the first 6 days, leading to increased CO2 production. Elevated C/N and C/P ratios in plants enhance the abundance of methanogenic bacteria and genes. Surplus carbon will be mineralized under anaerobic conditions, giving rise to mineralization of organics to CH4. These findings elucidate the mechanisms underlying CO2 and CH4 emissions during the decomposition of different aquatic plants and provide valuable insights for lake water environment management.},
}
@article {pmid40288073,
year = {2025},
author = {Song, Y and Baniakina, LFT and Jiang, L and Chai, L},
title = {Metagenomic insights into the alterations of gut microbial community in Bufo gargarizans tadpoles following lead exposure.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {55},
number = {},
pages = {101522},
doi = {10.1016/j.cbd.2025.101522},
pmid = {40288073},
issn = {1878-0407},
abstract = {Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of Bufo gargarizans tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 μg/L Pb group compared to the control group. Specifically, an increase in Bosea and Klebsiella was noted at 200 μg/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 μg/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 μg/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.},
}
@article {pmid40287860,
year = {2025},
author = {Li, Y and Liu, C and Wang, Y and Li, M and Zou, S and Hu, X and Chen, Z and Li, M and Ma, C and Obi, CJ and Zhou, X and Zou, Y and Tang, M},
title = {Urban wild bee well-being revealed by gut metagenome data: A mason bee model.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70051},
pmid = {40287860},
issn = {1744-7917},
support = {//Research Development Fund, Xi'an Jiaotong-Liverpool University/ ; //Summer Undergraduate Research Fellowship (SURF) Programme, Xi'an Jiaotong-Liverpool University/ ; },
abstract = {Wild bees are ecologically vital but increasingly threatened by anthropogenic activities, leading to uncertain survival and health outcomes in urban environments. The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors. Moving beyond bacteria, we propose a comprehensive analysis integrating diet, bacteriome, virome, resistome, and their association to understand the survival status of urban lives better. We conducted a study on mason bees (Osmia excavata) across 10 urban agricultural sites in Suzhou, China, using shotgun gut metagenome sequencing for data derived from total gut DNA. Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus, indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity. Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance. The gut bacterial community, dominated by Gammaproteobacteria, showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites. Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes, highlighting environmental threats to both bees and humans. The virome analysis identified honeybee pathogens, suggesting potential virus spillover. Many unknown bacteriophages were detected, some of which targeted the core gut bacteria, underscoring their role in maintaining gut homeostasis. These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats, thereby guiding probiotic development and city management for effective bee conservation.},
}
@article {pmid40287822,
year = {2025},
author = {Sun, C and Qin, Z and Liu, R and Guo, Y and Ge, Y and Du, Y},
title = {MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf340},
pmid = {40287822},
issn = {1362-4962},
support = {//University of Texas Systems STAR Program/ ; },
abstract = {Metagenomic Hi-C (metaHi-C) enables the reconstruction of microbial genome organization and interspecies interactions by capturing physical contacts between genomic fragments. However, raw metaHi-C data are often confounded by systematic biases and spurious contacts, which can obscure meaningful biological signals. Existing metaHi-C pipelines typically lack user-friendly normalization workflows and intuitive visualization tools, limiting the ability to explore microbial interaction networks. Here, we introduce MetaHiCNet, a web-based platform that supports widely used normalization methods with customizable parameters. MetaHiCNet provides a stepwise workflow for bias correction, spurious contact removal, and interactive visualization of microbial interactions. The platform supports multiple visualization modes, including taxonomic treemaps, cross-taxa networks, and cross-bin networks, enabling seamless transitions from community-wide overviews to detailed analyses of specific taxa or bins. This functionality facilitates the investigation of host-microbe interactions and the relationships between mobile genetic elements and their microbial hosts, offering deeper insights into microbial community structures and dynamics. MetaHiCNet is freely accessible at www.metahicnet.com without login.},
}
@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glycine max/microbiology/growth &amp; development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.<br><br>RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r&#x2009;= 0.5, p&#x2009;= 0.039) between microbial diversity and seed yield.<br><br>CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}
@article {pmid40287690,
year = {2025},
author = {Mohamed, FS and Jalal, D and Fadel, YM and El-Mashtoly, SF and Khaled, WZ and Sayed, AA and Ghazy, MA},
title = {Characterization and comparative profiling of piRNAs in serum biopsies of pediatric Wilms tumor patients.},
journal = {Cancer cell international},
volume = {25},
number = {1},
pages = {163},
pmid = {40287690},
issn = {1475-2867},
abstract = {Piwi-interacting RNAs (piRNAs) are small non-coding RNAs involved in transposon silencing and linked to cancer progression. However, their role in Wilms tumors (WT) remains unexplored. We conducted a thorough analysis and characterization of piRNAs in serum liquid biopsies of WT patients. Our study examined their expression patterns and functional annotations related to WT pathogenesis, as well as their clinical potential for diagnosis and monitoring. We identified 307 piRNAs expressed in WT serum samples, with 4% classified as repeat-related and 96% as non-repeat-related. The most abundant repeat-related piRNAs originated from LINEs retrotransposon, while tRNA-derived piRNAs were the most prevalent among non-repeat-related piRNAs. Furthermore, a distinct profile of 34 piRNAs showed significant differential expression in WT patients compared to healthy controls-22 downregulated and 12 upregulated. The target genes of differentially expressed piRNAs exhibited significant enrichment in biological pathways related to cytokine activity, inflammatory responses, TGF-beta signaling, p38 MAPK, and ErbB signaling. These genes are also involved in DNA damage response, DNA methylation, cell cycle regulation, as well as kidney development and function. Low expression levels of several piRNAs, especially piR-hsa-1,913,711, piR-hsa-28,190, piR-hsa-28,849, piR-hsa-28,848, and piR-hsa-28,318, showed significant diagnostic potential as non-invasive biomarkers for WT (AUC > 0.8, p < 0.05). Their expression levels also significantly correlated with adverse pathological features, including metastasis, anaplasia, and bilateral WT development. In conclusion, non-transposon-related piRNAs may serve as reliable biomarkers for WT and possess potential non-germline functions, particularly in regulating DNA methylation, cell growth, immune responses, and immune responses. Further studies are warranted to elucidate their functional significance.},
}
@article {pmid40287117,
year = {2025},
author = {Lu, W and Liu, Z and Song, Z and Wang, C and Yu, Z and Peng, S and Tian, Z and Lyu, A and Ning, Z},
title = {Vinegar-processed frankincense ameliorates ulcerative colitis by targeting BSH-active bacteria preference-mediated GDCA hydrolysis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119845},
doi = {10.1016/j.jep.2025.119845},
pmid = {40287117},
issn = {1872-7573},
abstract = {Frankincense, is extensively used in both traditional Chinese medicine (TCM) and Indian practices for the treatment of ulcerative colitis (UC). In TCM, it is typically subjected to process with vinegar, which is believed to enhance its therapeutic efficacy. However, the underlying mechanism has yet to be elucidated.<br><br>AIM OF THE STUDY: To elucidate the underlying mechanism of frankincense vinegar processing from the perspective of bile salt hydrolase (BSH)-active bacteria preference and glycodeoxycholic acid (GDCA) hydrolysis.<br><br>MATERIALS AND METHODS: Dextran sodium sulfate (DSS)-induced UC model was used to elucidate the superior improving effects of vinegar-processed frankincense (PF). 16S rRNA and metagenomic sequencing along with ultra-high performance liquid chromatography-triple quadrupole mass spectroscopy (UHPLC-TQ-MS) were employed to reveal the differential bacteria and its related disturbance of GDCA. The effects of PF and GDCA on BSH-active bacteria were confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) and in vitro experiments. Finally, the pro-inflammatory effects of GDCA and the mechanisms by which PF ameliorates UC were verified by establishing a UC pseudo-sterile mice model with GDCA intervention.<br><br>RESULTS: PF exhibited remarkable mitigating effects on UC (P<0.05 or P<0.01). Specifically, PF enhanced the BSH activity of Bifidobacterium longum and Lactobacillus acidophilus (P<0.01), thereby promoting their dissociation efficiency toward glycine-conjugated bile acids (G-CBAs), particularly GDCA (P<0.01). Furthermore, PF reduced GDCA levels by regulating the dissociation efficiency of Bifidobacterium longum and Lactobacillus acidophilus toward GDCA, thereby alleviating GDCA-induced exacerbation of UC.<br><br>CONCLUSION: PF exhibits its superior amelioration effects on UC by enhancing the dissociation efficiency of Bifidobacteruum longum and Lactobacillus acidophilus towards G-CBAs, particularly GDCA.},
}
@article {pmid40286758,
year = {2025},
author = {Gan, Y and Cui, J and Nie, A and Yang, Y and Zhao, X},
title = {Revealing the influence of Lacticaseibacillus paracasei C5 on the flavor formation of bread dough by metagenomics and flavouromics.},
journal = {International journal of food microbiology},
volume = {437},
number = {},
pages = {111220},
doi = {10.1016/j.ijfoodmicro.2025.111220},
pmid = {40286758},
issn = {1879-3460},
abstract = {This study investigated the impact of L. paracasei C5 on the generation of flavor compounds in bread through metagenomics and flavouromics. Metagenomic profiling revealed that L. paracasei C5 facilitated carbohydrate, amino acid, and lipid metabolism in the dough. Correlative analyses between specific microbial species and flavor compounds demonstrated a positive association between L. paracasei and key flavor compounds in bread, such as 2-nonenal,(E)-, 2-octenal,(E)-, benzeneacetaldehyde, and hexanoic acid, ethyl ester. A predictive network outlining the metabolic pathways responsible for L. paracasei C5 sourdough bread flavor compounds was established, elucidating the microbial annotation of pertinent genes and enzymes. The findings underscored the synergistic role of L. paracasei and S. cerevisiae in enhancing the activity of encoded enzymes involved in carbohydrate degradation, acetyl-CoA synthesis, succinate conversion, acyl-CoA production, transaminases, alcohol dehydrogenase, and carboxylesterases. These results offer novel insights into the mechanisms by which L. paracasei C5 augments bread flavor.},
}
@article {pmid40286682,
year = {2025},
author = {Xin, Y and Gao, Q and Zhang, S and Zhang, Z and Wang, J and Xia, X},
title = {Microbial regulatory mechanisms underlying methane emission in rivers with different land covers.},
journal = {Water research},
volume = {281},
number = {},
pages = {123680},
doi = {10.1016/j.watres.2025.123680},
pmid = {40286682},
issn = {1879-2448},
abstract = {Inland rivers play a crucial role in regulating the methane (CH4) budget via microbial carbon cycling. CH4 emissions vary significantly among rivers with different land covers, yet the regulatory mechanisms of CH4-cycling microorganisms across different land covers remain less understood. This study intergrates in-situ CH4 measurements with amplicon and metagenomic sequencing to investigate CH4-cycling microbial community composition and metabolic functions in regulating CH4 emissions across rivers with different land covers. Our results show that agricultural and urban rivers significantly increase riverine CH4 emission fluxes by 14 and 34 times than forest rivers, respectively. Urban and agricultural river sediments exhibited higher methanogenic abundance, but lower methanotrophic abundance than forest river sediments. Acetoclastic methanogens dominate the methanogenic communities of agricultural rivers, enhanced by high NO3[-] and DOC concentrations. Furthermore, methanogenic metagenome-assembled genomes (MAGs) recovered from agricultural rivers, which affiliated to Methanosarcina, carried the complete set of genes encoding for the enzymes in acetoclastic methanogenesis. In contrast, hydrogenotrophic methanogens drive CH4 production in urban rivers, favored by low DOC: NH4[+] ratios that enable methanogenesis independent of organic carbon. Lower CH4 emissions in agricultural rivers compared to urban rivers might be partly due to the greater sulfate-dependent anaerobic methane-oxidation. In forest rivers, type I methanotrophs outcompetes methanogens, aided by suitable sediment pH and larger sediment particle sizes, fostering oxic conditions that suppress CH4 emissions. This study reveals versatile microbial mechanisms underlying riverine CH4 emissions across land covers, enhancing understanding of microbial-mediated riverine CH4 cycling.},
}
@article {pmid40286059,
year = {2025},
author = {Men, C and Pan, Z and Liu, J and Miao, S and Yuan, X and Zhang, Y and Yang, N and Cheng, S and Li, Z and Zuo, J},
title = {Single and Combined Effects of Aged Polyethylene Microplastics and Cadmium on Nitrogen Species in Stormwater Filtration Systems: Perspectives from Treatment Efficiency, Key Microbial Communities, and Nitrogen Cycling Functional Genes.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {7},
pages = {},
doi = {10.3390/molecules30071464},
pmid = {40286059},
issn = {1420-3049},
support = {52400245//National Natural Science Foundation of China/ ; 2017ZX07103-007//National Key Research and Development Program of China/ ; 5221101156//National Natural Science Foundation of China/ ; },
mesh = {*Cadmium/chemistry ; *Microplastics/chemistry ; *Nitrogen Cycle/genetics/drug effects ; *Water Pollutants, Chemical ; *Nitrogen ; Filtration ; *Polyethylene/chemistry ; *Microbiota/drug effects ; Denitrification ; Water Purification/methods ; },
abstract = {Microplastics and heavy metal contamination frequently co-occur in stormwater filtration systems, where their interactions may potentially compromise nitrogen removal. Current research on microplastics and Cd contamination predominantly focuses on soils and constructed wetlands, with limited attention given to stormwater filtration systems. In this study, the single and synergistic effects of aged polyethylene microplastics (PE) and cadmium (Cd) contamination in stormwater infiltration systems were investigated from perspectives of nitrogen removal, microbial community structures, and predicted functional genes in nitrogen cycling. Results showed that PE single contamination demonstrated stronger inhibition on NO3[-]-N removal than Cd. Low-level PE contamination (PE content: 0.1% w/w) in Cd-contaminated systems showed stronger inhibitory effect than high-level PE contamination (PE content: 5% w/w). The mean NO3[-]-N removal efficiency under combined Cd50 (Cd concentration: 50 μg/L) and PE5 contamination during the sixth rainstorm event was 1.04 to 34.68 times that under other contamination scenarios. Metagenomic analysis identified keystone genera (Saccharimonadales, Enterobacter, Aeromonas, etc.), and critical nitrogen transformation pathways (nitrate reduction to ammonium, denitrification, nitrogen fixation, and nitrification) govern system performance. PE and Cd contamination effects were most pronounced on nitrification/denitrification enzymes beyond nitrite oxidase and nitrate reductase. These mechanistic findings advance our understanding of co-contaminant interactions in stormwater filtration systems.},
}
@article {pmid40285962,
year = {2025},
author = {Liao, J and Wei, JH and Liu, J and Ren, L and Zang, N and Liu, E},
title = {Respiratory virome in hospitalized children and analysis of its correlation with disease severity.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40285962},
issn = {1435-4373},
support = {Grant No. 82341111//The National Natural Science Foundation of China Special Project/ ; },
abstract = {PURPOSE: To investigate the composition of respiratory viromes and their association with disease severity among hospitalized pediatric patients.<br><br>METHODS: Clinical data and metagenomic next-generation sequencing (mNGS) results were collected from pediatric patients hospitalized at the Children's Hospital of Chongqing Medical University between January 2022 and September 2023. The analyzed specimens included sputum and bronchoalveolar lavage fluid (BALF).<br><br>RESULTS: The study included 229 patients (65.07% male, median age 3 years) with 25 sputum and 204 BALF samples, of whom 40.17% met the WHO criteria for severe acute respiratory infection (SARI). Herpesviruses were detected in 166 cases (72.49%), including 85 cases of cytomegalovirus (CMV), 64 cases of Epstein-Barr virus (EBV), 34 cases of human herpesvirus-7 (HHV-7), 12 cases of human herpesvirus-6 (HHV-6), and 6 cases of herpes simplex virus type 1 (HSV-1). Additionally, 53 cases of torque teno virus (TTV) and 7 cases of torque teno mini virus (TLMV) were detected. CMV prevalence was highest in neonates, while EBV peaked in the 3-6 year group (37.78%). HSV-1 and HHV-6 were predominantly identified in severe infections.<br><br>CONCLUSION: Herpesviruses, particularly CMV and EBV, were the most frequently detected viruses, followed by anelloviruses. The age-specific viral distribution patterns provide novel epidemiological perspectives for understanding pediatric respiratory pathogenesis, though their clinical significance requires validation through mechanistic studies.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40285778,
year = {2025},
author = {Alotaib, AS and Anwar, W and Albalawi, HQ and Albalawi, HS and Alshehri, MA and Al-Atawi, FM and Al Joundi, IT and Y Al Samini, A and Alqarni, RZ and Alzahrani, NE and Huraysi, MA},
title = {Metagenomic analysis microbial biodiversity of Trojena' the Mountains of Neom.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {71},
number = {4},
pages = {100-110},
doi = {10.14715/cmb/2025.71.4.13},
pmid = {40285778},
issn = {1165-158X},
mesh = {*Metagenomics/methods ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Saudi Arabia ; Soil Microbiology ; *Metagenome/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; },
abstract = {About 80% of the biosphere is constantly exposed to temperatures below 5 °C in cold environments. Microorganisms in cold environments can grow and decompose various organic compounds at sub-zero temperatures despite exposure to conditions that are harmful to their survival, such as sub-zero temperatures and low nutrient and water availability. The present study was designed to investigate metagenomic insights into the microbial diversity in (Al-Lawz Mountains / Trojena Mountains) Saudi Arabia. Metagenomic data sets are obtained by high-throughput sequencing of environmental soil samples and provide an aggregation of all the conceptually genetic materials of the intended area of this project. This study easily overcomes the bottlenecks associated with conventional molecular methods of retrieving genetic information and the unscientific shortage of microbial biodiversity research at Tabuk. High throughput bioinformatic analysis has been highlighted as the accurate exploration of the abundance and diversity of bacterial communities. Environmental DNA can be sequenced to identify the recent presence, relative abundance &amp; distribution of a prokaryotic species or whole communities of bacteria. A total of 333 bacterial metagenomes were sequenced over two seasons, fall and winter. The 16S rRNA genes were quantified during this period. The most significant species regarding the relative abundance and diversity were in the location of sample1 by, Klebsiella michiganensis (251), stenotrophomonass maltophilia (110), Escherichia coli USML2 (88), Zhongshania aliphaticivorans (40), Acidibrevibacterium fodinaquatile (12) Calothrix spp. &amp; Nibribacter ruber (10) Bacillus spp (10) respectively. On the other hand, the lowest abundances were in sample 4 location with Pseudomonas fluorescens (5) and Corynebacterium glutamicum (3) with (NA) species. This means these were unidentified yet. All these species have a growing demand for microbial biodiversity evaluations, given the pronounced impact of climate change in this region (Al-Lawz Mountains/Trojena Mountain). Benthic microbial communities are to be considered, given they have a potential role in CO2 and nitrogen fixation, which is related to plant growth-promoting properties. They can resist salinity, radiation, low-temperature adaptation, and biocontrol properties. Thus, eDNA cold-mountain biodiversity is a fraction of the time it costs to conduct conventional ecological monitoring.},
}
@article {pmid40285533,
year = {2025},
author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A},
title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70211},
doi = {10.1111/gcb.70211},
pmid = {40285533},
issn = {1365-2486},
support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; },
mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; },
abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.},
}
@article {pmid40285445,
year = {2025},
author = {Pérez Díaz, M and de Azevedo Gomes, AM and Quiroga Berdeal, MI and Bermúdez Pose, R},
title = {How to Dissect Zebrafish: A Standardized Sampling Protocol for Histological and Molecular Studies in Adult Zebrafish.},
journal = {Zebrafish},
volume = {},
number = {},
pages = {},
doi = {10.1089/zeb.2024.0184},
pmid = {40285445},
issn = {1557-8542},
abstract = {The zebrafish (Danio rerio) has become an essential model in fields such as developmental biology, toxicology, genetics, and regenerative medicine due to its low cost, small size, transparent embryos, and genetic similarity to humans. Nowadays, this model is increasingly recognized as a valuable tool in other fields, including veterinary medicine and animal production research, particularly aquaculture, due to its unique characteristics that make it suitable for studying economically significant diseases affecting production species. However, unlike established models such as mice, zebrafish lack standardized protocols for housing, feeding, anesthesia, and sample collection, which affects study reproducibility. In addition, it is a common practice to use whole zebrafish larvae or juveniles for metagenomic studies rather than analyzing individual organs, despite the fact that gene expression can vary between organs. This approach complicates the attribution of findings to specific biological processes. To address this, various authors proposed protocols for sample collection in larvae, juveniles, and adult zebrafish; however, comprehensive studies encompassing nearly all fish organs are scarce. Understanding zebrafish anatomy and the technical requirements of the study is essential for accurate sample collection. Some challenges present during zebrafish dissection include the small size of the fish, the fragility of their organs, and the faster onset of autolysis and heterolysis after the death of the animal. Using magnifying lenses, microdissection tools, and conducting dissections on cold surfaces can help mitigate these issues. This article aims to improve sample collection for histopathological and genetic studies in adult zebrafish by establishing a comprehensive, organized, and systematic dissection protocol that accounts for the anatomical specifics of this experimental model.},
}
@article {pmid40285000,
year = {2025},
author = {VanAcker, MC and Ergunay, K and Webala, PW and Kamau, M and Mutura, J and Lebunge, R and Ochola, GO and Bourke, BP and McDermott, EG and Achee, NL and Jiang, L and Grieco, JP and Keter, E and Musanga, A and Murray, S and Stabach, JA and Craft, ME and Fèvre, EM and Linton, YM and Hassell, J},
title = {A Novel Nobecovirus in an Epomophorus wahlbergi Bat from Nairobi, Kenya.},
journal = {Viruses},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/v17040557},
pmid = {40285000},
issn = {1999-4915},
support = {W81XWH-21-C-0001, W81XWH-22-C-0093 and HT9425-23-C-0059//United States Army Medical Research and Development Command/ ; George E. Burch Fellowship//Smithsonian Institution/ ; G1100783/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; CGIAR Trust Fund//CGIAR/ ; },
mesh = {Kenya ; *Chiroptera/virology ; Animals ; Phylogeny ; Genome, Viral ; Feces/virology ; *Coronaviridae/genetics/classification/isolation &amp; purification ; },
abstract = {Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species-Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)-in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa's most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.},
}
@article {pmid40284976,
year = {2025},
author = {Ibañez, JM and Zambrana, R and Carreras, P and Obregón, V and Irazoqui, JM and Vera, PA and Lattar, TE and Blanco Fernández, MD and Puebla, AF and Amadio, AF and Torres, C and López Lambertini, PM},
title = {Phylodynamic of Tomato Brown Rugose Fruit Virus and Tomato Chlorosis Virus, Two Emergent Viruses in Mixed Infections in Argentina.},
journal = {Viruses},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/v17040533},
pmid = {40284976},
issn = {1999-4915},
support = {INTA 2023-PEM-L01-I704//National Agricultural Technology Institute/ ; },
mesh = {Argentina ; *Solanum lycopersicum/virology ; *Plant Diseases/virology ; Genome, Viral ; Phylogeny ; *Crinivirus/genetics/classification/isolation &amp; purification ; Genetic Variation ; *Tobamovirus/genetics/classification/isolation &amp; purification ; Metagenomics ; Coinfection/virology ; Sewage/virology ; Evolution, Molecular ; },
abstract = {Tobamovirus fructirugosum (ToBRFV) and Crinivirus tomatichlorosis (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToCV from infected tomato plants and wastewater samples in Argentina to explore their global evolutionary dynamics. Additionally, it compared the genetic diversity of ToBRFV in plant tissue and sewage samples. Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. The analysis showed that ToBRFV exhibited higher genetic diversity in environmental samples than in plant samples. Phylodynamic analysis indicated that both viruses had a recent, single introduction in Argentina but predicted different times for ancestral diversification. The evolutionary analysis estimated that ToBRFV began its global diversification in June 2013 in Israel, with rapid diversification and exponential growth until 2020, after which the effective population size declined. Moreover, ToCV's global expansion was characterized by exponential growth from 1979 to 2010, with Turkey identified as the most probable location with the current data available. This study highlights how sequencing and monitoring plant viruses can enhance our understanding of their global spread and impact on agriculture.},
}
@article {pmid40284912,
year = {2025},
author = {Guo, M and Li, M and Liu, T and Sun, W and Du, K and Yang, S and Fu, Z and Kou, Z},
title = {Epidemiological and Genetic Characteristics of Sapovirus in Shandong, China, 2022-2023.},
journal = {Viruses},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/v17040469},
pmid = {40284912},
issn = {1999-4915},
support = {2021YFC2302003//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Sapovirus/genetics/classification/isolation &amp; purification ; China/epidemiology ; *Caliciviridae Infections/epidemiology/virology ; Child, Preschool ; Child ; Infant ; *Gastroenteritis/epidemiology/virology ; Male ; Female ; Adolescent ; Adult ; Phylogeny ; Middle Aged ; Young Adult ; Diarrhea/virology/epidemiology ; Genotype ; Prevalence ; Aged ; Genome, Viral ; Infant, Newborn ; Incidence ; Whole Genome Sequencing ; Feces/virology ; },
abstract = {Sapovirus (SaV) is a major pathogen responsible for acute gastroenteritis (AGE), and its incidence has been increasing in recent years. This study investigates the prevalence and the genetic characteristics of SaV in Shandong Province during 2022-2023, based on a surveillance network covering all age groups. Samples were obtained from a viral diarrhea surveillance network in Shandong Province during 2022-2023. SaVs were identified through quantitative reverse-transcription polymerase chain reaction (RT-qPCR). PCR amplification and Sanger sequencing were performed on positive samples, and whole-genome sequencing was conducted using metagenomic sequencing technology. Sequence analysis was conducted using BioEdit 7.0.9.0 and MEGA X, while statistical analysis was performed with SPSS 26.0. A total of 157 SaV-positive cases were identified, resulting in a positivity rate of 1.12%. The positivity rate for SaV was 0.75% in 2022 and it increased significantly to 1.42% in 2023. The highest positivity rates for both 2022 and 2023 were observed in November. The highest positivity rate was observed in the 3-5-year-old age group. In 2022, Dongying City had the highest positivity rate, while Zaozhuang City exhibited the highest rate in 2023. The incidence of vomiting in SaV-positive patients was significantly higher compared to SaV-negative patients (P = 0.002). Eight genotypes were identified in both the VP1 and RdRp regions. The complete genome sequence analysis of a GI.3 strain showed that NS1 (5.88%, 4/68) was the region most prone to amino acid variation, followed by VP2 (5.45%, 9/165) within the same genotype. SaV infections are more prevalent in cold weather, with young children being particularly susceptible. The SaV positivity rate in 2023 increased significantly accompanied by an increased diversity of genotypes, compared to that of 2022. The NS1 region exhibits the biggest variation within the same genotype, indicating that more attention should be paid to other regions besides VP1 in the future study. Ongoing surveillance of SaV is recommended for effective prevention and control.},
}
@article {pmid40284799,
year = {2025},
author = {Wang, Y and Cui, Q and Hou, Y and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Wang, W},
title = {Metagenomic Insights into the Diverse Antibiotic Resistome of Non-Migratory Corvidae Species on the Qinghai-Tibetan Plateau.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/vetsci12040297},
pmid = {40284799},
issn = {2306-7381},
support = {2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; },
abstract = {Antibiotic resistance represents a global health crisis with far-reaching implications, impacting multiple domains concurrently, including human health, animal health, and the natural environment. Wild birds were identified as carriers and disseminators of antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). A majority of studies in this area have concentrated on migratory birds as carriers for the spread of antibiotic resistance over long distances. However, there has been scant research on the resistome of non-migratory Corvidae species that heavily overlap with human activities, which limits our understanding of antibiotic resistance in these birds and hinders the development of effective management strategies. This study employed a metagenomics approach to examine the characteristics of ARGs and mobile genetic elements (MGEs) in five common Corvidae species inhabiting the Qinghai-Tibetan Plateau. The ARGs were classified into 20 major types and 567 subtypes. Notably, ARGs associated with multidrug resistance, including to macrolide-lincosamide-streptogramins, tetracyclines, beta-lactam, and bacitracin, were particularly abundant, with the subtypes acrB, bacA, macB, class C beta-lactamase, and tetA being especially prevalent. A total of 5 types of MGEs (166 subtypes) were identified across five groups of crows, and transposase genes, which indicated the presence of transposons, were identified as the most abundant type of MGEs. Moreover, some common opportunistic pathogens were identified as potential hosts for these ARGs and MGEs. Procrustes analysis and co-occurrence network analysis showed that the composition of the gut microbiota shaped the ARGs and MGEs, indicating a substantial association between these factors. The primary resistance mechanisms of ARGs in crows were identified as multidrug efflux pumps, alteration of antibiotic targets, and enzymatic inactivation. High-risk ARGs which were found to potentially pose significant risks to public health were also analyzed and resulted in the identification of 81 Rank I and 47 Rank II ARGs. Overall, our study offers a comprehensive characterization of the resistome in wild Corvidae species, enhancing our understanding of the potential public health risks associated with these birds.},
}
@article {pmid40284724,
year = {2025},
author = {Brinkerhoff, RJ and Pandian, J and Leber, M and Hauser, ID and Gaff, HD},
title = {Impacts of Tick Parasitism on the Rodent Gut Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040888},
pmid = {40284724},
issn = {2076-2607},
support = {5R01AI136035/GF/NIH HHS/United States ; },
abstract = {Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in treated versus control BALB/c mice. Whereas there is variation in the fecal microbiome associated with each of the host species we tested, some of the same microbial taxa, notably members of the family Muribaculaceae, occurred at higher relative abundance in tick-parasitized hosts in both the field and laboratory studies, suggesting that there are consistent impacts of tick parasitism on the host gut microbiome. We recommend future studies to test the hypothesis that epithelial cell secretions, generated as part of the host's immune response to tick parasitism, could provide resources that allow particular microbial lineages in the mammalian gut to flourish.},
}
@article {pmid40284718,
year = {2025},
author = {Wu, X and Liao, H and Zhang, X and Ma, Z and Fu, Z},
title = {Unraveling the Impact of Microplastic-Tetracycline Composite Pollution on the Moon Jellyfish Aurelia aurita: Insights from Its Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040882},
pmid = {40284718},
issn = {2076-2607},
support = {2022GXNSFBA035473//Natural Science Foundation of Guangxi Province China/ ; 2023A1515011859//Guangdong Natural Science Foundation of China/ ; 2021KJQD18//Guangxi&#xa0;Minzu&#xa0;University&#xa0;Research&#xa0;Fund/ ; },
abstract = {Microplastics have emerged as a pervasive marine contaminant, with extreme concentrations reported in deep-sea sediments (e.g., 1.9 million particles/m[2]) and localized accumulations near Antarctic research stations. Particular concern has been raised regarding their synergistic effects with co-occurring antibiotics, which may potentiate toxicity and facilitate antibiotic resistance gene dissemination through microbial colonization of plastic surfaces. To investigate these interactions, a 185-day controlled exposure experiment was conducted using Aurelia aurita polyps. Factorial combinations of microplastics (0, 0.1, 1 mg/L) and tetracycline (0, 0.5, 5 mg/L) were employed to simulate environmentally relevant pollution scenarios. Microbiome alterations were characterized using metagenomic approaches. Analysis revealed that while alpha and beta diversity measures remained unaffected at environmental concentrations, significant shifts occurred in the relative abundance of dominant bacterial taxa, including Pseudomonadota, Actinomycetota, and Mycoplasmatota. Metabolic pathway analysis demonstrated perturbations in key functional categories including cellular processes and environmental signal transduction. Furthermore, microplastic exposure was associated with modifications in polyp life-stage characteristics, suggesting potential implications for benthic-pelagic population dynamics. These findings provide evidence for the impacts of microplastic-antibiotic interactions on cnidarian holobionts, with ramifications for predicting jellyfish population responses in contaminated ecosystems.},
}
@article {pmid40284693,
year = {2025},
author = {Olivos-Caicedo, KY and Fernandez-Materan, FV and Daniel, SL and Anantharaman, K and Ridlon, JM and Alves, JMP},
title = {Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040857},
pmid = {40284693},
issn = {2076-2607},
support = {1R03AI147127-20A1/NH/NIH HHS/United States ; },
abstract = {Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of Clostridioides difficile infection. We determined the presence and absence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes among C. scindens strains and the features of the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the C. scindens cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.},
}
@article {pmid40284690,
year = {2025},
author = {Galanova, OO and Mitkin, NA and Danilova, AA and Pavshintsev, VV and Tsybizov, DA and Zakharenko, AM and Golokhvast, KS and Grigoryeva, TV and Markelova, MI and Vatlin, AA},
title = {Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040854},
pmid = {40284690},
issn = {2076-2607},
support = {202760-2-000//RUDN University Scientific Projects Grant System/ ; },
abstract = {Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species-Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.},
}
@article {pmid40284681,
year = {2025},
author = {Wang, X and Li, Y and Zuo, L and Li, P and Lou, H and Zhao, R},
title = {Revealing the Characteristics and Correlations Among Microbial Communities, Functional Genes, and Vital Metabolites Through Metagenomics in Henan Mung Bean Sour.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040845},
pmid = {40284681},
issn = {2076-2607},
support = {231100110300//the Major Science and Technology Project of Henan, China/ ; 221100110700//Major Science and Technology Project of Henan, China/ ; },
abstract = {Henan mung bean sour (HMBS) is the raw material for mung bean sour noodles (MBSNs), a traditional fermented food. To investigate the characteristic flavor compounds, we have detected the content of free amino acids (FAAs) and key metabolites including organic acids, sugars, and alcohols. The results revealed that the content associated with umami, sweetness, and bitterness (TVA > 1) showed significant differences. Metagenomic analysis indicated that Lactobacillus delbrueckii was the dominant and characteristic species in WJ and LY15, whereas Bifidobacterium mongoliense, Lactiplantibacillus plantarum, and Acetobacter indonesiensis were the dominant species in GY. The abundance of functional genes related to carbohydrate and amino acid metabolism was higher in WJ and LY15. There was a strong correlation between dominant genera and vital metabolites (r |>| 0.7). This study provides a theoretical foundation for the development of HMBS.},
}
@article {pmid40284671,
year = {2025},
author = {de Obeso Fernández Del Valle, A and Membrillo-Hernández, J},
title = {Metagenomics Analysis of the Microbial Consortium in Samples from Lake Xochimilco, a World Cultural Heritage Site.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040835},
pmid = {40284671},
issn = {2076-2607},
support = {1/CX/CSRD VA/United States ; },
abstract = {Since ancient times, the community of Xochimilco in the south of Mexico City has provided vegetables for the entire city. Today, Lake Xochimilco is listed as a UNESCO World Heritage Site because it is the last remaining bastion of Aztec culture and preserves the extraordinary ecological landscape of chinampas, a system of arable islands that has endured for over 1000 years. Here, we report on the microbiological communities currently existing in the lake. This is relevant since the water irrigates crops on the islands, known as chinampas. To achieve this, samples from the lake were collected at two different sites, and metagenomics analysis of the 16S gene was conducted. The results indicate the presence of five dominant bacterial phyla: Actinobacteria (44.5%), Proteobacteria (22.5%), Firmicutes (13%), Bacteroidota (6%), and Chloroflexi (4.6%). The most abundant families were Micrococcaceae, Intrasporangiaceae, and Rhodobacteraceae. The results correlate with current anthropogenic activity, indicating a moderate problem associated with contamination. Our findings suggest that immediate actions and increased awareness are necessary to preserve this cultural and natural heritage site and to take steps to comply with Sustainable Development Goal 11 (Sustainable Cities and Communities). Furthermore, this is the first report to characterize microbial communities in the water of Lake Xochimilco using 16S rRNA gene sequencing.},
}
@article {pmid40284644,
year = {2025},
author = {Xin, ZZ and Ma, K and Che, YZ and Dong, JL and Xu, YL and Zhang, XT and Li, XY and Zhang, JY},
title = {Differences in Microbial Community Structure Determine the Functional Specialization of Gut Segments of Ligia exotica.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040808},
pmid = {40284644},
issn = {2076-2607},
support = {CARS-47//the earmarked fund for the China Agriculture Research System/ ; ZR2022QC250//the Natural Science Foundation of Shandong Province/ ; 32173019//National Natural Science Foundation of China/ ; },
abstract = {Ligia feed on seashore algae and remove organic debris from the coastal zone, thereby playing an important role in the intertidal ecosystem. Nevertheless, the specific roles of distinct gut segments in the gut transit remain unclear. We collected and identified Ligia exotica specimens in the coast of Aoshanwei, Qingdao, Shandong Province, and analyzed their foreguts and hindguts for 16S rRNA, metagenomics, metabolomics, and proteomics. The concentrations of common metabolites, NO3[-]-N and NH4[+]-N, and the contents of C and N were measured. The gut transit decreased the abundances of the dominant phyla Cyanobacteria but increased Proteobacteria, Firmicutes, and Actinobacteria, and Planctomycetes and Bacteroidetes remained relatively constant. The foregut gut microbiota is involved in the carbohydrates and amino acids metabolism, as well as the decomposition of polysaccharides. The hindgut gut microbiota performs a variety of functions, including carbohydrate and amino acid metabolism, fermentation, cell motility, intracellular transport, secretion, and vesicular translocation, and the decomposition of polysaccharides, disaccharides, and oligosaccharides. The results of omics analyses and molecular experiments demonstrated that the metabolic processes involving amino acids and carbohydrates are more active in the foregut, whereas the fermentation, absorption, and assimilation processes are more active in the hindgut. Taken together, the differences in microbial community structure determine the functional specialization of different gut segments, i.e., the foregut appears to be the primary site for digesting food, while the hindgut further processes and absorbs nutrients and then excretes them.},
}
@article {pmid40284617,
year = {2025},
author = {Mohapatra, A and Trivedi, S and Tejpal, CS and Aware, MJ and Vaswani, S and Prajapati, VJ and Kolte, AP and Malik, PK and Sahoo, A and Ravishankar, CN and Bhatta, R},
title = {Effect of Two Selected Levels of Padina gymnospora Biowaste and Enteric Methane Emission, Nutrient Digestibility, and Rumen Metagenome in Growing Sheep.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040780},
pmid = {40284617},
issn = {2076-2607},
support = {Outreach Methane//Indian Council of Agricultural Research/ ; },
abstract = {A study was conducted on growing sheep to investigate the effect of two selected levels of biowaste of Padina gymnospora on feed intake, digestibility, daily enteric methane (CH4) emission, growth performance, and rumen metagenome. We randomly divided the 18 growing male sheep into three groups of six animals each. The animals were fed on a basal diet comprising finger millet straw (Eleusine coracana) and a concentrate mixture in a 35:65 ratio. The sheep in the control group (C) were offered a concentrate mixture without waste, whereas the wheat bran in the concentrate mixture in test group I (A2) and test group II (A5) was replaced (w/w) with the biowaste of Padina gymnospora at a level of 3.07 and 7.69%, respectively. The biowaste of Padina gymnospora at the above levels in concentrate constituted 2 and 5% of the diet. A significant decrease of 28.4% in daily enteric CH4 emission (g/d) was reported in the A5 group, whereas the difference in daily enteric CH4 emission between the C and A2 &amp; A2 and A5 groups did not prove significant. The inclusion of Padina gymnospora biowaste did not affect the nutrient intake and digestibility among the groups. The inclusion of Padina gymnospora biowaste in the A5 group resulted in a significant reduction (p = 0.0012) in daily CH4 emissions compared with group C; however, no significant differences were observed in daily CH4 emissions between groups C-A2 (p = 0.0793) and A2-A5 (p = 0.3269). Likewise, the adjustment of data to CH4 emissions per 100 g of organic matter intake indicated a substantial decrease in the A5 group relative to C. The energy loss in CH4 as a percentage of GE relative to group C decreased significantly (-23.4%) in the A5 group; however, this reduction was not associated with an increase in productivity, as almost similar average daily gain (p = 0.827) was observed in the groups. The replacement of wheat bran with the biowaste of Padina gymnospora significantly decreased the numbers of total protozoa and holotrichs in the A5 group. Irrespective of the group, the Bacteroidota was the single largest phylum in the rumen metagenome, representing >60% of the microbiota. However, the abundance of Bacteroidota was similar among the groups. The methanogenic phyla Euryarchaeota was the 5th most abundant; however, it constituted only 3.14% of the metagenome. The abundance of Desulfovibrio was significantly higher in the A5 group as compared with the control. In conclusion, the significant increase in the abundance of sulfate-reducing bacteria and reduction in protozoal numbers led to a significant reduction in CH4 emissions with the incorporation of biowaste of Padina gymnospora at a 5% level of the diet.},
}
@article {pmid40284605,
year = {2025},
author = {Xiao, C and Wan, K and Chen, Y and Jin, Y and Zhou, F and Yu, J and Chi, R},
title = {Metagenomic Analysis Revealed the Changes in Antibiotic Resistance Genes and Heavy Metal Resistance Genes in Phosphate Tailings Compost.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040768},
pmid = {40284605},
issn = {2076-2607},
abstract = {Phosphate tailings are usually rich in phosphorus and some other mineral nutrients, which is very suitable for composting. In this study, 60 days of composting using phosphate tailings, chicken manure, and straw resulted in a significant decrease in total nitrogen (TN) content from 1.75 ± 0.12 g/kg to 0.98 ± 0.23 g/kg (p < 0.01), with a nitrogen retention of 56%, an increase in water-soluble phosphorus (Ws-P) from 3.24 ± 0.14 mg/kg to 7.21 ± 0.09 mg/kg, and an increase in immediate potassium (AK) from 0.56 ± 0.21 mg/kg to 1.90 ± 0.11 mg/kg (p < 0.05). Metagenomic sequencing showed little changes in the diversity and abundance of microbial communities before and after composting, but changes in species composition and the abundance of archaea, bacteria, and fungi resulted in differences in community structure before and after composting. Composting contributed to a lower gene abundance of ARGs and MRGs. The addition of phosphate tailings combined the functions of chemical regulation and nutrient enrichment, and its synergistic effect significantly optimized the nutrient cycling in the composting system.},
}
@article {pmid40284601,
year = {2025},
author = {Song, Z and Zhang, T and Liang, Y and Mcminn, A and Wang, M and Jiao, N and Luo, T},
title = {Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040764},
pmid = {40284601},
issn = {2076-2607},
abstract = {Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 Synechococcus cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of Synechococcus. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance Synechococcus strains underdetected by in situ samples. In addition, 24 clades representing Synechococcus subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of Synechococcus in the coastal waters of Xiamen. Furthermore, the Synechococcus community displayed pronounced seasonal variations, and temperature significantly influenced the variations in Synechococcus community composition. Additionally, Synechococcus populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of Synechococcus.},
}
@article {pmid40284573,
year = {2025},
author = {Russell, G and Alegoz, R and Hester, K and Sierzega, KL and Szul, MJ and Hubert, N and Rylander, T and Jensen, S and Ciancio, MJ and Martinez-Guryn, K and Evans, CC},
title = {The Microbiome of an Outpatient Sports Medicine Clinic During a Global Pandemic: Effects of Implementation of a Microbiome-Specific Cleaning Program.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040737},
pmid = {40284573},
issn = {2076-2607},
support = {2018//Illinois Physical Therapy Association/ ; 2020//Illinois Physical Therapy Association/ ; },
abstract = {Outpatient healthcare facilities represent potential sources of healthcare-associated infections (HAIs). The purpose of this study was to survey high-contact surfaces in an outpatient physical therapy clinic, characterize the microbiome of those surfaces, and investigate the effects of a microbiome-specific cleaning and hygiene plan. Hand sanitizer containing a fluorescent probe used by patients and staff identified surface contact. High-contact surfaces were analyzed for bacterial DNA and SARS-CoV-2. A microbiome-specific cleaning and hygiene plan was developed based on initial analysis. After the implementation of the revised cleaning regimen, microbial community diversity and predicted metagenome content (PICRUSt) were employed for differential analysis. Patients had greater surface contact than staff. Ralstonia pickettii was the dominant species pre-cleaning, comprising 49.76% of the total, and observed on 79.5% of surfaces. The cleaning and hygiene plan significantly increased Shannon diversity, and R. pickettii decreased to 4.05% of total bacteria. SARS-CoV-2 was not observed on any surfaces. This study found ecological dominance by a single species in this outpatient clinic, suggesting a potential source of HAIs. However, a microbiome-specific cleaning strategy was successful in diversifying the microbiome and reducing ecological dominance. Additional research is needed to confirm these findings.},
}
@article {pmid40284568,
year = {2025},
author = {Ma, W and Han, Z and Liu, X and Cui, W and Zhen, D and Zhou, X and Song, Y and Jiang, S},
title = {Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040731},
pmid = {40284568},
issn = {2076-2607},
abstract = {The intestinal tract extends several times the length of bodies, with varying environmental conditions across different segments (small intestinal and large intestinal), thereby harboring distinct gut microbiota. Most studies focused on the quantitative responses of gut microbiota upon probiotics entering the gut, without an in-depth analysis of how the genetic change in local gut microbiota. Therefore, in this experiment, C57BL/6J male mice were once administered Lactiplantibacillus plantarum HNU082 (Lp082). Then, the mice were euthanized on the 1st, 3rd, and 7th days after gavage, and the contents of the small and large intestines of the mice were scraped for metagenomic analysis. Based on the characterization of large intestine and small intestine bacteria, changes in the diversity and abundance of single-nucleotide variants (SNVs) of microbiota were analyzed. There were observable distinct responses at the genetic level. A significant number of SNVs were identified in Ligilactobacillus murinus in the large intestine. These SNVs may impact the utilization of carbohydrates in L. murinus. Ingested probiotics traversed the entire gut and interacted with the indigenous microbiota, driving the evolution of the indigenous gut microbiota in the different intestinal segments, thereby influencing microbial growth and metabolism. This study investigates the role of probiotics in the evolution of gut microbiota. It offers new probiotic insights and a basis for targeted interventions.},
}
@article {pmid40284547,
year = {2025},
author = {Alzahrani, AJ and Al-Hebshi, BM and Yahia, ZA and Al-Judaibi, EA and Alsaadi, KH and Al-Judaibi, AA},
title = {Impact of Microbiota Diversity on Inflammatory Bowel Disease.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040710},
pmid = {40284547},
issn = {2076-2607},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition that includes two main types, Crohn's disease (CD) and ulcerative colitis (UC), involving inflammation of the gastrointestinal (GI) tract. The exact cause of IBD is unknown but could be a combination of genetic, environmental, and immune system factors. This study investigated the impact of IBD on microbiota diversity by evaluating the differences in microbial composition and the microbiota of a control group (A) of healthy individuals and a group (B) of IBD patients. Sixty biopsies were collected from participants recruited from hospitals in Makkah, Saudi Arabia. Biopsy specimens were taken during colonoscopy examination, and bacterial identification was performed by extracting ribosomal DNA from sigmoid colon biopsies using a DNeasy Blood &amp; Tissue Kit. Metagenomics and bioinformatics analyses were then conducted to analyze and compare the microbiota in the two groups. The results showed that the varieties of core microbiome species were 3.81% greater in the IBD patients than in the members of the control group. Furthermore, the differences between the groups were significantly greater than the variations within each group. Differences between the two groups were detected in the relative abundance of Clostridium nexile, Ruminococcus gnavus, Ruminococcus faecis, and Escherichia coli. These results indicate that microbiota could play a role in the pathogenesis of IBD and suggest that microbial diversity can serve as a biomarker for diagnosing the disease and monitoring its progression.},
}
@article {pmid40284188,
year = {2025},
author = {Bonomo, MG and D'Angelo, S and Picerno, V and Carriero, A and Salzano, G},
title = {Recent Advances in Gut Microbiota in Psoriatic Arthritis.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081323},
pmid = {40284188},
issn = {2072-6643},
mesh = {Humans ; *Arthritis, Psoriatic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.},
}
@article {pmid40284057,
year = {2025},
author = {Lan, W and Ding, H and Zhang, Z and Li, F and Feng, H and Guo, Q and Qin, F and Zhang, G and Xu, M and Xu, Y},
title = {Diversified Soil Types Differentially Regulated the Peanut (Arachis hydropoaea L.) Growth and Rhizosphere Bacterial Community Structure.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/plants14081169},
pmid = {40284057},
issn = {2223-7747},
support = {24-4-4-zrjj-132-jch//Natural Science Foundation of Qingdao/ ; CXGC2025D19//2025 Innovation Project of Shandong Academy of Agricultural Sciences/ ; ZR2024QC012//Natural Science Foundation of Shandong Province/ ; 110202201029(LS-13)//Major Science and Technology Project/ ; },
abstract = {Peanut (Arachis hydropoaea L.) demonstrates a prominent adaptability to diverse soil types. However, the specific effects of soil types on peanut growth and bacterial communities remain elusive. This study conducted a thorough examination of the agronomic traits, the corresponding physicochemical properties, and bacterial structure of rhizosphere soil in acidic (AT), neutral (NT), and saline-alkali (ST) soils, elucidating the internal relationship between soil type and peanut yield. Our results showed that different soil types exhibited significant differences in peanut yield, with ST demonstrating the lowest yield per plant, showing an 85.05% reduction compared to NT. Furthermore, available phosphorus content, urease, and invertase activities were substantially reduced in both ST and AT, particularly in ST by 95.35%, 38.57%, and 62.54%, respectively. Meanwhile, metagenomic sequencing unveiled a notable decline in Bradyrhizobium and Streptomyces in these soils, which is crucial for soil improvement. Further metabolic pathway analysis revealed that the reduction in pathways related to soil remediation, fertility improvement, and stress response in AT and ST may lead to slower peanut growth. In conclusion, peanuts cultivated in acidic and saline-alkali soils can increase yield via implementing soil management practices such as improving soil quality and refining micro-environments. Our study provides practical applications for enhancing peanut yield in low- to medium-yield fields.},
}
@article {pmid40283102,
year = {2025},
author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD},
title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/life15040547},
pmid = {40283102},
issn = {2075-1729},
support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; },
abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.},
}
@article {pmid40282815,
year = {2025},
author = {Lee, JH and Moon, H and Park, HR and Noh, JI and Kim, SS},
title = {Metagenomic Analysis of Raw Milk and the Inactivation of Foodborne Pathogens Using Ultraviolet-C.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081414},
pmid = {40282815},
issn = {2304-8158},
support = {WISET-2024-056//Ministry of Science and ICT/ ; },
abstract = {The purpose of this study was to identify the microbial community of raw milk samples before and after UV-C irradiation and to establish fundamental data on UV-C treatment to improve the safety and shelf life of raw milk. Metagenomic analysis revealed that Lactococcus spp., Lactobacillus spp., and Staphylococcus spp. were the dominant genera in raw milk, while Pseudomonas spp. became more prevalent after 14 days of refrigerated storage. The microorganisms in raw milk were isolated using selective media and identified as Serratia quinivorans 4364 and Latilactobacillus curvatus DSM 20019. To compare the UV resistance of these microorganisms, Pseudomonas aeruginosa, Staphylococcus aureus, Lactococcus lactis, and Latilactobacillus curvatus were inoculated into sterilized milk and subjected to UV-C treatment. The reduction rates of P. aeruginosa were significantly lower than those of the other strains (S. aureus, L. lactis, and L. curvatus). These findings provide insights into the microbial distribution in raw milk and the degree of resistance to UV treatment, which can serve as fundamental data for the pasteurization of raw milk.},
}
@article {pmid40282811,
year = {2025},
author = {Dong, K and Song, D and Li, S and Wang, X and Dai, L and Pei, X and Yang, X and Jiang, Y},
title = {Significance of Whole-Genome Sequencing for the Traceability of Foodborne Pathogens: During the Processing of Meat and Dairy Products.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081410},
pmid = {40282811},
issn = {2304-8158},
support = {No. 2023-JSGG-29//National Center of Technology Innovation for Dairy/ ; },
abstract = {The complexity of tracing foodborne pathogens in the food chain has increased significantly due to the long and complicated chain, the involvement of numerous links, and the presence of various types of pathogens at different stages and environments. Traditional typing techniques are not sufficient to meet the requirements of tracing pathogens in the food chain. Whole-Genome Sequencing (WGS) has gradually become an important technological tool for characterizing and tracing pathogens in the food chain due to comprehensive information, speed, and superior discriminatory power. This paper provides an overview of the advantages of WGS and its application in foodborne pathogen traceability. This paper focused on foodborne pathogen contamination pathways during the processing of animal foods in commercial restaurant kitchens and the potential contamination of milk, milk powder, and other dairy products by pathogens during processing in the dairy industry chain and environments. Improper handling practices during meat processing (i.e., using cloths, washing hands without soap, and cleaning boards with knives) were a critical point of foodborne pathogen cross-contamination in commercial kitchen premises. However, in dairy products, contamination of pathogens in raw milk was the main cause of foodborne disease outbreaks. Therefore, preventing the contamination of pathogens in food should not only be focused on hygiene measures during processing and in environments but also on the quality and hygiene of raw materials to prevent the spread of foodborne pathogens throughout the entire production chain. Further, Whole-Metagenome Sequencing and DNA sequence markers are considered to be the future direction of WGS. The purpose of this work is to promote the wider application of WGS during the processing of meat and dairy products and provide theoretical support for the rapid investigation and accurate traceability of foodborne pathogen outbreaks in food.},
}
@article {pmid40282779,
year = {2025},
author = {Nie, X and Chen, X and Lu, X and Yang, S and Wang, X and Liu, F and Yang, J and Guo, Y and Shi, H and Xu, H and Zhang, X and Fang, M and Tao, Y and Liu, C},
title = {Metagenomics Insights into the Role of Microbial Communities in Mycotoxin Accumulation During Maize Ripening and Storage.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081378},
pmid = {40282779},
issn = {2304-8158},
support = {No. 32060710//the National Natural Science Foundation of China/ ; },
abstract = {Mycotoxins are among the primary factors compromising food quality and safety. To investigate mycotoxin contamination, microbial diversity, and functional profiles in maize across distinct geographic regions, this study analyzed samples from Xuanwei, Fuyuan, and Zhanyi. Mycotoxin concentrations were quantified through standardized assays, while microbial community structures were characterized using metagenomics sequencing. Metabolic pathways, functional genes, and enzymatic activities were systematically annotated with the KEGG, eggNOG, and CAZy databases. The results demonstrated an absence of detectable aflatoxin (AF) levels. Deoxynivalenol (DON) concentrations varied significantly among experimental cohorts, although all values remained within regulatory thresholds. Zearalenone (ZEN) contamination exceeded permissible limits by 40%. The metagenomic profiling identified 85 phyla, 1219 classes, 277 orders, 590 families, 1171 genera, and 2130 species of microorganisms, including six mycotoxigenic fungal species. The abundance and diversity of microorganisms were similar among different treatment groups. Among 32,333 annotated KEGG pathways, primary metabolic processes predominated (43.99%), while glycoside hydrolases (GH) and glycosyltransferases (GT) constituted 76.67% of the 40,202 carbohydrate-active enzymes. These empirical findings establish a scientific framework for optimizing agronomic practices, harvest scheduling, and post-harvest management in maize cultivation.},
}
@article {pmid40282295,
year = {2025},
author = {Laguerre, H and Noël, C and Jégou, C and Fleury, Y and Le Chevalier, P},
title = {The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040430},
pmid = {40282295},
issn = {2079-7737},
abstract = {In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the same habitat in the Glénan Archipelago (Brittany, France) at different times for 2 years. The cœlomic microbiota were analyzed by targeted metagenomic with V4-16S metabarcoding and by a culturable approach with the isolation of strains and antimicrobial activity assays. Most of the OTUs of the cœlomic microbiota were affiliated with the phylum Proteobacteria and, notably, five orders: Burkholderiales, Flavobacteriales, Alteromonadales, Vibrionales and Pseudomonadales. Significant differences were observed regarding richness, biodiversity and composition between species and sampling dates. They could be explained by sub-abundant taxa that represented the global diversity. Cœlomic microbiota also revealed shared and unshared bacterial communities, validating a potential "specific" microbiota among the three Echinoderm species. Moreover, significant variations of the microbiota occurred among the sampling dates, suggesting a plasticity and, thus, a potential selection of these microbiota. Finally, out of the 831 bacterial strains isolated from culturable microbiota, 20 strains exhibited antibacterial activities, most of them assigned to the genera Shewanella, Pseudoalteromonas and Vibrio.},
}
@article {pmid40281970,
year = {2025},
author = {Khalid, N and Bukhari, SM and Ali, W and Sheikh, AA and Abdullah, HM and Nazmi, A},
title = {Probiotic Lactocaseibacillus casei NK1 Enhances Growth and Gut Microbiota in Avian Pathogenic Escherichia coli Challenged Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/ani15081136},
pmid = {40281970},
issn = {2076-2615},
abstract = {The present study was conducted to assess the efficacy of Laboratory-Isolated Lactocaseibacillus casei NK1 (Lc. NK1) in broilers hypothesizing that, Lc. NK1 supplementation will enhance growth performance, modulate the gut microbiome, and reduce fecal pathogenic Escherichia coli in broilers. The experiment spanned 35 days where 60 one-day-old broiler chicks were randomly assigned to four treatment groups (n = 15); control-group with no treatment (NC), APEC (challenged with E. coli only), CProb (received commercial probiotics), and LNK1 (treated with Lc. NK1). The APEC, CProb, and LNK1 groups were infected with E. coli O78 strain at 11 days of age. Growth performance analysis revealed that the LNK1 group by day 35 gained body weight similar to the CProb group, with both groups significantly outperforming the APEC group (p < 0.001). Both the LNK1 and CProp groups exhibited similar reduction in E. coli while increasing Lactobacillus colorizations in the cloacal swabs from day 21 to 35 of age (p > 0.05). Metagenomic analysis using 16S rRNA sequencing showed that the LNK1 group maintained a diverse and balanced gut microbiota, characterized by increased Firmicutes and reduced Proteobacteria. In contrast, the APEC group exhibited reduced diversity and dominance of Escherichia-Shigella (p < 0.001). These findings suggest Lc. NK1 could be a promising probiotic for enhancing gut health and growth performance in broilers, even under pathogenic challenges, offering a potential alternative to antibiotics in poultry production.},
}
@article {pmid40281939,
year = {2025},
author = {Hu, J and An, X and Yang, P and Tan, R and Chen, T and Chen, J and Tao, Y and Li, X and Sun, R and Zhang, S and Liu, S and Yang, L},
title = {Analysis of the Primary Pathogenic Bacteria in Abscess Disease of Musk Deer Using Metagenomic Approaches.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/ani15081105},
pmid = {40281939},
issn = {2076-2615},
support = {Grant No. 5242015//Beijing Municipal Natural Science Foundation/ ; 2024HXFWBH-LSQ-03//Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd/ ; 2024HXFWBH-LSQ-01//Huailai Zhiyangtianbao Technical development Co., Ltd/ ; },
abstract = {Abscesses are among the diseases affecting the survival of captive musk deer and are difficult to identify in their early stages. In this study, metagenomic sequencing, 16S rRNA sequencing, and paraffin sectioning were used to analyze the microbiota in the abscess musk deer pus group (AMP), abscess musk deer oral group (AMO), and healthy musk deer oral group (HMO) to compare the differences in microbiota in musk deer. By detecting differences in the oral microbiota through throat swabs, we aimed to monitor the early onset of abscess disease to facilitate timely intervention and treatment. The results showed that the alpha diversity of HMO microbiota was significantly higher than that of the AMP and AMO samples. Beta diversity results indicated that there were significant differences in the bacterial communities of HMO and AMO samples, and no significant difference was found between AMO and AMP samples. A taxonomic analysis of the bacterial species indicated that differences between HMO and AMP groups were found in the Fusobacterium and Trueperella species. Fusobacterium and Trueperella were the main pathogenic bacteria responsible for the occurrence of abscess diseases in forest musk deer in this study. Furthermore, the appearance of Fusobacterium and Trueperella in the oral cavity can serve as biomarkers for the early diagnosis of abscess disease in musk deer.},
}
@article {pmid40280794,
year = {2025},
author = {Ruppé, E and Lazarevic, V and Schrenzel, J},
title = {9th International Conference on Clinical Metagenomics (ICCMg9): meeting report.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.03.012},
pmid = {40280794},
issn = {1878-4380},
}
@article {pmid40280386,
year = {2025},
author = {An, X and Zhao, R and Wang, L and Xiao, X and Xu, Z and Zhang, S and Xie, D and Xiao, Y and Zhang, Q},
title = {Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121688},
doi = {10.1016/j.envres.2025.121688},
pmid = {40280386},
issn = {1096-0953},
abstract = {Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated. Metagenomic analysis showed that Thiobacillus (77.73 %) were the primary degraders for the efficient degradation of thiocyanate. A total of 27 genes related to thiocyanate biodegradation were identified, including SCNase, COSase, sulfur oxidation, denitrification and carbon fixation. Metaproteomic revealed the high expression of chemotaxis protein and thioredoxin enhances cellular oxidative stress and maintains normal physiological metabolism. Additionally, the differentially expressed proteins were primarily involved in metabolic pathways including sphingolipid metabolism, energy metabolism, oxidative phosphorylation, two-component system and amino acid metabolism. Then the lipid, organic acid and amino acid metabolism were up-regulated by metabolomic analysis, thereby achieving the degradation of thiocyanate. Using a combination of qRT-PCR and parallel reaction monitoring (PRM), 27 key genes involved in thiocyanate biodegradation have been identified, providing a theoretical basis for developing microbial strategies to mitigate thiocyanate pollution. Molecular docking deepens the understanding of the interaction between degrading enzyme and thiocyanate. This study provides a theoretical basis for the microbial remediation of thiocyanate-containing wastewater.},
}
@article {pmid40280272,
year = {2025},
author = {Bačnik, K and Kranjc, L and Botella, L and Maguire, I and Pavić, D and Patoka, J and Dragičević, P and Bláha, M and Bielen, A and Kouba, A and Kutnjak, D and Hudina, S},
title = {Crayfish pet trade as a pathway for the introduction of known and novel viruses.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108345},
doi = {10.1016/j.jip.2025.108345},
pmid = {40280272},
issn = {1096-0805},
abstract = {Expanding international pet trade has emerged as one of the main introduction pathways of aquatic invasive species, with ornamental crayfish species commonly available on the EU and global markets. Besides most frequently studied crayfish pathogens, such as Aphanomyces astaci and white spot syndrome virus (WSSV), ornamental crayfish carry associated microbial communities, which may potentially lead to the emergence of known or even novel diseases following intentional or unintentional release of animals into the wild. This is especially problematic in the case of viruses, which represent an important, yet considerably understudied, group of crayfish pathogens. Here we analyzed viromes of hepatopancreas tissue of four crayfish species acquired in the international pet trade in Europe (Procambarus clarkii, Procambarus alleni, Cherax holthuisi, and Cherax quadricarinatus) using a high throughput sequencing based metagenomic approach. Seven different known viruses were identified, which were previously either directly associated with crayfish (WSSV, Cherax quadricarinatus reovirus, chequa iflavirus, athtab bunya-like virus) or with hosts from subphylum Crustacea or invertebrates associated with freshwater environment (Shahe ispoda virus 5, Dicistroviridae sp.). Additional sequences represented 8 potential novel and divergent RNA viruses, most similar to sequences belonging to members of Picornavirales, Elliovirales, Reovirales, Hepelivirales, Tolivirales and Ghabrivirales orders. We discuss our findings in relation to their phylogenetic relationships, geographical origins, and putative pathogenicity implications. The results highlight the need for further research into the risks related to disease emergence associated with the pet trade.},
}
@article {pmid40280009,
year = {2025},
author = {Gao, FZ and Hu, LX and Liu, YS and Yang, HY and He, LY and Bai, H and Liu, F and Jin, XW and Ying, GG},
title = {Unveiling the prevalence of metal resistance genes and their associations with antibiotic resistance genes in heavy metal-contaminated rivers.},
journal = {Water research},
volume = {281},
number = {},
pages = {123699},
doi = {10.1016/j.watres.2025.123699},
pmid = {40280009},
issn = {1879-2448},
abstract = {Heavy metals can drive antibiotic resistance through co-selection mechanisms. Current knowledge predominantly focuses on relationships between metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) at the river reach scale. It remains unclear the links between MRGs and ARGs at the large river basin scale, as does the role of MRG-ARG colocalization in resistance dissemination. This study employed metagenomics to investigate the prevalence of MRGs in the Xiangjiang River, a historically heavy metal-contaminated river, and their connections with ARGs by combining resistome profiling with colocalization analyses. Results revealed the significant prevalence of MRGs in the river compared to nationwide rivers, but it showed weak correlations with metal concentrations in either water or sediment. The prevalence of MRGs in water was weakly driven by abiotic parameters, but was strongly influenced by microbial composition. The proportion of water MRGs attributable to sewage sources was tightly positively correlated with MRG abundances, suggesting the significant contribution of external waste input. Plasmid-originated MRGs were more abundant in water, while chromosomal MRGs dominated in sediment, indicating medium-specific transfer dynamics. The profile of MRGs were strongly correlated with that of ARGs in both media, encompassing several clinically high-risk ARGs. However, MRG-ARG colocalization events were rarely detected (eight instances in total), consistent with low frequencies in nationwide rivers (3.5 % in sediment; 2.0 % in water), implying their limited roles in resistance dissemination. Overall, the findings enhance our understanding of riverine metal resistome and its associations with antibiotic resistome, while emphasize the rare presence of MRG-ARG colocalization in riverine environments.},
}
@article {pmid40280002,
year = {2025},
author = {Liu, X and Yang, Y and Graham, NJD and Takizawa, S and Ng, HY},
title = {Deciphering membrane biofouling induced by micro-/nano-plastics in nanofiltration: Metagenomic insights and spacer-driven mitigations.},
journal = {Water research},
volume = {281},
number = {},
pages = {123682},
doi = {10.1016/j.watres.2025.123682},
pmid = {40280002},
issn = {1879-2448},
abstract = {Nanofiltration (NF) is an effective process for micro-/nano-plastics (MNPs) interception, but the impact of accumulated MNPs on the microbial community structure and metabolic pathways of biofilms on NF membranes remains unclear. This provides uncertainty with respect to membrane biofouling behavior and the risks to efficient NF operations. In this study, the size-dependent (20 nm-25 μm) and concentration-dependent (0.1-50 mg·L[-1]) effects of MNPs on the biofouling of a NF membrane treating secondary wastewater effluent were studied. Three MNPs-tolerant, hypermetabolic and polystyrene-degradable genera (i.e., Acinetobacter, Novosphingobium and Asticcacaulis) were detected in biofilms as dominant taxonomic compositions. MNPs led to an increase of 19.3 %-76.7 % in biomass contents and a more rapid decrease in permeate flux, with 0.1 mg·L[-1] of 80 nm NPs causing the most severe membrane biofouling. Metagenomic analysis revealed that MNPs upregulated enzymes involved in exopolysaccharide (ExoA/L/M/P/Q/X/Y/Z) and tyrosine (COMT, FeaB and AOC3) biosynthesis and quorum sensing (PhzF and CiaH/R), and suppressed cell motility pathways including flagellar assembly and bacterial chemotaxis. Novel types of perforated column spacer (PCS) enhanced the hydrodynamics of the membrane feed with a lower pressure drop and higher fluid velocity, introduced micro-jets and greater mass transfer inside feed channels, thus eliminating the deposition of MNPs and mitigating membrane biofouling. Overall, a greater understanding of the interaction mechanisms between MNPs and membrane biofouling in secondary effluent filtration will help develop more effective MNPs management strategies and achieve more sustainable NF operations.},
}
@article {pmid40279015,
year = {2025},
author = {Han, X and Ma, P and Liu, C and Yao, C and Yi, Y and Du, Z and Liu, P and Zhang, M and Xu, J and Meng, X and Liu, Z and Wang, W and Ren, R and Xie, L and Han, X and Xiao, K},
title = {Pathogenic profiles and lower respiratory tract microbiota in severe pneumonia patients using metagenomic next-generation sequencing.},
journal = {Advanced biotechnology},
volume = {3},
number = {2},
pages = {13},
pmid = {40279015},
issn = {2948-2801},
support = {82100096//National Science Foundation/ ; },
abstract = {INTRODUCTION: The homeostatic balance of the lung microbiota is important for the maintenance of normal physiological function of the lung, but its role in pathological processes such as severe pneumonia is poorly understood.<br><br>METHODS: We screened 34 patients with community-acquired pneumonia (CAP) and 12 patients with hospital-acquired pneumonia (HAP), all of whom were admitted to the respiratory intensive care unit. Clinical samples, including bronchoalveolar lavage fluid (BALF), sputum, peripheral blood, and tissue specimens, were collected along with traditional microbiological test results, routine clinical test data, and clinical treatment information. The pathogenic spectrum of lower respiratory tract pathogens in critically ill respiratory patients was characterized through metagenomic next-generation sequencing (mNGS). Additionally, we analyzed the composition of the commensal microbiota and its correlation with clinical characteristics.<br><br>RESULTS: The sensitivity of the mNGS test for pathogens was 92.2% and the specificity 71.4% compared with the clinical diagnosis of the patients. Using mNGS, we detected more fungi and viruses in the lower respiratory tract of CAP-onset severe pneumonia patients, whereas bacterial species were predominant in HAP-onset patients. On the other hand, using mNGS data, commensal microorganisms such as Fusobacterium yohimbe were observed in the lower respiratory tract of patients with HAP rather than those with CAP, and most of these commensal microorganisms were associated with hospitalization or the staying time in ICU, and were significantly and positively correlated with the total length of stay.<br><br>CONCLUSION: mNGS can be used to effectively identify pathogenic pathogens or lower respiratory microbiome associated with pulmonary infectious diseases, playing a crucial role in the early and accurate diagnosis of these conditions. Based on the findings of this study, it is possible that a novel set of biomarkers and predictive models could be developed in the future to efficiently identify the cause and prognosis of patients with severe pneumonia.},
}
@article {pmid40278577,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Tian, F and Shi, H and Wei, S and Li, X and Li, X and Gao, Y and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {A Multi-Omics Study of Neurodamage Induced by Growth-Stage Real-Time Air Pollution Exposure in Mice via the Microbiome-Gut-Brain Axis.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278577},
issn = {2305-6304},
support = {82203988//National Natural Science Foundation of China/ ; 2022A1515010695//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515010465//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A04J2071//Science and Technology Program of Guangzhou/ ; 23qnpy107//the Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
abstract = {Air pollution has been widely recognized as a risk factor for neurological disorders, and the gut microbiome may play a mediating role. However, current evidence remains limited. In this study, a mouse model was employed with continuous exposure to real-time air pollution from conception to late adolescence. Effects of growth-stage air pollution exposure on the gut microbiome, host metabolites, and brain tissue were assessed. Pathological damage in the hippocampus and cortex was observed. Fecal metagenomic sequencing revealed alterations in both compositions and functions of the gut microbiome. Metabolic disturbances in unsaturated fatty acids and glycerophospholipids were identified in the intestine, serum, and brain tissues, with significant changes in metabolites (e.g., gamma-linolenic acid, alpha-linolenic acid, docosahexaenoic acid (DHA), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and phosphatidylserine (PS). Serum levels of the pro-inflammatory mediator leukotriene C4 were also elevated. Correlation analysis identified a group of different gut microbiome species that were associated with host metabolites. Furthermore, mediation analysis showed that intestinal and serum metabolites mediated the associations between the key gut microbiome and brain microbiome. These findings indicate that the metabolic crosstalk in the gut-brain axis mediates the neuronal damage in mice induced by growth-stage air pollution exposure, potentially through pathways involving lipid metabolism and inflammation.},
}
@article {pmid40278377,
year = {2025},
author = {Xiong, S},
title = {Gut-Microbiota-Driven Lipid Metabolism: Mechanisms and Applications in Swine Production.},
journal = {Metabolites},
volume = {15},
number = {4},
pages = {},
pmid = {40278377},
issn = {2218-1989},
support = {32272831//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: The gut microbiota plays a pivotal role in host physiology through metabolite production, with lipids serving as essential biomolecules for cellular structure, metabolism, and signaling. This review aims to elucidate the interactions between gut microbiota and lipid metabolism and their implications for enhancing swine production. Methods: We systematically analyzed current literature on microbial lipid metabolism, focusing on mechanistic studies on microbiota-lipid interactions, key regulatory pathways in microbial lipid metabolism, and multi-omics evidence (metagenomic/metabolomic) from swine models. Results: This review outlines the structural and functional roles of lipids in bacterial membranes and examines the influence of gut microbiota on the metabolism of key lipid classes, including cholesterol, bile acids, choline, sphingolipids, and fatty acids. Additionally, we explore the potential applications of microbial lipid metabolism in enhancing swine production performance. Conclusions: Our analysis establishes a scientific framework for microbiota-based strategies to optimize lipid metabolism. The findings highlight potential interventions to improve livestock productivity through targeted manipulation of gut microbial communities.},
}
@article {pmid40278299,
year = {2025},
author = {Wu, K and Xu, G and Tian, Y and Li, G and Yi, Z and Tang, X},
title = {Synthesis and Evaluation of Aquatic Antimicrobial Peptides Derived from Marine Metagenomes Using a High-Throughput Screening Approach.},
journal = {Marine drugs},
volume = {23},
number = {4},
pages = {},
pmid = {40278299},
issn = {1660-3397},
support = {2021J02015//Fujian Provincial Natural Science Foundation of China/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; K240301(1)//Xiamen Ocean Research and Development Institute/ ; },
mesh = {Animals ; High-Throughput Screening Assays/methods ; *Antimicrobial Peptides/pharmacology/chemical synthesis/chemistry ; *Metagenome ; Penaeidae ; *Anti-Bacterial Agents/pharmacology/chemistry ; Aquaculture ; Aquatic Organisms ; Microbial Sensitivity Tests ; *Antimicrobial Cationic Peptides/pharmacology ; Machine Learning ; },
abstract = {Bacterial diseases cause high mortality and considerable losses in aquaculture. The rapid expansion of intensive aquaculture has further increased the risk of large-scale outbreaks. However, the emergence of drug-resistant bacteria, food safety concerns, and environmental regulations have severely limited the availability of antimicrobial. Compared to traditional antibiotics, antimicrobial peptides (AMPs) offer broad spectrum activity, physicochemical stability, and lower resistance development. However, their low natural yield and high extraction costs along with the time-consuming and expensive nature of traditional drug discovery, pose a challenge. In this study, we applied a machine-learning macro-model to predict AMPs from three macrogenomes in the water column of South American white shrimp aquaculture ponds. The AMP content per megabase in the traditional earthen pond (TC1) was 1.8 times higher than in the biofloc pond (ZA1) and 63% higher than in the elevated pond (ZP11). A total of 1033 potential AMPs were predicted, including 6 anionic linear peptides, 616 cationic linear peptides, and 411 cationic cysteine-containing peptides. After screening based on structural, and physio-chemical properties, we selected 10 candidate peptides. Using a rapid high-throughput cell-free protein expression system, we identified nine peptides with antimicrobial activity against aquatic pathogens. Three were further validated through chemical synthesis. The three antimicrobial peptides (K-5, K-58, K-61) showed some inhibitory effects on all four pathogenic bacteria. The MIC of K-5 against Vibrio alginolyticus was 25 μM, the cell viability of the three peptides was higher than 70% at low concentrations (≤12.5 μM), and the hemolysis rate of K-5 and K-58 was lower than 5% at 200 μM. This study highlights the benefits of machine learning in AMP discovery, demonstrates the potential of cell-free protein synthesis systems for peptide screening, and provides an efficient method for high-throughput AMP identification for aquatic applications.},
}
@article {pmid40278100,
year = {2025},
author = {El Jaddaoui, I and Sehli, S and Al Idrissi, N and Bakri, Y and Belyamani, L and Ghazal, H},
title = {The Gut Mycobiome for Precision Medicine.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
pmid = {40278100},
issn = {2309-608X},
abstract = {The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.},
}
@article {pmid40278085,
year = {2025},
author = {Guo, MC and Wu, BC and Luo, CY and Sa, W and Wang, L and Li, ZH and Shang, QH},
title = {The Effects of Fungal Pathogen Infestation on Soil Microbial Communities for Morchella sextelata Cultivation on the Qinghai-Xizang Plateau.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040264},
pmid = {40278085},
issn = {2309-608X},
support = {2023-NK-134//Key R &amp; D and Transformation Projects of Science and Technology Department of Qinghai Province/ ; },
abstract = {Fungi infestation as a disease has serious impacts on the cultivation of Morchella species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating Morchella sextelata, we sampled soil samples of Morchella cultivars in the Qinghai-Xizang Platea and used metagenome sequencing technology to identify the disease fungi and analyze the differences in microbial diversity and structure between disease-infested and healthy soils. The disease fungi identified were Tricharina gilva and Peziza lohjaoensis, and the microbial diversity of T. gilva-infected soil was higher than that of healthy soil, while the diversity of P. lohjaoensis-infected soil was lower. Interestingly, whether infected with T. gilva or P. lohjaoensis, the soil microbial community was changed, and the dominant phyla and genera were different in different soil samples. When infected with P. lohjaoensis, the dominant phyla with relatively high abundances included Proteobacteria, Bacteroidetes, and Ascomycota, with average relative abundances of 44%, 18%, and 15%, respectively, and the dominant genera with high relative abundances encompassed Pseudomonadaceae, Terfezia, and Pedobacter, with average relative abundances of 8%, 9%, and 5%, respectively. Following infection with T. gilva, the dominant phyla with higher relative abundances were Proteobacteria, Acidobacteria, and Bacteroidetes, with average relative abundances of 46%, 15%, and 12%, respectively, and the dominant genera with high relative abundances included Hydrogenophaga, Sphingomonas, and Polaromonas, with average relative abundances of 9%, 3%, and 2%, respectively. Additionally, we found that lipid-metabolism-related genes were less abundant in the soil infected with P. lohjaoensis than in the other soil samples, and glycoside hydrolase diversity was lower in the soil infected with T. gilva than in other healthy soils. The results showed that the effects of different disease fungi on soil microbial communities and functional genes were different, which provided a theoretical basis for the sustainable cultivation of Morchella.},
}
@article {pmid40278081,
year = {2025},
author = {Wicaksono, S and Ngokwe, ZB and McCullough, M and Yap, T},
title = {The Role of Oral Yeasts in the Development and Progression of Oral Squamous Cell Carcinoma: A Scoping Review.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040260},
pmid = {40278081},
issn = {2309-608X},
support = {202403220801271//Lembaga Pengelola Dana Pendidikan/ ; },
abstract = {The role of oral yeasts in oral squamous cell carcinoma (OSCC) has gained attention due to evidence linking fungal dysbiosis to carcinogenesis. While Candida albicans has been the primary focus, emerging studies highlight the importance of non-Candida species yeast genera. This scoping review synthesises the evidence on the role of oral yeasts, including Candida spp. and non-Candida species, in the development and progression of OSCC. A PRISMA-ScR-guided search was conducted in Medline, Embase, EBM Reviews, and CINAHL. Observational and experimental studies involving humans with OSCC, oral potentially malignant disorders (OPMDs), or oral epithelial dysplasia (OED) were included. This review analysed 75 studies. Research on oral yeast in OSCC has progressed since the 1970s, with advancements in identification techniques-from conventional culture methods to metagenomic sequencing and multi-omics approaches-alongside improved animal and cellular models of OSCC. These methodological advancements have identified notable distinctions in the oral mycobiome between carcinomatous and healthy states. Clinical findings reinforce the hypothesis that oral yeasts, particularly Candida spp., actively contribute to the dysplasia-carcinoma sequence. Emerging evidence suggests that oral yeasts may significantly modulate events contributing to OSCC progression. However, further mechanistic studies and robust clinical evidence are essential to establish causality and clarify their role in OSCC.},
}
@article {pmid40278065,
year = {2025},
author = {Li, XZ and Li, YL and Zhu, JS},
title = {Three-Dimensional Structural Heteromorphs of Mating-Type Proteins in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungal Complex.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040244},
pmid = {40278065},
issn = {2309-608X},
support = {2021-SF-A4//the Major Science and Technology Projects of Qinghai Province, China/ ; LHZX-2022-01//the Joint Science Project of the Chinese Academy of Sciences, Qinghai Provincial Government, and Sanjiangyuan National Park/ ; QHCY-2023-057//Qinghai Province of China/ ; 2024-NK-P67//Qinghai Province Science and Technology Commissioner Special Project/ ; },
abstract = {The MAT1-1-1 and MAT1-2-1 proteins are essential for the sexual reproduction of Ophiocordyceps sinensis. Although Hirsutella sinensis has been postulated to be the sole anamorph of O. sinensis and to undergo self-fertilization under homothallism or pseudohomothallism, little is known about the three-dimensional (3D) structures of the mating proteins in the natural Cordyceps sinensis insect-fungal complex, which is a valuable therapeutic agent in traditional Chinese medicine. However, the alternative splicing and differential occurrence and translation of the MAT1-1-1 and MAT1-2-1 genes have been revealed in H. sinensis, negating the self-fertilization hypothesis but rather suggesting the occurrence of self-sterility under heterothallic or hybrid outcrossing. In this study, the MAT1-1-1 and MAT1-2-1 proteins in 173 H. sinensis strains and wild-type C. sinensis isolates were clustered into six and five clades in the Bayesian clustering trees and belonged to 24 and 21 diverse AlphaFold-predicted 3D structural morphs, respectively. Over three-quarters of the strains/isolates contained either MAT1-1-1 or MAT1-2-1 proteins but not both. The diversity of the heteromorphic 3D structures of the mating proteins suggested functional alterations of the proteins and provided additional evidence supporting the self-sterility hypothesis under heterothallism and hybridization for H. sinensis, Genotype #1 of the 17 genome-independent O. sinensis genotypes. The heteromorphic stereostructures and mutations of the MAT1-1-1 and MAT1-2-1 proteins in the wild-type C. sinensis isolates and natural C. sinensis insect-fungi complex suggest that there are various sources of the mating proteins produced by two or more cooccurring heterospecific fungal species in natural C. sinensis that have been discovered in mycobiotic, molecular, metagenomic, and metatranscriptomic studies, which may inspire future studies on the biochemistry of mating and pheromone receptor proteins and the reproductive physiology of O. sinensis.},
}
@article {pmid40277368,
year = {2025},
author = {Martins, DT and Alegria, OVC and Dantas, CWD and De Los Santos, EFF and Pontes, PRM and Cavalcante, RBL and Ramos, RTJ},
title = {CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0147024},
doi = {10.1128/aem.01470-24},
pmid = {40277368},
issn = {1098-5336},
abstract = {UNLABELLED: Viruses are the most abundant biological entities in all ecosystems of the world. Their ubiquity makes them suitable candidates for indicating fecal contamination in rivers. Recently, a group of Bacteroidetes bacteriophages named CrAssphages, which are highly abundant, sensitive, and specific to human feces, were studied as potential viral biomarkers for human fecal pollution in water bodies. In this study, we evaluated the presence, diversity, and abundance of viruses with a focus on crAssphages via metagenomic analysis in an Amazonian river and conducted correlation analyses on the basis of physicochemical and georeferencing data. Several significant differences in viral alpha diversity indexes were observed among the sample points, suggesting an accumulation of viral organisms in the river mouth, whereas beta diversity analysis revealed a significant divergence between replicates of the most downstream point (IT4) when compared to the rest of the samples, possibly due to increased human impact at this point. In terms of the presence of crAssphage, the analysis identified 61 crAssphage contigs distributed along the Itacaiúnas River. Moreover, our analysis revealed significant correlations between 19 crAssphage contigs and human population density, substantiating the use of these viruses as possible markers for human fecal pollution in the Itacaiúnas River. This study is the first to assess the presence of crAssphages in an Amazonian river, with results suggesting the potential use of these viruses as markers for human fecal pollution in the Amazon.<br><br>IMPORTANCE: The Amazon biome is one of the most diverse ecosystems in the world and contains the most vast river network; however, the continuous advance of urban centers toward aquatic bodies exacerbates the discharge of pollutants into these water bodies. Fecal contamination contributes significantly to water pollution, and the application of an improved fecal indicator is essential for evaluating water quality. In this study, we evaluated the presence, diversity, and abundance of crAssphages in an Amazonian river and performed correlation analysis on the basis of physicochemical and georeferencing data to test whether crAssphages are viable fecal pollution markers. Our analysis revealed both the presence of crAssphages and their correlation with physicochemical data and showed significant correlations between the relative abundance of crAssphages and human density. These results suggest the potential use of these viruses as markers for water quality assessment in Amazonian rivers.},
}
@article {pmid40276513,
year = {2025},
author = {Xu, X and Li, Y and Huang, X},
title = {Case Report: A rare case of community-acquired Roseomonas mucosa sepsis that presented with persistently normal host-response biomarkers.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1521161},
pmid = {40276513},
issn = {1664-3224},
mesh = {Humans ; Female ; Middle Aged ; Biomarkers/blood ; *Gram-Negative Bacterial Infections/diagnosis/microbiology/drug therapy ; *Community-Acquired Infections/microbiology/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Methylobacteriaceae ; *Sepsis/microbiology/diagnosis/drug therapy ; Meropenem/therapeutic use ; },
abstract = {Community-acquired Roseomonas mucosa sepsis can lead to significant morbidity and mortality if not diagnosed promptly. We report a case of a 59-year-old woman with community-acquired Roseomonas mucosa sepsis who presented with persistent fever progressing to septic shock, despite repeatedly negative host-response biomarker results. Initial metagenomic analysis of peripheral blood suggested Pseudomonas aeruginosa infection. However, a peripheral blood culture identified Roseomonas mucosa as the causative pathogen. She was cured after switching to meropenem according to blood cultures and antimicrobial susceptibility testing.},
}
@article {pmid40276369,
year = {2025},
author = {Boshuizen, B and De Maré, L and Oosterlinck, M and Van Immerseel, F and Eeckhaut, V and De Meeus, C and Devisscher, L and Vidal Moreno de Vega, C and Willems, M and De Oliveira, JE and Hosotani, G and Gansemans, Y and Meese, T and Van Nieuwerburgh, F and Deforce, D and Vanderperren, K and Verdegaal, EL and Delesalle, C},
title = {Aleurone supplementation enhances the metabolic benefits of training in Standardbred mares: impacts on glucose-insulin dynamics and gut microbiome composition.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1565005},
pmid = {40276369},
issn = {1664-042X},
abstract = {INTRODUCTION: Aleurone, derived from the bran layer of grains like wheat and barley, has demonstrated positive effects on energy metabolism in pigs, mice, and untrained horses, influencing glucose-insulin dynamics and gut microbiome composition. Training itself enhances insulin sensitivity in horses, similar to the improvements in performance capacity observed in human athletes. This study aimed to investigate whether aleurone supplementation provides additional benefits to training by modulating insulin metabolism and gut microbiota in Standardbred mares.<br><br>METHODS: Sixteen Standardbred mares (aged 3-5 years) participated in a cross-over study with two 8-week training periods separated by 8 weeks of detraining. Each horse received either 200 g/day aleurone supplementation or a control diet. Insulin metabolism was evaluated using oral (OGTT) and intravenous (FSIGTT) glucose tolerance tests, measuring parameters such as Maximumglucose, AUCglucose, Maximuminsulin, AUCinsulin, Time to peakinsulin (OGTT), Acute Insulin Response to Glucose (AIRg), glucose effectiveness (Sg), and disposition index (DI) (FSIGTT). Fecal samples underwent metagenomic analysis to assess alpha and beta diversity and microbial composition.<br><br>RESULTS: Training alone: Training significantly improved OGTT parameters by decreasing Maximuminsulin (P = 0.005) and AUCinsulin (P = 0.001), while increasing Time to peakinsulin (P = 0.03), indicating enhanced insulin sensitivity. FSIGTT results also showed a decrease in logAIRg (P = 0.044). Training with Aleurone: Aleurone supplementation further reduced FSIGTT AIRg (P = 0.030), logAIRg (P = 0.021) while increasing glucose effectiveness (Sg; P = 0.031). These findings suggest aleurone improves insulin sensitivity, glucose disposal, and fasting glucose regulation beyond training. Microbiome analysis revealed training decreased Pseudomonas, associated with dysbiosis, while aleurone reduced inflammation-associated Desulfovibrio. Beta diversity metrics showed no significant changes.<br><br>CONCLUSION: Aleurone supplementation enhances training-induced improvements in glucose metabolism and fecal microbiota composition, which could offer potential benefits for equine athletes by optimizing metabolic flexibility. It also supports improvements in glucose and insulin dynamics, particularly by further enhancing insulin sensitivity and glucose-mediated disposal. Future studies should investigate the mechanisms of aleurone at the muscle and gut level and explore its potential applications for metabolic disorders such as Equine Metabolic Syndrome.},
}
@article {pmid40275546,
year = {2025},
author = {Jungpraditphol, I and Sutthiboonyapan, P and Khamwachirapitak, C and Krasaesin, A and Srithanyarat, S and Porntaveetus, T and Wiriyakijja, P},
title = {Shotgun Metagenomics of Biofilm Microbiome in Oral Lichen Planus With Desquamative Gingivitis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15349},
pmid = {40275546},
issn = {1601-0825},
support = {68-032,68-059//Health Systems Research Institute/ ; HEA_FF_68_008_3200_001,HEA_FF_68_223_3200_015//Thailand Science Research and Innovation Chulalongkorn University/ ; DRF68_007//Faculty of Dentistry, Chulalongkorn University/ ; },
abstract = {INTRODUCTION: Oral lichen planus (OLP) is a chronic inflammatory condition often associated with desquamative gingivitis (DG). The oral microbiome's role in OLP and DG (OLP-DG) is gaining recognition, but prior 16S rRNA studies lacked taxonomic resolution. This study introduced shotgun metagenomic sequencing to thoroughly compare the supragingival and subgingival plaque microbiomes of individuals with and without OLP-DG.<br><br>METHODS: Twenty-seven participants (9 OLP-DG, 18 non-OLP) were recruited. Supra- and subgingival plaque samples were collected separately. Genomic DNA was analyzed using shotgun metagenomic sequencing. Microbial abundance and diversity were assessed through bioinformatic and statistical analyses.<br><br>RESULTS: We observed significant changes in the supragingival and subgingival microbiomes in OLP-DG. Supragingival plaque showed reduced Corynebacteriaceae and Porphyromonadaceae, with enrichment of an unnamed Synergistaceae genus and three unnamed species (Candidatus Saccharibacteria bacterium oral taxon 955 and 488 and GGB10852_SGB17523). Subgingival plaque revealed increased Flavobacteriaceae and Rhodocyclaceae, and reduced Actinomycetaceae. Although alpha or beta diversity was not significantly different, common commensals like Corynebacterium matruchotii and Streptococcus mitis were less abundant in OLP-DG patients.<br><br>CONCLUSION: This first-time application of metagenomic sequencing revealed a distinct microbiome in OLP-DG, characterized by novel bacterial species and reduced commensals, suggesting a potential role in OLP-DG pathogenesis, and warranting further study.},
}
@article {pmid40275408,
year = {2025},
author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K},
title = {Unveiling plasmid diversity and functionality in pristine groundwater.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {42},
pmid = {40275408},
issn = {2524-6372},
abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).<br><br>RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.<br><br>CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.},
}
@article {pmid40275402,
year = {2025},
author = {Maaskant, A and Lee, D and Ngo, H and Montijn, RC and Bakker, J and Langermans, JAM and Levin, E},
title = {AI for rapid identification of major butyrate-producing bacteria in rhesus macaques (Macaca mulatta).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {39},
pmid = {40275402},
issn = {2524-4671},
abstract = {BACKGROUND: The gut microbiome plays a crucial role in health and disease, influencing digestion, metabolism, and immune function. Traditional microbiome analysis methods are often expensive, time-consuming, and require specialized expertise, limiting their practical application in clinical settings. Evolving artificial intelligence (AI) technologies present opportunities for developing alternative methods. However, the lack of transparency in these technologies limits the ability of clinicians to incorporate AI-driven diagnostic tools into their healthcare systems. The aim of this study was to investigate an AI approach that rapidly predicts different bacterial genera and bacterial groups, specifically butyrate producers, from digital images of fecal smears of rhesus macaques (Macaca mulatta). In addition, to improve transparency, we employed explainability analysis to uncover the image features influencing the model's predictions.<br><br>RESULTS: By integrating fecal image data with corresponding metagenomic sequencing information, the deep learning (DL) and machine learning (ML) algorithms successfully predicted 16 individual bacterial genera (area under the curve (AUC)&#x2009;>&#x2009;0.7) among the 50 most abundant genera in rhesus macaques (Macaca mulatta). The model was successful in predicting functional groups, major butyrate producers (AUC 0.75) and a mixed group including fermenters and short-chain fatty acid (SCFA) producers (AUC 0.81). For both models of butyrate producers and mixed fermenters, the explainability experiments revealed no decline in the AUC when random noise was added to the images. Increased blurring led to a gradual decline in the AUC. The model's performance was robust against the impact of fecal shape from smearing, with a stable AUC maintained until patch 4 for all groups, as assessed through scrambling. No significant correlation was detected between the prediction probabilities and the total fecal weight used in the smear; r&#x2009;=&#x2009;0.30&#x2009;&#xb1;&#x2009;0.3 (p&#x2009;>&#x2009;0.1) and r&#x2009;=&#x2009;0.04&#x2009;&#xb1;&#x2009;0.36 (p&#x2009;>&#x2009;0.8) for the butyrate producers and mixed fermenters, respectively.<br><br>CONCLUSION: Our approach demonstrated the ability to predict a wide range of clinically relevant microbial genera and microbial groups in the gut microbiome based on digital images from a fecal smear. The models proved to be robust to the smearing method, random noise and the amount of fecal matter. This study introduces a rapid, non-invasive, and cost-effective method for microbiome profiling, with potential applications in veterinary diagnostics.},
}
@article {pmid40275259,
year = {2025},
author = {He, H and Cai, L and Xue, X and Zhang, K and Huang, Q and Qiu, A and Fan, H and Lin, Y and Xu, B and Pan, W},
title = {Disseminated talaromycosis in HIV-negative patients with lung cancer: a rare case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {601},
pmid = {40275259},
issn = {1471-2334},
support = {2024SSY06041//Jiangxi Key Laboratory of oncology/ ; JDLCZDZK-PWH//the National Natural Science Foundation of China/ ; SHDC22022302//the Clinical Research Plan of SHDC/ ; 2023YJBF-FH03, 2020YCGPZ-102//the Clinical Research Project of Second Affiliated Hospital of Naval Medical University/ ; 2023ZD005//2023 Key Project for Science and Technology Innovation of Jiangxi Provincial Health Commission/ ; 2024DZXYYXK-104//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; Male ; *Lung Neoplasms/complications/microbiology ; Talaromyces/isolation &amp; purification ; Fatal Outcome ; *Mycoses/complications/microbiology/diagnosis/drug therapy ; Middle Aged ; Antifungal Agents/therapeutic use ; *Carcinoma, Squamous Cell/complications ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Talaromycosis has long been considered to be exclusively associated with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). In recent years, with effective control measures for HIV, the number of talaromycosis patients without HIV infection has been increasing annually. All of these patients have various immunosuppressive factors, including tumors. However, we find that talaromycosis among HIV-negative lung cancer patients remains a rarity and is without comprehensive reviews, contributing to significant gaps in clinical knowledge.<br><br>CASE PRESENTATION: We report a case of lung squamous cell carcinoma combined with Talaromyces marneffei (T.marneffei) infection in an HIV-negative patient. The patient, a male with a history of long-term smoking, presented with recurrent fever and cough. Chest computed tomography (CT) scans revealed pleural effusion and nodules. The patient was diagnosed with lung squamous cell carcinoma and talaromycosis through sputum cytology and blood/cerebrospinal fluid metagenomics next-generation sequencing (mNGS). The patient underwent only antifungal therapy and succumbed to respiratory failure, liver and kidney failure, and sepsis in January 2024, before receiving any anti-tumor therapy.<br><br>CONCLUSION: The mortality rate of talaromycosis combined with lung cancer is extremely high. Therefore, regardless of whether patients have a history of travel to endemic areas of T. marneffei infection, it is crucial to test for HIV and anti-IFN-&#x3b3; autoantibodies (AIGA) in patients suspected of having a pulmonary fungal infection, as well as conducting multiple cultures of specimens from different sites and utilizing mNGS to enhance diagnostic accuracy. Additionally, it is essential to perform biopsies in various methods from multiple sites to ascertain the presence of lung cancer. With effective control of T. marneffei infection and timely diagnosis and treatment of lung cancer, there can be a significant improvement in patient survival rates.},
}
@article {pmid40274091,
year = {2025},
author = {Huo, X and He, M and Qiao, J and Zhao, J and Yang, B},
title = {Regulatory effects of nano-carbon on poplar growth and rhizosphere soil organic carbon accumulation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121628},
doi = {10.1016/j.envres.2025.121628},
pmid = {40274091},
issn = {1096-0953},
abstract = {The positive effects of nano-carbon on plant growth and soil C sequestration within the rhizosphere have been widely recognized. Nevertheless, information is seriously deficient in understanding the underlying mechanisms based on microbial communities and carbon cycle functional genes. Here, metagenomic sequencing was employed to explore different responses of poplar seedling growth and organic carbon fractions to nano-carbon fertilizers at concentrations of 0 ml/kg (CK), 5 ml/kg (NC-5), 10 ml/kg (NC-10) and 20 ml/kg (NC-20). We observed that, after 120 days of nano-carbon fertilizers treatments, the growth indexes (height and biomass) of poplar were significantly increased by 53-173 %, and C fractions in the rhizosphere soil were significantly increased by 1.6-8.2 % with the NC-5 treatment having a greater impact on organic carbon components than the NC-10 and NC-20 treatments. Compared to CK, the additions of nano-carbon fertilizers significantly increased the content of total nitrogen (TN), nitrate nitrogen (NN), and available potassium (AK) in the rhizosphere soil and decreased the pH, and improved stochastic processes in microbial communities, which elevates the abundance of microbes involved in carbon fixation (e.g., Proteobacteria, Actinobacteria) and carbon-cycling genes. In addition, network complexity and stability of microbes were significantly enhanced by nano-carbon treatments. Structural equation model indicated that microbial community assembly processes directly alter rhizosphere SOC accumulation. Carbon functional genes influenced by microbial structure have positive effects on biomass of poplar and SOC contents. Our observations provide key evidence for evaluating how nano-carbon fertilizers may influence functional changes in C cycle that are mediated by microbial synergy.},
}
@article {pmid40273857,
year = {2025},
author = {Yu, H and Zhang, D and Xiong, R and Liu, S and Hu, R and Chen, P and Wu, X and Zou, H and Hu, N and Ding, D and Yan, Q and He, Z},
title = {Soil-dependent responses of bacterial communities, phosphorus and carbon turnover to uranium stress in different soil ecosystems.},
journal = {Journal of hazardous materials},
volume = {493},
number = {},
pages = {138383},
doi = {10.1016/j.jhazmat.2025.138383},
pmid = {40273857},
issn = {1873-3336},
abstract = {Uranium (U) can impact microbially driven soil phosphorus (P) and carbon (C) cycling. However, the response of microbial P and C turnover to U in different soils is not well understood. Through the quantitative assay of P pools and soil organic C (SOC) quantitative assay and sequencing of 16S rRNA gene amplicons and metagenomes, we investigated the effect of U on P and C biotransformation in grassland (GL), paddy soil (PY), forest soil (FT). U (60 mg kg[-1]) impacted the diversity, interaction and stability of soil bacterial communities, leading to a decrease in available P (AP). Under U stress, organophosphate mineralization substantially contributed to the AP in GL and FT, whereas intracellular P metabolism dominated the AP in PY. Also, the reductive citrate cycle (rTCA cycle) promoted the content of SOC in GL, while the rTCA cycle and complex organic C degradation pathways enhanced the SOC in PY and FT, respectively. Notably, functional bacteria carrying organic C degradation genes could decompose SOC to enhance soil AP. Bacteria developed various resistance strategies to cope with U stress. This study reveals soil-dependent response of microbial P and C cycling and its ecological functions under the influence of radioactive contaminants in different soil systems.},
}
@article {pmid40273693,
year = {2025},
author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH},
title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123627},
doi = {10.1016/j.watres.2025.123627},
pmid = {40273693},
issn = {1879-2448},
abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.},
}
@article {pmid40273602,
year = {2025},
author = {Hu, C and Lu, JN and Chen, Z and Tian, L and Yin, Y and Jiang, G and Fei, YH and Tang, YT and Wang, S and Jin, C and Qiu, R and Chao, Y},
title = {Viral diversity and auxiliary metabolic genes in rare earth element mine drainage in South China.},
journal = {Water research},
volume = {281},
number = {},
pages = {123666},
doi = {10.1016/j.watres.2025.123666},
pmid = {40273602},
issn = {1879-2448},
abstract = {In extreme environments, viruses play a crucial role in regulating the structure and metabolic activities of microbial communities, thereby impacting the overall biogeochemical cycles. Previous research found that rare earth element acid mine drainage (REE-AMD) harbors a wide array of microbial species. However, our understanding of the viruses that infect these microorganisms remains limited. In this study, we utilized metagenomic analysis to explore the viral diversity, interactions between viruses and their hosts, as well as the viruses encoded auxiliary metabolic genes (AMGs) within REE-AMD. The results demonstrated that viral communities showed increased diversity with REEs pollution. Furthermore, AMGs exhibited habitat and host specificity. Viruses in water samples contaminated with REEs tended to encode AMGs related to cellular metabolic processes and stress responses to protect their hosts. In contrast, viruses in sediment samples were more likely to encode AMGs associated with nutrient competition, thereby expanding the ecological niches of hosts and viruses. Viruses would carry more AMGs from the dominant prokaryotes. Additionally, under REEs stress, viruses encode a greater number of carbon- and sulfur-related AMGs, influencing the carbon and sulfur cycles of microorganisms in REE-AMD. Overall, our study provides a first systematic characterization of the viral community in REE-AMD, which is crucial for understanding the intricate interactions among viruses, their hosts, and the surrounding environment.},
}
@article {pmid40273394,
year = {2025},
author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH},
title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.},
journal = {Neurology},
volume = {104},
number = {10},
pages = {e213592},
doi = {10.1212/WNL.0000000000213592},
pmid = {40273394},
issn = {1526-632X},
abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.<br><br>METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.<br><br>RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.<br><br>DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.},
}
@article {pmid40272442,
year = {2025},
author = {Diao, Z and Zhao, Z and Han, Y and Chen, Y and Huang, T and Feng, L and Ma, Y and Li, J and Zhang, R},
title = {A Comprehensive Assessment of Metagenomic cfDNA Sequencing for Microbe Detection.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf044},
pmid = {40272442},
issn = {1530-8561},
support = {2024-2-40510//Capital's Funds for Health Improvement and Research/ ; 2022YFC2603800//National Key R&amp;D Program of China/ ; },
abstract = {BACKGROUND: Metagenomic cell-free DNA (cfDNA) sequencing provides a new avenue for diagnosing infectious diseases. Owing to the low concentration and highly fragmented nature of microbial cfDNA in plasma, coupled with methodological complexity, ensuring accurate and comparable metagenomic cfDNA sequencing results has proved challenging. This study aims to evaluate the performance of metagenomic cfDNA sequencing for detecting microorganisms in plasma across various laboratories and to examine factors affecting accuracy.<br><br>METHODS: A reference panel consisting of 18 microbial cfDNA communities was designed and used to investigate the performance of metagenomic cfDNA sequencing across 130 laboratories. We comprehensively assessed the accuracy, repeatability, anti-interference, limit of detection (LoD), and linear correlation.<br><br>RESULTS: The results showed that the performance of most laboratories was excellent, with an average F1 score of 0.98. Most contamination in metagenomic cfDNA sequencing originated from "wet labs," as 68.25% (475/696) of the false-positive sequences matched reported microorganisms. The chief cause (74.24%, 49/66) of false-negative errors in metagenomic cfDNA sequencing was from "dry labs." Laboratories showed favorable reproducibility, LoD, and linearity. Interference from elevated human cfDNA concentrations was minimal, whereas interference from genetically similar microorganisms was more pronounced. Overall, viral cfDNA detection showed weaker performance compared to bacterial and fungal detection.<br><br>CONCLUSIONS: This study presented the performance of metagenomic cfDNA sequencing in real-world settings, identifying key factors critical for its development and optimization. These findings provide valuable guidance for accurate pathogen detection in infectious diseases and promote the adoption of metagenomic cfDNA sequencing in diagnostics.},
}
@article {pmid40272326,
year = {2025},
author = {Adi, A and Lebrun, S and Kondo, M and Alvarez Villela, M and Fontes, JD},
title = {Culture-Negative Subacute Lactobacillus Endocarditis Diagnosed by Microbial Cell-Free DNA Sequencing.},
journal = {JACC. Case reports},
volume = {},
number = {},
pages = {103505},
doi = {10.1016/j.jaccas.2025.103505},
pmid = {40272326},
issn = {2666-0849},
abstract = {BACKGROUND: Lactobacillus endocarditis is a rare infection generally occurring in patients with heart disease and immunosuppression. Although Lactobacillus is typically a benign part of the gastrointestinal and genitourinary flora, it can cause invasive infections.<br><br>CASE SUMMARY: We present a case of a 74-year-old patient with low-grade fever and a nonproductive cough following recent cardiac surgery. Transesophageal echocardiography revealed vegetations, suggestive of endocarditis, despite negative blood cultures. Due to high suspicion for endocarditis, advanced genetic testing identified Lactobacillus fermentum as the causative pathogen. The patient disclosed daily probiotic use, likely the infection source. Treatment with intravenous ampicillin resulted in significant symptom improvement.<br><br>DISCUSSION: This case underscores the importance of considering probiotics as a potential source of bacteremia in patients with negative cultures after surgery and highlights how metagenomic sequencing can identify pathogens and guide effective therapy in challenging cases.},
}
@article {pmid40272234,
year = {2025},
author = {Wang, X and Zhang, J and Yang, B and Mao, H and Yu, Q and Zhang, Y},
title = {Intermittent Microaeration Enhanced Anaerobic Digestion: The Key Role of Fe(III)/Fe(II) Cycle and Reactive Oxygen Species.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04187},
pmid = {40272234},
issn = {1520-5851},
abstract = {Microaeration has been reported to improve anaerobic digestion, which is generally attributed to increased microbial diversity, but a thorough explanation is lacking. In this study, it was found that intermittent microaeration (IMA) supplied to an anaerobic digester could oxidize Fe(II) produced by dissimilatory iron reduction (DIR) to form a Fe(III)/Fe(II) cycle and generate extracellular reactive oxygen species (ROS) to improve anaerobic treatment of phenol-containing wastewater. The results showed that compared to the control group without IMA, the removal rates of COD and phenol increased by 29.54 and 49.68 percentage points, respectively, and daily average methane production increased by 85.44%. The Fe(III)/Fe(II) cycle slowed down the loss of iron (13.97%) released from sludge due to the lower solubility of Fe(III) and facilitated [•]OH generation (1.22 ± 0.04 μM) via Fenton-like reactions. The DIR and the generation of [•]OH accelerated phenol degradation. Metagenomic analysis revealed that the abundance of methanogens and antioxidant enzymes-encoding genes in response to oxidative stress significantly increased in the IMA group compared to the control, enabling methanogenesis to proceed smoothly under microaeration. This study investigated the extracellular ROS generation induced by microaeration during anaerobic digestion and their roles in promoting anaerobic performance, thereby providing a new perspective for optimizing anaerobic systems with microaeration.},
}
@article {pmid40272147,
year = {2025},
author = {Dai, X and Cao, Y and Li, L and Gao, Y-X and Wang, J-X and Liu, Y-J and Ma, T-T and Zheng, J-M and Zhan, P-P and Shen, Z-Y},
title = {Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0162624},
doi = {10.1128/msystems.01626-24},
pmid = {40272147},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiome and metabolome play crucial roles in renal allograft rejection progression. Integrated multiomics analyses may provide a comprehensive understanding of specific underlying mechanisms, which remain elusive. This study aimed to identify new approaches for clinical renal allograft rejection diagnosis and treatment. Thirty-five patients were divided into three groups: the rejection (n = 16), dysfunction (n = 7), and control (n = 12) groups. Metagenomic sequencing and nontargeted metabolomics were used to analyze stool and plasma samples. Significant microbiota, metabolites, and signaling pathways were identified. LASSO regression was used to construct a diagnostic model, and its diagnostic value was assessed via receiver operating characteristic curves. The microbiota composition and the related genes in the rejection group significantly differed from that in the dysfunction and control groups at the phylum, genus, and species levels (P < 0.001). The core species in the rejection group networks were Escherichia coli and Ruminococcus gnavus, while core species in the dysfunction group networks were Faecalibacterium prausnitzii and Bacteroides ovatus. The balance of specific microbial species was associated with kidney function in rejection patients. Spearman analysis revealed that specific differential species like Agathobaculum butyriciproducens and Gemmiger qucibialis were closely linked to the levels of serum 4-pyridoxic acid, 4-acetamidobutanoate, and fecal tryptamine from specific differential pathways. Finally, we constructed four clinical models to distinguish the rejection and dysfunction groups, and the model had excellent diagnostic performance. Altered gut microbiota may contribute to changes in metabolic pathway activity and metabolite abundance in rejection and dysfunction patients, which are strongly correlated with host immunological rejection. The diagnostic model, developed based on the gut microbiota and metabolites, has high clinical value for diagnosing renal rejection.<br><br>IMPORTANCE: This study aimed to screen new markers for non-invasive diagnosis by the gut microbiome and metabolome analysis, providing new insights into rejection mechanisms and identifying new approaches for clinical renal allograft rejection diagnosis.},
}
@article {pmid40271228,
year = {2025},
author = {Liu, J and Wu, X},
title = {Rare Bloodstream Infection of Rhodococcus rhodochrous as the Prodromal Signal for Malignancy.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1951-1959},
doi = {10.2147/IDR.S512213},
pmid = {40271228},
issn = {1178-6973},
abstract = {Rhodococcus-associated infections are extremely rare, and previous publications have indicated that such infections are primarily observed among individuals with HIV. Limited information is available regarding therapy, and no clear consensus has been reached to guide treatment. Here, we report the first case of bloodstream infection with Rhodococcus rhodochrous in a non-HIV patient with a viral intracranial infection. During follow-up, lymph node biopsy and bone marrow aspiration were performed because superficial lymphadenectasis had failed to regress as expected within 3 months. The patient was newly diagnosed with nodal T-follicular helper cell lymphoma, angioimmunoblastic-type. For cases of rare infection or co-infection, screening for pathogenic microorganisms is the priority, and several methods should be employed, such as microorganism culture, antigen and antibody detection, and metagenomic next-generation sequencing. In retrospect to integrated case management, our case indicated that early malignancy screening is significant for early diagnosis and treatment of occult cancer during patients with rare opportunistic infections.},
}
@article {pmid40270817,
year = {2025},
author = {Onohuean, H and Olot, H and Onohuean, FE and Bukke, SPN and Akinsuyi, OS and Kade, A},
title = {A scoping review of the prevalence of antimicrobial-resistant pathogens and signatures in ready-to-eat street foods in Africa: implications for public health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1525564},
doi = {10.3389/fmicb.2025.1525564},
pmid = {40270817},
issn = {1664-302X},
abstract = {BACKGROUND AND OBJECTIVE: Despite its critical role in individual and societal health, food hygiene remains underexplored. Antibiotic-resistant pathogenic bacteria in ready-to-eat (RTE) food threaten public health. This scoping review collected data on the epidemiological prevalence of RTE food-contaminated pathogens resistant to antimicrobial drugs and resistance genes in Africa.<br><br>METHOD: Using electronic databases, such as PubMed, Scopus, and Web of Science (WoS), handpicked from references, pre-reviewed published articles were retrieved and analyzed according to the PRISMA-ScR guidelines.<br><br>RESULTS: The findings indicate 40 previewed published articles qualified for meta-synthesis in the scoping review with a population/case ratio of 11,653/5,338 (45.80%). The most frequently reported RTE foods were meat or beef/beef-soup, chicken or poultry products, salads, vegetable salads, and sandwiches, which harboured pathogens such as E. coli, Salmonella, and Staphylococcus. Antibiotic susceptibility tests revealed the use of 48 antibiotics to manage infections, following CLSI (Clinical and Laboratory Standards Institute) protocols. Moreover, 10 authors reported 54 resistance genes associated with pathogenic resistant bacteria. In addition, only 15 studies received funding or financial support.<br><br>CONCLUSION: These findings from several researchers indicate that RTE street foods in African and resource-limited nations harbour enteric pathogens and are a significant concern to the public health system and reservoir of the spread of antibiotic resistance. This underscores the necessity of implementing effective control strategies to address challenges and limit the spread of resistant bacteria in RTE foods. The antimicrobial resistance surveillance system in the region is a significant concern. Notably, Africa needs to strengthen the national and international regulatory bodies and a health surveillance system on antimicrobial resistance, particularly among developing nations.},
}
@article {pmid40270812,
year = {2025},
author = {Fagerlund, A and Møretrø, T and Jensen, MR and Langsrud, S and Moen, B},
title = {Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541481},
doi = {10.3389/fmicb.2025.1541481},
pmid = {40270812},
issn = {1664-302X},
abstract = {Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.},
}
@article {pmid40270585,
year = {2025},
author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L},
title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf057},
doi = {10.1093/ismeco/ycaf057},
pmid = {40270585},
issn = {2730-6151},
abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.},
}
@article {pmid40270483,
year = {2025},
author = {McElwee-Adame, A and Esplin-Stout, R and Mugoya, T and Vourlitis, G and Welch, N and Henning, J and Afram, K and Jeshvaghane, MA and Bingham, N and Dockter, A and Eslava, J and Gil, G and Mergens, J and Mohamed, A and Nguyen, T and Noor, F and Salcedo, N and Sethuraman, A},
title = {Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17769},
doi = {10.1111/mec.17769},
pmid = {40270483},
issn = {1365-294X},
support = {2017-06423//USDA; National Institute of Food and Agriculture/ ; 2022-77040-38529//USDA; National Institute of Food and Agriculture/ ; 1564659//NSF; Division of Biological Infrastructure/ ; 2147812//NSF; Division of Biological Infrastructure/ ; },
abstract = {Humulus lupulus L., commonly known as hop, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hop has undergone intense artificial selection, with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavour and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study explores the global population structure and domestication history of 98 hop cultivars. We assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Our study revealed that worldwide hop cultivars cluster into four subpopulations: Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modelling the evolutionary history of domesticated hop reveals divergence of the common ancestors of modern US cultivars around 2800 years before present (ybp), and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition under common-garden settings in the United States.},
}
@article {pmid40270118,
year = {2025},
author = {Murtaza, N and Collins, L and Yao, CK and Thwaites, PA and Veitch, P and Varney, JE and Gill, PA and Gibson, PR and Morrison, M and Muir, JG},
title = {Effects of dietary FODMAP content on the faecal microbiome and gastrointestinal physiology in healthy adults: a randomised, controlled cross-over feeding study.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-39},
doi = {10.1017/S0007114525000868},
pmid = {40270118},
issn = {1475-2662},
abstract = {The effect dietary FODMAPs (fermentable oligo-, di- and mono-saccharides and polyols) in healthy adults is poorly documented. This study compared specific effects of low and moderate FODMAP intake (relative to typical intake) on the faecal microbiome, participant-reported outcomes and gastrointestinal physiology. In a single-blind cross-over study, 25 healthy participants were randomised to one of two provided diets, 'low' (LFD) <4 g/d or 'moderate' (MFD) 14-18 g/d, for 3 weeks each, with ≥2-week washout between. Endpoints were assessed in the last week of each diet. The faecal bacterial/archaeal and fungal communities were characterised in 18 participants in whom high quality DNA was extracted by 16S rRNA and ITS2 profiling, and by metagenomic sequencing. There were no differences in gastrointestinal or behavioural symptoms (fatigue, depression, anxiety), or in faecal characteristics and biochemistry (including short-chain fatty acids). Mean colonic transit time (telemetry) was 23 (95% confidence interval: 15, 30) h with the MFD compared with 34 (24, 44) h with LFD (n=12; p=0.009). Fungal diversity (richness) increased in response to MFD, but bacterial richness was reduced, coincident with expansion of the relative abundances of Bifidobacterium, Anaerostipes, and Eubacterium. Metagenomic analysis showed expansion of polyol-utilising Bifidobacteria, and Anaerostipes with MFD. In conclusion, short-term alterations of FODMAP intake are not associated with symptomatic, stool or behavioural manifestations in healthy adults, but remarkable shifts within the bacterial and mycobiome populations were observed. These findings emphasise the need to quantitatively assess all microbial Domains and their interrelationships to improve understanding of consequences of diet on gut function.},
}
@article {pmid40270064,
year = {2025},
author = {Basu, A and Chalasani, D and Sarma, PVSRN and Uikey, S and Chenna, VR and Choudhari, PL and Podile, AR},
title = {Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {41},
pmid = {40270064},
issn = {2524-6372},
abstract = {BACKGROUND: Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.<br><br>RESULTS: Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.<br><br>CONCLUSIONS: These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.},
}
@article {pmid40269715,
year = {2025},
author = {Poopedi, E and Pierneef, R and Singh, T and Gomba, A},
title = {Antibiotic resistance profiles and mutations that might affect drug susceptibility in metagenome-assembled genomes of Legionella pneumophila and Aeromonas species from municipal wastewater.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {237},
pmid = {40269715},
issn = {1471-2180},
support = {121333//National Research Foundation/ ; K5/2885//3//Water Research Commission/ ; },
mesh = {*Wastewater/microbiology ; *Aeromonas/genetics/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Legionella pneumophila/genetics/drug effects/isolation &amp; purification ; Genome, Bacterial ; Mutation ; *Metagenome ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic resistance (AR) has emerged as a significant global health issue. Wastewater treatment plants (WWTPs) contain diverse bacterial communities, including pathogens, and have been identified as crucial reservoirs for the emergence and dissemination of AR. The present study aimed to identify antibiotic resistance genes (ARGs) and screen for the presence of mutations associated with AR in Legionella pneumophila and Aeromonas spp. from municipal wastewater. Metagenome-assembled genomes (MAGs) of L. pneumophila and Aeromonas spp. were reconstructed to investigate the molecular mechanisms of AR in these organisms. A total of 138 nonsynonymous single nucleotide variants (SNVs) in seven genes associated with AR and one deletion mutation in the lpeB gene were identified in L. pneumophila. In Aeromonas spp., two (aph(6)-Id and aph(3'')-Ib) and five (blaMOX-4, blaOXA-1143, blaOXA-724, cepH, and imiH) ARGs conferring resistance to aminoglycosides and β-lactams were identified, respectively. Moreover, this study presents β-lactam resistance genes, blaOXA-1143 and blaOXA-724, for the first time in Aeromonas spp. from a municipal WWTP. In conclusion, these findings shed light on the molecular mechanisms through which clinically relevant pathogenic bacteria such as L. pneumophila and Aeromonas spp. found in natural environments like municipal wastewater acquire AR.},
}
@article {pmid40269516,
year = {2025},
author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D},
title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf177},
pmid = {40269516},
issn = {1477-4054},
support = {U24HG006620/NH/NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; },
abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.<br><br>AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.},
}
@article {pmid40269515,
year = {2025},
author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH},
title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf176},
pmid = {40269515},
issn = {1477-4054},
support = {2430236//National Science Foundation/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; },
abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.},
}
@article {pmid40269473,
year = {2025},
author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL},
title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70088},
doi = {10.1111/1758-2229.70088},
pmid = {40269473},
issn = {1758-2229},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; },
mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation &amp; purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation &amp; purification ; Machine Learning ; Brazil ; },
abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.},
}
@article {pmid40269059,
year = {2025},
author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M},
title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14204},
pmid = {40269059},
issn = {2045-2322},
support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration &amp; dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; },
abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.},
}
@article {pmid40268958,
year = {2025},
author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L},
title = {The dynamics of microbiome and virome in migratory birds of southwest China.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {64},
pmid = {40268958},
issn = {2055-5008},
mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; },
abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.},
}
@article {pmid40268922,
year = {2025},
author = {Patsis, AC and Schuler, CJ and Toner, BM and Santelli, CM and Sheik, CS},
title = {The potential for coupled organic and inorganic sulfur cycles across the terrestrial deep subsurface biosphere.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3827},
pmid = {40268922},
issn = {2041-1723},
support = {EAR-1813526//National Science Foundation (NSF)/ ; EAR-1813526//National Science Foundation (NSF)/ ; },
mesh = {*Sulfur/metabolism ; Ecosystem ; *Sulfur Compounds/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenome ; Sulfides/metabolism ; Metagenomics ; Sulfites/metabolism ; Soil Microbiology ; Sulfonium Compounds ; },
abstract = {Organosulfur compounds (OrgS) are fundamental components of life's biomass, yet the cycling of these compounds in the terrestrial deep subsurface, one of Earth's largest ecosystems, has gone relatively unexplored. Here, we show that all subsurface microbial genomes reconstructed from Soudan Underground Mine State Park have the capacity to cycle organic sulfur species. Our findings suggest that OrgS degradation may be an integral link between the organic and inorganic sulfur cycle via the production of sulfite and sulfide. Furthermore, despite isolation from surface ecosystems, most Soudan microorganisms retained genes for dimethylsulfoniopropionate and taurine biosynthesis. Metagenomic analyses of an additional 54 deep subsurface sites spanning diverse lithologies revealed the capacity for OrgS cycling to be widespread, occurring in 89% of assembled metagenomes. Our results indicate that consideration of OrgS cycling may be necessary to accurately constrain sulfur fluxes, discern the energetic limits of deep life, and determine the impact of deep subsurface biogeochemical sulfur cycling on greater Earth system processes.},
}
@article {pmid40268850,
year = {2025},
author = {Zhao, J and Zhuge, R and Hu, B and Wang, Y and Wang, X and Zhang, Y and Yuan, L and Qiu, C and Yan, Y and Zhang, X and Hua, Z and Tang, J and Guo, K and Sun, Y and Wang, K and Qiu, L and Luo, J and Zhang, W and Zhuge, J and Fang, H},
title = {Clinical impact of bronchoalveolar lavage fluid metagenomic next-generation sequencing in immunocompromised patients with severe community-acquired pneumonia in ICU: a multicenter retrospective study.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {40268850},
issn = {1439-0973},
support = {2023KY1296//The Project of Zhejiang Provincial Department of Health/ ; 2022K71//Quzhou Bureau of Science and Technology/ ; },
abstract = {BACKGROUND: An increasing number of critically ill patients are immunocompromised. These patients are at high risk of intensive care unit (ICU) admission because of numerous complications. Acute respiratory failure due to severe community-acquired pneumonia (SCAP) is one of the leading causes of admission. Early targeted antibiotic therapy is crucial for improving the prognosis of these patients. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) has shown significant value in pathogen detection in recent years. However, there are few studies on summarizing pathogen profiles of SCAP in immunocompromised patients.<br><br>METHODS: We performed a multicenter retrospective analysis of patients with SCAP in the ICU diagnosed between May 2021 to October 2024. Bronchoalveolar lavage fluid (BALF), blood, and sputum samples were collected and subjected to mNGS and conventional microbiological tests (CMTs). The pathogen profiles detected by the two methods were compared.<br><br>RESULTS: In our study, compared to CMTs, mNGS increased the detection rates of mixed infections in the immunocompromised group (58.82% vs 17.96%, P&#x2009;<&#x2009;0.05) and immunocompetent group (44.58% vs 18.72%, P&#x2009;<&#x2009;0.05), while also reducing the rate of no pathogen detected (4.90% vs 38.73%, P&#x2009;<&#x2009;0.05; 8.37% vs 32.76%, P&#x2009;<&#x2009;0.05). In both groups, the proportion of positive clinical impacts (diagnosis) resulting from mNGS results exceeded 90% (96.57% vs 93.84%), and the treatment effectiveness rate in the immunocompromised group was higher than in the immunocompetent group (65.69% vs 56.40%, P&#x2009;<&#x2009;0.05). Further analysis showed that when mNGS-guided treatment was effective, the 28-day mortality rate significantly improved in both the immunocompromised group (31.34% vs 74.29%, P&#x2009;<&#x2009;0.05) and the immunocompetent group (42.36% vs 40.68%, P&#x2009;<&#x2009;0.05) compared to when the treatment was ineffective.<br><br>CONCLUSION: This study indicates that ICU patients with SCAP, particularly those who are immunocompromised, are more likely to have polymicrobial infections. mNGS in BALF provides rapid and comprehensive pathogen profiling of pulmonary infections, thereby having a positive impact on both the diagnosis, treatment and prognosis of immunocompromised patients with SCAP.},
}
@article {pmid40268777,
year = {2025},
author = {Claverie, JM and Legendre, M and Rigou, S and Abergel, C},
title = {Refining the taxonomy of pithovirus-related giant DNA viruses within the order Pimascovirales.},
journal = {Archives of virology},
volume = {170},
number = {5},
pages = {111},
pmid = {40268777},
issn = {1432-8798},
mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure ; *Giant Viruses/classification/genetics/ultrastructure ; DNA, Viral/genetics ; },
abstract = {The first member of the family Pithoviridae (Pithovirus sibericum) was isolated from ancient Siberian permafrost and characterized in 2014. Since then, many relatives have been isolated, characterized, and classified as members of the genera Alphapithovirus, Alphacedratvirus, and Alphaorpheovirus. In addition, one complete circular genome sequence was assembled from metagenomic data (hydrivirus). All of these viruses form distinctive giant elongated ovoid particles, up to 2 µm in length, but they differ significantly in the size of their genome, their nucleotide composition, and their gene content. Based on their shared ovoid virion shape, common replication strategy, and core gene similarity, we recently proposed to update their taxonomic status by classifying them in three distinct families (Pithoviridae, Orpheoviridae, and Hydriviridae) within a new suborder, the Ocovirineae, to separate them clearly from the other more distant families (Marseilleviridae, Ascoviridae, Iridoviridae) of the order Pimascovirales. This new taxonomy, validated by the last ICTV Ratification vote held in March 2025, extends the previous partition from three clades to four (to include hydrivirus) while keeping the genera Alphacedratvirus and Alphapithovirus in the same family, Pithoviridae (but split into two subfamilies), due to their much greater similarity to each other than to orpheovirus and hydrivirus.},
}
@article {pmid40268631,
year = {2025},
author = {Pemán, J and Ruiz-Gaitán, A},
title = {Diagnosing invasive fungal infections in the laboratory today: It's all good news?.},
journal = {Revista iberoamericana de micologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.riam.2025.01.004},
pmid = {40268631},
issn = {2173-9188},
abstract = {Despite the advances in medical science, invasive fungal infections (IFI) remain a diagnostic challenge. The increasing prevalence of IFI, driven by immunosuppressive therapies, advances in intensive care and emerging pathogens, underscores the need for early and accurate diagnosis. This review evaluates current laboratory methods for the diagnosis of IFI, highlighting their strengths and limitations. Conventional techniques, including fungal culture, direct microscopy, and histopathology, remain the gold standard for the diagnosis of proven IFIs. These methods allow pathogen isolation, species identification and antifungal susceptibility testing. However, these techniques have limitations in terms of sensitivity and turnaround times. Although microscopy is a rapid technique, its sensitivity and species discrimination profile are limited. Modern serological assays, such as β-d-glucan and galactomannan detection, have improved the diagnostic accuracy of probable IFI cases. Integration of these assays with clinical and radiological findings, enables earlier intervention, although this is accompanied by an increased risk of false positives and necessitates careful clinical correlation. Molecular diagnostics, particularly polymerase chain reaction (PCR), allow rapid, species-specific identification directly from clinical samples. The advent of MALDI-TOF mass spectrometry has further improved diagnostic efficiency, particularly for yeast identification, although challenges remain for filamentous fungi. Innovative techniques, such as metagenomic sequencing, lateral-flow assays, and loop-mediated isothermal amplification, offer the potential for rapid and precise detection, even in resource-limited settings. The combination of conventional and innovative methods provides a comprehensive diagnostic framework. The continuous refinement of these tools, in conjunction with multidisciplinary collaboration, is imperative to improve the early diagnostic and targeted treatment of patients with IFI.},
}
@article {pmid40268236,
year = {2025},
author = {Emon, MI and Cheung, YF and Stoll, J and Rumi, MA and Brown, C and Choi, JM and Moumi, NA and Ahmed, S and Song, H and Sein, J and Yao, S and Khan, A and Gupta, S and Kulkarni, R and Butt, A and Vikesland, P and Pruden, A and Zhang, L},
title = {CIWARS: a web server for antibiotic resistance surveillance using longitudinal metagenomic data.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169159},
doi = {10.1016/j.jmb.2025.169159},
pmid = {40268236},
issn = {1089-8638},
abstract = {The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://ciwars.cs.vt.edu/.},
}
@article {pmid40271438,
year = {2017},
author = {Lu, J and Breitwieser, FP and Thielen, P and Salzberg, SL},
title = {Bracken: estimating species abundance in metagenomics data.},
journal = {PeerJ. Computer science},
volume = {3},
number = {},
pages = {},
doi = {10.7717/peerj-cs.104},
pmid = {40271438},
issn = {2376-5992},
abstract = {Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.},
}
@article {pmid40268215,
year = {2025},
author = {Sun, X and Hu, P and Xiao, M and Zhang, S and Shi, J and Cai, D and Wang, D and Xu, L and Liu, L and Liu, Y},
title = {Synergy of Multi-Enzyme Pretreatment and Paraclostridium benzoelyticum Bioaugmentation: A Dual Strategy for Enhancing Methane Production in Dry Anaerobic Digestion of Kitchen Waste.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121671},
doi = {10.1016/j.envres.2025.121671},
pmid = {40268215},
issn = {1096-0953},
abstract = {Dry anaerobic digestion (DAD) of kitchen waste (KW) has low methane production due to the poor mass transfer and the low abundance of functional microorganisms. This study employed multi-enzyme pretreatment (PRE), bioaugmentation with Paraclostridium benzoelyticum (BIO), and their combination (COM) to enhance methane production. Interestingly, the COM group had the highest methane production, which was increased by 18.51%, 9.91% and 12.39% compared with the control, PRE and BIO groups, respectively, which indicated that there was a synergy between multi-enzyme pretreatment and bioaugmentation. Further analysis of microbial community and metagenome was conducted to reveal the synergistic mechanism. The results showed that in COM group, the enrichment of the Rikenellaceae, Methanobacteriaceae and Methanosaetaceae was the directly reason for enhancing methane production. Additionally, key metabolic functions including biosynthesis of cofactors, methane metabolism and oxidative phosphorylation also played a pivotal role in boosting methane production. Furthermore, the enhancement of the hydrogenotrophic methanogenesis pathway has been demonstrated to be a critical factor in the synergistic effects. It provided a reliable theoretical basis for the practical application of the multi-enzyme pretreatment combined with Paraclostridium benzoelyticum bioaugmentation for DAD.},
}
@article {pmid40268122,
year = {2025},
author = {Highmore, C and Cooper, K and Parker, J and Robinson, J and Castangia, R and Webb, JS},
title = {Real-time detection of Foodborne Pathogens and Biofilm in the food processing environment with Bactiscan, a macro-scale fluorescence device.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100511},
doi = {10.1016/j.jfp.2025.100511},
pmid = {40268122},
issn = {1944-9097},
abstract = {Food safety relies on rapid detection methods and rigorous sampling of the food processing environment, and is challenged by recurrent biofilm contamination and by sub-lethally injured bacteria that can evade detection. Bactiscan is investigated as an alternative detection approach, a macro-scale and reagentless device that detects microbial contamination through activating green fluorescence of glycoproteins in the bacterial cell wall. The detection capability of Bactiscan was tested on foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Detection by Bactiscan was assessed using 3 independent observers viewing bacterial samples dried on stainless steel, using 3 biological repeats and 5 technical repeats. Detection by Bactiscan was possible to 1.20*10[6] colony forming units (CFU), compared to 1.36*10[4] CFU by ATP swab testing, where Bactiscan detection limits were defined by the concentration at which 50% of the samples were observed under illumination of the device. Heat-killed and chlorine stressed E. coli and S. enterica caused a 2-log reduction in detection by ATP swab tests (p≤0.05), while detection by Bactiscan was unaffected (p≥0.05). Pathogen biofilms were detectable via Bactiscan with >80% accuracy at 4 days of growth; E. coli and L. monocytogenes biofilms were visible at 2 days of growth. In situ contamination studies determined that Bactiscan can detect microbial contamination on chicken, salmon, and yoghurt samples with stronger fluorescence than a competitor UV torch. The presence of one of the pathogens on the food samples was confirmed by metagenome sequencing, determining that S. aureus was present in 7 samples out of 9 with a relative abundance of >0.5%. These data demonstrate that Bactiscan can effectively detect bacteria present in the food processing environment and can complement existing technologies to improve food industry cleaning practices and infection prevention.},
}
@article {pmid40267797,
year = {2025},
author = {Sun, X and Sun, Y and Li, P and Gao, Y and Han, M and Zhang, P},
title = {Intensive oyster farming alters the microbial-regulated blue carbon storage in sediment.},
journal = {Marine pollution bulletin},
volume = {216},
number = {},
pages = {118016},
doi = {10.1016/j.marpolbul.2025.118016},
pmid = {40267797},
issn = {1879-3363},
abstract = {Intensive oyster farming enhances the organic matter coupling from water to sediment through biodeposition, potentially contributing to carbon storage. Microbes play a key role in regulating biogeochemical cycling in the coastal sediment. However, their specific contributions to carbon storage under oyster farming remain poorly understood. This study investigates microbial necromass and associated biogeochemical processes in sediments from an intensive oyster farm in Sanggou Bay, China, and compares these indicators with adjacent seagrass beds and bare zones. Additionally, carbon use efficiency (CUE) was employed to indicate microbial-regulated carbon cycling and storage in sediment. The results demonstrate that oyster farming promotes organic carbon accumulation in surface sediments but reduces its stability. Microbial necromass was identified as a critical driver of sedimentary organic carbon in oyster farm sediments, supported by enhanced nitrogen and sulfur cycling pathways. Notably, contrasting relationships between CUE and organic carbon were observed between the seagrass bed and the oyster farm. Functional metagenomic analysis further revealed distinct microbial metabolic pathways across habitats, highlighting the role of biodeposition in shaping microbial functions. These findings enhance our understanding of microbial contributions to blue carbon storage in aquaculture systems and provide new insights into coastal carbon storage beyond vegetated ecosystems.},
}
@article {pmid40267563,
year = {2025},
author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T},
title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105138},
doi = {10.1016/j.psj.2025.105138},
pmid = {40267563},
issn = {1525-3171},
abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.},
}
@article {pmid40266944,
year = {2025},
author = {Herzog, F and Crissman, KR and Beckers, KF and Zhou, G and Liu, CC and Sones, JL},
title = {Lactobacillus Genus Complex Probiotic-Induced Changes on the Equine Clitoral Microbiome.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030232},
pmid = {40266944},
issn = {2306-7381},
support = {2022//Louisiana State University Charles V. Cusimano/ ; },
abstract = {Dysbiosis of the lower reproductive tract (LRT) in mares may play a role in clinical diseases, including endometritis and placentitis. Metagenomic/metagenetic analysis of bacterial DNA can identify organisms that are not readily cultured and, thus, may go undetected. In this study, we tested the following hypotheses: (1) the clitoris of estrual mares harbors a unique resident microbiome, (2) topical Lactobacillus genus complex (LGC)-containing probiotic will alter the equine clitoral microbiome, and (3) early pregnancy rates following clitoral LGC application will not differ significantly from industry standards. Mares (n = 12) in estrus had sterile clitoral swabs collected (0) prior to daily topical LGC for 4 days. Second (12 h) and third clitoral swabs (48 h) were collected following final LGC application. During the next estrus, the mares were bred by artificial insemination. Genomic DNA was extracted and used for 16S rRNA sequencing via the Illumina Miseq platform. Abundance was evaluated via Friedman test with pairwise Dunn's post hoc comparisons. Statistical significance was set at p < 0.05. Compared to time 0, Desulfobacterota decreased and Corynebacterium spp. increased at 12 h and 48 h compared to 0, while Actinobacillus and Fusobacterium spp. increased in a time-dependent manner. Furthermore, Mobiluncus spp. and Christensenellacea_R-7_group decreased at 12 h and 48 h compared to 0. LGC changed the beta but not alpha diversity at both 12 h and 48 h. Mares with LGC application achieved an 85% pregnancy rate in the subsequent estrus. Future investigations are needed to understand the role of the LRT microbiome and probiotics in equine breeding.},
}
@article {pmid40266232,
year = {2025},
author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y},
title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf076},
pmid = {40266232},
issn = {1751-7370},
support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; },
abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria, which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of segmented filamentous bacteria from the chicken gut microbiota, which displayed common metabolic deficiency with segmented filamentous bacteria of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of segmented filamentous bacteria in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.},
}
@article {pmid40265464,
year = {2025},
author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q},
title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12984},
pmid = {40265464},
issn = {1749-4877},
support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.},
}
@article {pmid40265338,
year = {2025},
author = {Venkatraman, K and Lipp, NF and Budin, I},
title = {Origin and evolution of mitochondrial inner membrane composition.},
journal = {Journal of cell science},
volume = {138},
number = {9},
pages = {},
doi = {10.1242/jcs.263780},
pmid = {40265338},
issn = {1477-9137},
support = {GM142960/NH/NIH HHS/United States ; GBMF9734//Gordon and Betty Moore Foundation/ ; //University of California/ ; },
mesh = {*Mitochondrial Membranes/metabolism/chemistry ; *Mitochondria/metabolism/genetics ; Humans ; Animals ; Mitochondrial Proteins/metabolism ; *Evolution, Molecular ; },
abstract = {Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.},
}
@article {pmid40265160,
year = {2025},
author = {Fässler, D and Heinken, A and Hertel, J},
title = {Characterising functional redundancy in microbiome communities via relative entropy.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1482-1497},
pmid = {40265160},
issn = {2001-0370},
abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.},
}
@article {pmid40264979,
year = {2025},
author = {Zhong, Y and Chi, H and Wu, T and Fan, W and Su, H and Li, R and Jiang, W and Du, X and Ma, Z},
title = {Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537846},
pmid = {40264979},
issn = {1664-302X},
abstract = {Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.},
}
@article {pmid40264936,
year = {2025},
author = {Hou, F and Qiao, Y and Qiao, Y and Shi, Y and Chen, M and Kong, M and Hu, X and Jiang, L and Liu, X},
title = {A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1530486},
pmid = {40264936},
issn = {2235-2988},
abstract = {INTRODUCTION: The application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. A total of 180 patients with severe infections were included in this study.<br><br>METHODS: Based on their different symptoms, bronchoalveolar lavage fluid (BALF) or blood samples were collected for conventional microbiological testing (CMT) and mNGS.<br><br>RESULTS: The results indicated that the etiological diagnosis rate of mNGS (78.89%) was significantly higher than that of CMT (20%) (p<0.001). Notably, mNGS exhibited greater sensitivity towards rare pathogens such as Chlamydia pneumoniae, Mycobacterium tuberculosis complex, and Legionella pneumophila, which were undetectable by CMT. Additionally, 64 cases underwent blood culture, BALF culture, and mNGS testing. Analysis revealed that the positive rate of blood culture (3.1%) was lower than that of BALF (25%), and the positive rate of CMT from both types was significantly lower than that of mNGS (89.1%) (p<0.001). In this study, 168 mNGS results were accepted, and 116 patients had their antibiotic therapy adjustment based on mNGS. Paired analysis indicated that white blood cell count (WBC), procalcitonin (PCT), C-reactive protein (CRP), and neutrophil (NEU) percentage provided valuable therapeutic guidance. The survival rate of patients was 55.36%, influenced by patient physical condition and age.<br><br>DISCUSSION: Our data indicated that mNGS had significant auxiliary value in the clinical diagnosis and treatment for critically ill patients, especially for those with negative CMT results and clinically undefined infections. mNGS could broaden the detection scope, especially for special pathogens, and improve the detection rate, providing powerful assistance for early clinical diagnosis and treatment.},
}
@article {pmid40263874,
year = {2025},
author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y},
title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116061},
doi = {10.1016/j.foodres.2025.116061},
pmid = {40263874},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; },
abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.},
}
@article {pmid40263747,
year = {2025},
author = {Liu, CG and Lin, MX and Xin, Y and Sun, M and Cui, J and Liu, D and Zang, D and Chen, J},
title = {Metagenomics and Non-Targeted Metabolomics Reveal the Role of Gut Microbiota and Its Metabolites in Brain Metastasis of Non-Small Cell Lung Cancer.},
journal = {Thoracic cancer},
volume = {16},
number = {8},
pages = {e70068},
doi = {10.1111/1759-7714.70068},
pmid = {40263747},
issn = {1759-7714},
support = {2022RQ091//Science and Technology Talent Innovation Support Plan of Dalian/ ; 82203056//National Natural Science Foundation of China/ ; 2022LCYJYB01//The "1+X" program for Clinical Competency enhancement-Clinical Research Incubation Project of the Second Hospital of Dalian Medical University/ ; 2023-BS-167//Natural Science Foundation of Liaoning Province/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/secondary/metabolism ; *Lung Neoplasms/pathology/metabolism/microbiology ; *Metabolomics/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; Prognosis ; },
abstract = {BACKGROUND: Brain metastasis is a common and severe complication in non-small cell lung cancer (NSCLC) patients, significantly affecting prognosis. However, the role of gut microbiota and its metabolites in NSCLC brain metastasis remains poorly understood. This study aims to explore the relationship between gut microbiota, metabolites, and the development of brain metastasis in NSCLC.<br><br>METHODS: We conducted an integrative analysis combining metagenomics and non-targeted metabolomics on baseline fecal samples from NSCLC patients with brain metastasis (n&#x2009;=&#x2009;18) and those without distant metastasis (n&#x2009;=&#x2009;12). Gut microbiota composition and metabolite profiles were detected and analyzed, and statistical methods, including machine learning models, were applied to identify differences and potential biomarkers.<br><br>RESULTS: Significant differences in gut microbiota composition were found between the two groups, with higher microbial diversity observed in patients with brain metastasis. Specific genera, such as Paenibacillus, Fournierella, and Adlercreutzia, were enriched in the brain metastasis group. Metabolomic analysis revealed altered levels of short-chain fatty acids and other metabolites associated with immune modulation and vascular permeability, including angiotensin (1-7). These changes were linked to the metastatic process and may influence brain metastasis development. Furthermore, machine learning models identified key biomarkers, such as Raoultibacter, Mobilibacterium, and N-acetyl-L-glutamic acid, which could serve as valuable indicators for brain metastasis.<br><br>CONCLUSIONS: Our findings suggest that gut microbiota dysbiosis and its metabolic products may contribute to the development of brain metastasis in NSCLC. The identification of microbiota-derived biomarkers holds potential for early detection and therapeutic intervention in NSCLC brain metastasis.},
}
@article {pmid40263712,
year = {2025},
author = {Hör, J},
title = {Advancing RNA phage biology through meta-omics.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
doi = {10.1093/nar/gkaf314},
pmid = {40263712},
issn = {1362-4962},
mesh = {*Bacteria/virology/genetics ; *RNA Phages/genetics/physiology/classification ; Genome, Viral ; *Metagenomics/methods ; *Genomics/methods ; Transcriptome ; Bacteriophages/genetics ; },
abstract = {Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.},
}
@article {pmid40263502,
year = {2025},
author = {Canderan, J and Ye, Y},
title = {Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13926},
pmid = {40263502},
issn = {2045-2322},
support = {R01AI143254//U.S. Department of Health &amp; Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; EF-202545//National Science Foundation (NSF)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Proteomics/methods ; *Bacterial Proteins/metabolism ; Aspergillus/metabolism ; },
abstract = {Microbiome research has revealed associations between microbial species and colorectal cancer (CRC). Most of the existing research relied on metagenomic data. We leveraged a tool that we recently developed for detecting human and microbial peptides from (meta)proteomics data to reanalyze Clinical Proteomic Tumor Analysis Consortium CRC proteomics datasets. Our analyses revealed potential microbial species and proteins that are associated with CRC, especially when analyzing multiplexed proteomics data consisting of cancerous and healthy tissue taken from the same individuals. Many of the identified proteins are associated with species with known links to CRC, such as the fungi Aspergillus kawachii, but many are unstudied or their specific roles unknown. Proteins from other microbial species, such as Paenibacillus cellulosilyticus, were also identified in the samples. We showed that Aspergillus kawachii and others are depleted overall in cancer samples, which is consistent with a previous genomic-based multi-cohort study. Our analysis also revealed that some proteins belonging to this species are more abundantly detected, while others in this and other species are not. Further, we showed that microbial identifications could be used to build predictive models for tumor detection, but caution needs to be taken when applying such models trained on one dataset to another due to the substantial impacts of different experimental techniques on peptide detection profiles.},
}
@article {pmid40263397,
year = {2025},
author = {Li, C and Zhu, J and Wang, Y and Jiang, W and Lin, Y},
title = {Metagenomic NGS reveals determinants of polymicrobial spinal infection pathogenesis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13959},
pmid = {40263397},
issn = {2045-2322},
support = {20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; Risk Factors ; *Coinfection/microbiology ; *Metagenomics/methods ; ROC Curve ; Adult ; *Spinal Diseases/microbiology ; },
abstract = {To explore the influencing factors of spinal mixed infection under mNGS-assisted detection. A retrospective analysis was conducted on the general clinical data of patients diagnosed with spinal infections at Guilin People's Hospital, covering the period from October 2022 to October 2024, to evaluate the effectiveness of different treatment modalities including conservative, pharmacological, and surgical interventions. In the end, a total of 45 cases were included, including 18 cases of mixed infection and 27 cases of single infection. The receiver operating characteristic (ROC) curve was utilized to evaluate the predictive efficacy of various indices for the occurrence of mixed infection in patients with spinal infections, with the curve's proximity to the top left corner indicating higher diagnostic accuracy. Multivariate Logistic regression was used to analyze the independent risk factors affecting the development of mixed infection in patients with spinal infection. No significant differences were found between the two groups regarding gender, smoking, alcohol consumption, hypertension, albumin levels, liver function, malignancy, or rheumatic immune disease history (P > 0.05). However, the mixed infection group had significantly higher proportions of patients aged > 60 years (78% (14/18) vs. 48% (13/27)), diabetes mellitus (44% (8/18) vs. 15% (4/27)), chronic kidney disease (17% (3/18) vs. 0.00 (0/27)), and previous spinal surgery (39% (7/18) vs. 11% (3/27)), along with lower BMI (20.70 ± 2.15 vs. 24.04 ± 3.76) and hemoglobin levels (105.17 ± 14.05 g/L vs. 117.48 ± 18.08 g/L). The results of the ROC curve analysis showed that the area under the curve for BMI and hemoglobin in predicting the occurrence of mixed infection in patients was 0.787 and 0.704, respectively, with optimal cutoff values of 21.12 kg/m[2] and 119 g/L. Multivariate logistic regression identified BMI < 21.12 kg/m[2], hemoglobin < 119 g/L, and diabetes as independent risk factors. Lower BMI, diabetes and hemoglobin are independent risk factors for spinal mixed infection. Increasing BMI, effectively controlling blood glucose and improving anemia are helpful to reduce the occurrence of spinal mixed infection.},
}
@article {pmid40263287,
year = {2025},
author = {Gao, D and Zhuang, Y and Liu, S and Ma, B and Xu, Y and Zhang, H and Nuermaimaiti, Y and Chen, T and Hou, G and Guo, W and You, J and Huang, Z and Xiao, J and Wang, W and Li, M and Li, S and Cao, Z},
title = {Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {61},
pmid = {40263287},
issn = {2055-5008},
support = {2024BBF01006//Key Research and Development Program of Ningxia/ ; 2023YFD1300904//National Key Research and Development Program of China/ ; 2024-KFKT-026//National Center of Technology Innovation for Dairy/ ; PC2023B02002//Pinduoduo-China Agricultural University Research Fund/ ; },
mesh = {Animals ; Cattle ; *Oxidative Stress ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Mice ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Metagenomics ; *Clostridiales/genetics/metabolism/isolation &amp; purification ; Multiomics ; },
abstract = {An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10[8] cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.},
}
@article {pmid40263159,
year = {2025},
author = {Pandey, A and Israr, J and Pandey, J and Misra, S},
title = {Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {258},
pmid = {40263159},
issn = {1432-0991},
mesh = {*Biological Products/metabolism/pharmacology/isolation &amp; purification/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/genetics ; Multigene Family ; Biosynthetic Pathways/genetics ; Microbiota ; },
abstract = {Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.},
}
@article {pmid40262434,
year = {2025},
author = {Lima, RAT and Garay, AV and Frederico, TD and de Oliveira, GM and Quirino, BF and Barbosa, JARG and Freitas, SM and Krüger, RH},
title = {Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome.},
journal = {Enzyme and microbial technology},
volume = {189},
number = {},
pages = {110654},
doi = {10.1016/j.enzmictec.2025.110654},
pmid = {40262434},
issn = {1879-0909},
abstract = {Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe[2 +]. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10[-5] μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.},
}
@article {pmid40262432,
year = {2025},
author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z},
title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.},
journal = {Water research},
volume = {282},
number = {},
pages = {123626},
doi = {10.1016/j.watres.2025.123626},
pmid = {40262432},
issn = {1879-2448},
abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.},
}
@article {pmid40261735,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {40261735},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}
@article {pmid40261409,
year = {2025},
author = {Zhao, S and Guo, H and Wang, Z and Zhang, B and Chen, H and Klitzsch, N and Yue, L and Xia, D},
title = {Clay mineral content modulates biogenic gas production in coal: divergent microbial responses in low- and medium-rank coals revealed by multi-omics.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {40261409},
issn = {1615-7605},
support = {23ZX015//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 42172195//National Natural Science Foundation of China/ ; 42172199//National Natural Science Foundation of China/ ; AQ20240302//Double First-Class Initiative for Safety Discipline Construction Project/ ; 2024B03002//Xinjiang Key R &amp; D Task Project/ ; },
abstract = {The influence of clay mineral content on biogenic gas production in coal seams remains insufficiently understood. This study systematically investigated the mechanisms by which clay minerals affect biogas production in low- and medium-rank coals by integrating simulated biogas production experiments with multidimensional analytical techniques, including infrared spectroscopy, X-ray diffraction, scanning electron microscopy, gas chromatography-mass spectrometry, fluorescence spectroscopy, and metagenomic analysis. The results demonstrated that in low-rank coal, increasing the clay content from 2.78 to 4.75 g per 20 g of coal reduced the biogas yield from 6.30 to 3.47 mL/g. Conversely, in medium-rank coal, increasing the clay content from 1.66 to 2.65 g per 20 g of coal enhanced the biogas yield from 3.45 to 5.28 mL/g. These contrasting outcomes are primarily attributed to the distinct mechanistic roles of clay minerals across coal ranks. In low-rank coal, the hydration-induced swelling of clay minerals intensified pore blockage, impeded gas diffusion, decreased the abundance of genes involved in propionate degradation, and suppressed microbial metabolic activity, ultimately limiting methane production. In contrast, in medium-rank coal, clay minerals facilitated the enrichment of key functional microbial taxa, such as Acetobacteroides and Methanoculleus, promoted the degradation of fatty acids, hydroxyls, and amines, and enhanced the activity of acidogenic and methanogenic pathways, thereby increasing methane yield. This study elucidates the microbial mechanisms underlying the regulatory role of clay minerals in biogas production, offering new theoretical insights into the origin of coalbed methane (CBM) and providing a scientific foundation for optimizing biogenic CBM recovery.},
}
@article {pmid40261207,
year = {2025},
author = {Liao, X and Li, Y and Wu, Y and Li, X and Shang, X},
title = {Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00174},
pmid = {40261207},
issn = {2161-5063},
abstract = {With the widespread application of the CRISPR-Cas system in gene editing and related fields, along with the increasing availability of metagenomic data, the demand for detecting and classifying CRISPR-Cas systems in metagenomic data sets has grown significantly. Traditional classification methods for CRISPR-Cas systems primarily rely on identifying cas genes near CRISPR arrays. However, in cases where cas gene information is absent, such as in metagenomes or fragmented genome assemblies, traditional methods may fail. Here, we present a deep learning-based method, CRISPRclassify-CNN-Att, which classifies CRISPR loci solely based on repeat sequences. CRISPRclassify-CNN-Att utilizes convolutional neural networks (CNNs) and self-attention mechanisms to extract features from repeat sequences. It employs a stacking strategy to address the imbalance of samples across different subtypes and uses transfer learning to improve classification accuracy for subtypes with fewer samples. CRISPRclassify-CNN-Att demonstrates outstanding performance in classifying multiple subtypes, particularly those with larger sample sizes. Although CRISPR loci classification traditionally depends on cas genes, CRISPRclassify-CNN-Att offers a novel approach that serves as a significant complement to cas-based methods, enabling the classification of orphan or distant CRISPR loci. The proposed tool is freely accessible via https://github.com/Xingyu-Liao/CRISPRclassify-CNN-Att.},
}
@article {pmid40261064,
year = {2025},
author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES},
title = {Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0156824},
doi = {10.1128/msystems.01568-24},
pmid = {40261064},
issn = {2379-5077},
abstract = {UNLABELLED: The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome among individuals living with HIV is not fully characterized. Here, we describe the nasopharyngeal microbiome before, during, and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (P-values < 0.0001). In both mothers and children, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.<br><br>IMPORTANCE: The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.},
}
@article {pmid40261045,
year = {2025},
author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD},
title = {TEAL-Seq: targeted expression analysis sequencing.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0098424},
doi = {10.1128/msphere.00984-24},
pmid = {40261045},
issn = {2379-5042},
abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.},
}
@article {pmid40260991,
year = {2025},
author = {López-Gálvez, R and Orenes-Piñero, E and Rivera-Caravaca, JM and Pérez-Sanz, F and Ramos-Bratos, MP and Roca, MI and Mandaglio-Collados, D and López-García, C and Gil-Pérez, P and Esteve-Pastor, MA and Marín, F},
title = {Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70046},
doi = {10.1002/mnfr.70046},
pmid = {40260991},
issn = {1613-4133},
support = {//Instituto de Salud Carlos III/ ; //Centro de investigaci&#xf3;n Biom&#xe9;dica en Red/ ; },
abstract = {Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.},
}
@article {pmid40260089,
year = {2025},
author = {Xu, P and Pan, C and Yuan, M and Zhu, Y and Wei, S and Lu, H and Zhang, W},
title = {Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1564755},
pmid = {40260089},
issn = {1664-302X},
abstract = {INTRODUCTION: Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.<br><br>METHODS: In this study, fecal samples from children with ARI were investigated using viral metagenomics.<br><br>RESULTS: The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.<br><br>DISCUSSION: We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.},
}
@article {pmid40260085,
year = {2025},
author = {Perez, LJ and Perez-Restrepo, LS and Ciuoderis, K and Usuga, J and Moreno, I and Vargas, V and Arévalo-Arbelaez, AJ and Berg, MG and Cloherty, GA and Hernández-Ortiz, JP and Osorio, JE},
title = {Emergence, persistence, and positive selection of yellow fever virus in Colombia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1548556},
pmid = {40260085},
issn = {1664-302X},
abstract = {Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.},
}
@article {pmid40260047,
year = {2025},
author = {Guo, L and Wu, X and Cao, L},
title = {Clinical Characteristics of Miliary Pulmonary Tuberculosis in Pregnancy After In Vitro Fertilization-Embryo Transfer: A Retrospective Clinical Study.},
journal = {Health science reports},
volume = {8},
number = {4},
pages = {e70705},
pmid = {40260047},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Miliary pulmonary tuberculosis (MPTB) is rare in patients treated with In Vitro fertilization-embryo transfer (IVF-ET), and can be life-threatening to pregnant women and fetuses. We aimed to describe the clinical characteristics of MPTB after IVF-ET and pregnancy outcomes to provide reference for early diagnosis and treatment.<br><br>METHODS: Clinical data from patients who developed MPTB after IVF-ET from January 2018-December 2021 were retrospectively and statistically analyzed.<br><br>RESULTS: Ultimately, 21 patients (mean age: 29.81&#x2009;&#xb1;&#x2009;3.79 years) were included. Three patients had a history of pulmonary or extrapulmonary tuberculosis (TB), and were cured or showed no suggestive TB activity before pregnancy. Patients presented with atypical early symptoms, fever (39.16&#x2009;&#xb1;&#x2009;0.74&#xb0;C), and vaginal bleeding, and lung imaging changes. Patients became febrile 78.90&#x2009;&#xb1;&#x2009;26.04 days after IVF-ET; the time from fever to diagnosis was 17.76&#x2009;&#xb1;&#x2009;9.05 days. Patients were admitted 96.05&#x2009;&#xb1;&#x2009;25.33 days after IVF-ET. Sputum Mycobacterium tuberculosis smear and culture, purified protein derivative, TB polymerase chain reaction, and other routine TB examinations had low positivity rates; the erythrocyte sedimentation rate was generally within normal limits. Chest imaging during pregnancy is limited, further increasing the diagnosis time. Two critically ill patients were diagnosed by metagenomic next-generation sequencing. Seven patients had TB meningitis or encephalitis. Pregnancy was terminated in all but three patients. All patients received anti-TB therapy; however, two patients died during hospitalization (mean hospitalization: 58.29&#x2009;&#xb1;&#x2009;33.40 days).<br><br>CONCLUSIONS: Comprehensive TB screening before IVF-ET is necessary for infertile patients. MPTB develops after IVF-ET with atypical symptoms and poor pregnancy outcomes. Clinicians should use multiple methods to confirm TB diagnoses early on, without delaying chest imaging.},
}
@article {pmid40259990,
year = {2025},
author = {Chen, Y and Liu, Y and Ji, M and Zhang, Z and Xing, T and Pan, H and Liu, K and Li, Y and Liu, P},
title = {Metabolic diversity and adaptation of carbon-fixing microorganisms in extreme glacial cryoconite.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf056},
pmid = {40259990},
issn = {2730-6151},
abstract = {Understanding the diversity and functionality of carbon-fixing microorganisms in glacial ecosystems is crucial for elucidating carbon cycling processes in extreme environments. This study investigates the composition, diversity, and metabolic potential of carbon-fixing microorganisms in Tibetan cryoconite. Through metagenomic sequencing, we identified 13 carbon-fixing metagenome-assembled genomes spanning ten known and three unclassified genera. Deoxyribonucleic acid -stable isotope probing experiments with [13]C-labeled sodium bicarbonate confirmed the metabolic activity of key genera, including Cyanobacteria (Microcoleus and Phormidesmis) and Proteobacteria (Rhizobacter and Rhodoferax). Our results reveal a diverse array of carbon fixation pathways, with the Calvin-Benson-Bassham cycle and 3-hydroxypropionate bicycle being the most prominent. In addition to photoautotrophic microorganisms, chemoautotrophic microorganisms also contribute to carbon fixation through mechanisms such as sulfur oxidation and atmospheric reducing gas utilization. The study highlights the adaptability of microbial communities to varying environmental conditions, including fluctuations in oxygen, light, and substrate availability. The findings underscore the complex interplay between carbon fixation pathways and environmental factors in cryoconite ecosystems. It also emphasizes the importance of exploring alternative carbon fixation pathways to gain a more comprehensive understanding of carbon cycling in these harsh and dynamic ecosystems.},
}
@article {pmid40259731,
year = {2025},
author = {Sun, YS and Zhao, L and Zheng, CL and Yan, XT and Li, Y and Gao, XL and Xue, TF and Zhang, YM and Li, ZP and Heller, R and Feng, CG and Xu, C and Wang, K and Qiu, Q},
title = {Convergent musk biosynthesis across host and microbiota in musk deer and muskrat.},
journal = {Zoological research},
volume = {46},
number = {3},
pages = {505-517},
doi = {10.24272/j.issn.2095-8137.2025.094},
pmid = {40259731},
issn = {2095-8137},
mesh = {Animals ; *Deer/microbiology/metabolism ; *Fatty Acids, Monounsaturated/metabolism ; *Microbiota ; Scent Glands/metabolism ; *Arvicolinae/microbiology/metabolism ; },
abstract = {Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.},
}
@article {pmid40259344,
year = {2025},
author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE},
title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {101},
pmid = {40259344},
issn = {2049-2618},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation &amp; purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation &amp; purification ; Cecum/microbiology ; },
abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.<br><br>RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.<br><br>CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.},
}
@article {pmid40258842,
year = {2025},
author = {Duru, IC and Lecomte, A and Laine, P and Shishido, TK and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P},
title = {Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13723},
pmid = {40258842},
issn = {2045-2322},
support = {NNF22OC0080109//Novo Nordisk Foundation/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/isolation &amp; purification ; Aged ; *Plasmids/genetics ; Male ; Female ; Middle Aged ; Feces/microbiology/virology ; Case-Control Studies ; Metagenomics/methods ; Machine Learning ; },
abstract = {The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.},
}
@article {pmid40258509,
year = {2025},
author = {Fang, C and Zhu, J and Xu, H and Qian, M and Jin, Y},
title = {Polystyrene microplastics and cypermethrin exposure interfered the complexity of antibiotic resistance genes and induced metabolic dysfunction in the gut of adult zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126288},
doi = {10.1016/j.envpol.2025.126288},
pmid = {40258509},
issn = {1873-6424},
abstract = {Environmental pollutants such as microplastics (MPs) and pesticides are becoming prevalent in aquatic ecosystems, posing risks to wildlife and human health. This study investigated the toxicological effects of polystyrene microplastics (PS-MPs) and cypermethrin (CYP) on adult female zebrafish (Danio rerio), focusing on intestinal microenvironment. Adsorption kinetics experimental results showed that PS-MPs can adsorb a certain amount of CYP on its surface, thereby forming a new type of composite pollutant. After exposure to red fluorescent PS-MPs for 4 days, it was found that the PS-MPs could enter the zebrafish and accumulate in the intestines. Five-month-old female zebrafish were exposed to PS-MPs, CYP, and a mixture of both for 21 days. After exposure, feces were collected and analyzed using metagenomic sequencing to determine microbial composition and functional changes. Metagenomic sequencing of naturally excreted feces showed that co-exposure synergistically reduced α-diversity and shifted community structure, with marked losses of beneficial Fusobacteriota, Firmicutes and Cetobacterium somerae and enrichment of pathogenic Preplasmiviricota. Functional annotation indicated that PS-MPs alone up-regulated glycoside hydrolases and glycosyl-transferases, whereas CYP and the co-exposure group suppressed a great number of the top 50 carbohydrate-active enzymes and decreased secondary metabolic pathways linked to amino-acid, lipid and carbohydrate metabolism pathways. Antibiotic-resistance gene (ARGs) profiling identified 57 ARG types (such as sul1, adeF, lnuC and mphA) after co-exposure. Finally, key genes related to amino acid metabolism, carbohydrate metabolism, and lipid metabolism in intestinal tissue were significantly altered. Collectively, our data demonstrated that PS-MPs and CYP exposure amplified gut dysbiosis, metabolic dysfunction and ARG complexity in zebrafish. Overall, the study highlighted the potential risks of combined environmental pollutants on intestinal microbiota, with implications for ecosystem health.},
}
@article {pmid40258462,
year = {2025},
author = {He, R and Li, X and Zhang, X},
title = {Methane enhancing nitrous oxide consumption in microaerobic sludge systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121658},
doi = {10.1016/j.envres.2025.121658},
pmid = {40258462},
issn = {1096-0953},
abstract = {Nitrous oxide (N2O) reduction is traditionally known to be active under extremely low oxygen concentrations and hypoxic conditions. Herein, microaerobic sludge systems (∼38.2 and ∼12.1 μM dissolved oxygen) were conducted to investigate the performance of simultaneous methane (CH4) oxidation and N2O consumption compared with hypoxic conditions. During the whole experiment, the average N2O consumption rate in the high dissolved oxygen sludge system with CH4 was 3.4-4.9 times that of the others. A positively linear correlation was observed between the CH4 oxidation rate and the N2O consumption rate in the sludge systems. Compared to the treatment without CH4, the N2O consumption rate was higher in the treatment with CH4, indicating that aerobic CH4 oxidation might be related with the N2O consumption in the systems. The N2O consumption in the microaerobic system was influenced by the O2, CH4 and NH4[+]-N concentrations and was regulated by the microbial species. Type I methane-oxidizing bacteria (MOB) including Methylococcus, Methylocaldum, Methylomagnum, Methylosarcina, Methylobacter and Methylogaea, type II MOB Methylocystis and NC10 phylum Candidatus Methylomirabilis were the main methanotrophs in the systems. Compared with type II MOB, type I MOB were more abundant in the system. Anaerolinea and Lautropia were the main denitrifying bacteria in the microaerobic system with CH4 and N2O. Clad I nosZ and clad II nosZ were both rich in the microaerobic system. These findings suggest that an appropriate oxygen concentration would be favorable for simultaneous mitigation of CH4 and N2O emission in the sludge systems.},
}
@article {pmid40257249,
year = {2025},
author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS},
title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0133524},
doi = {10.1128/mra.01335-24},
pmid = {40257249},
issn = {2576-098X},
abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.},
}
@article {pmid40257199,
year = {2025},
author = {Wang, X and Wang, M and Zhang, W and Li, H and Tiedje, JM and Zhou, J and Topp, E and Luo, Y and Chen, Z},
title = {Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf077},
pmid = {40257199},
issn = {1751-7370},
abstract = {Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Here, leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, qPCR, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment units in a full-scale antibiotic-manufacturing wastewater treatment plant processing wastewater from a β-lactam manufacturing facility. We demonstrated that both bacterial communities and antibiotic resistance gene compositions varied across the treatment units, but were associated. Certain antibiotic resistance gene persisted through treatment, either carried by identical bacterial species, or linked to mobile genetic elements in different species. Despite the satisfactory performance in chemical removal, the antibiotic-manufacturing wastewater treatment plant continuously enriched zoonotic antibiotic-resistant Aeromonas veronii (an emerging pathogen responsible for substantial economic losses in aquaculture and human health) from influent to effluent, probably due to prolonged β-lactam selection pressure and aquatic nature of A. veronii. This enrichment resulted in a significantly higher abundance of A. veronii in the antibiotic-manufacturing wastewater treatment plant compared to other aquatic samples worldwide. Furthermore, the closest evolutionary relative to the antibiotic-manufacturing wastewater treatment plant derived A. veronii was an isolate obtained from the stool of a local diarrhea patient. These findings highlighted a substantial public health risk posed by antibiotic-manufacturing wastewater treatment plants, underlining their potential role in enriching and disseminating zoonotic antibiotic-resistant pathogens. Beyond chemical monitoring, enhanced surveillance of antibiotic-resistant pathogens and antibiotic resistance genes is needed in antibiotic-manufacturing wastewater treatment plants to avoid creating environmental hotspots of antibiotic resistant pathogens from discharging wastewater effluents.},
}
@article {pmid40256453,
year = {2025},
author = {Shen, D and Ju, H and Wang, H and Wang, X and Li, G},
title = {The clinic application of mNGS and ENA-78 assays to identify intra-amniotic infection/inflammation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1510671},
pmid = {40256453},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology/chemistry ; Adult ; *Chorioamnionitis/diagnosis ; *Inflammation/diagnosis ; *Pregnancy Complications, Infectious/diagnosis ; Biomarkers/analysis ; High-Throughput Nucleotide Sequencing ; Obstetric Labor, Premature/diagnosis ; Pregnancy Outcome ; Cerclage, Cervical ; Young Adult ; *Chemokine CXCL5/analysis ; },
abstract = {OBJECTIVE: The objective of this study is to explore whether metagenomic next-generation sequencing (mNGS) and Epithelial Neutrophil Activating Peptide-78 (ENA-78) assays in the amniotic fluid (AF) of patients with preterm labor (PTL) could be employed for diagnosing intra-amniotic infection/inflammation (IAI/I) and predict the outcomes of emergency cerclage in women with cervical insufficiency(CI).<br><br>METHODS: AF samples from 40 patients were subjected to PTL were subjected to mNGS and microbial culture to diagnose intra-amniotic infection known as microbial invasion of the amniotic cavity (MIAC); ELISA was used to analyze ENA-78 levels for prediction of intra-amniotic inflammation (IAI). Pregnancy outcomes were compared, the predictive performance of mNGS and ENA-78 were assessed to evaluate the efficacy of emergency cervical cerclage.<br><br>RESULTS: The diagnosis rate of MIAC was higher with mNGS (17.5%) compared to microbial culture (2.5%). AF ENA-78 levels were significantly higher in IAI patients than in non-IAI/I patients. ENA-78 demonstrated certain accuracy in identifying IAI, with sensitivity and specificity of 73.3% and 100%, respectively. Compared with non-IAI/I patients, patients with MIAC or IAI exhibited poor pregnancy outcomes after cervical cerclage.<br><br>CONCLUSIONS: mNGS and ENA-78 assays are valuable means for assessing the state of infection/inflammation in the amniotic cavity and predicting the outcomes of emergency cerclage.},
}
@article {pmid40255248,
year = {2025},
author = {Favale, N and Costa, S and Summa, D and Sabbioni, S and Mamolini, E and Tamburini, E and Scapoli, C},
title = {Comparison of microbiome community structure and dynamics during anaerobic digestion of different renewable solid wastes.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100383},
pmid = {40255248},
issn = {2666-5174},
abstract = {This study analysed the effect of the different lignocellulose composition of two crop substrates on the structure and dynamics of bacterial communities during anaerobic digestion (AD) processes for biogas production. To this end, cereal grains and grape pomace biomasses were analysed in parallel in an experimental AD bench-scale system to define and compare their metagenomic profiles for different experimental time intervals. The bacterial community structure and dynamics during the AD process were detected and characterised using high-resolution whole metagenomic shotgun analyses. Statistical evaluation identified 15 strains as specific to two substrates. Some strains, like Clostridium isatidis, Methanothermobacter wolfeii, and Methanobacter sp. MB1 in cereal grains, and Acetomicrobium hydrogeniformans and Acetomicrobium thermoterrenum in grape pomace, were never before detected in biogas reactors. The presence of bacteria such as Acetomicrobium sp. and Petrimonas mucosa, which degrade lipids and protein-rich substrates, along with Methanosarcina sp. and Peptococcaceae bacterium 1109, which tolerate high hydrogen pressures and ammonia concentrations, suggests a complex syntrophic community in lignin-cellulose-enriched substrates. This finding could help develop new strategies for the production of a tailor-made microbial consortium to be inoculated from the beginning of the digestion process of specific lignocellulosic biomass.},
}
@article {pmid40255076,
year = {2025},
author = {Buttler, L and Velázquez-Ramírez, DA and Tiede, A and Conradi, AM and Woltemate, S and Geffers, R and Bremer, B and Spielmann, V and Kahlhöfer, J and Kraft, ARM and Schlüter, D and Wedemeyer, H and Cornberg, M and Falk, C and Vital, M and Maasoumy, B},
title = {Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2487209},
doi = {10.1080/19490976.2025.2487209},
pmid = {40255076},
issn = {1949-0984},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Dysbiosis/microbiology ; *Fungi/classification/isolation &amp; purification/genetics ; *Inflammation/microbiology ; *Liver Cirrhosis/microbiology ; *Mycobiome ; Prospective Studies ; Metagenomics ; Intestinal Mucosa/microbiology ; *End Stage Liver Disease/microbiology/drug therapy ; Adult ; },
abstract = {Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation, and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were prospectively collected from 95 dLC-patients between 2017 and 2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing distinct microbial patterns. G1 (n = 39) displayed lowest diversity and highest Enterococcus abundance, G2 (n = 24) was dominated by Bifidobacteria, G3 (n = 29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed the lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp. (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n = 33; 86.8%), had highest plasma-levels of Zonulin (p = 0.044) and a proinflammatory cytokine profile along with numerically higher incidences of subsequent infections (p = 0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotic treatment significantly contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.},
}
@article {pmid40254830,
year = {2025},
author = {Pham, CM and Rankin, TJ and Stinear, TP and Walsh, CJ and Ryan, FJ},
title = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf173},
pmid = {40254830},
issn = {1477-4054},
support = {GNT1194325//National Health and Medical Research Council of Australia/ ; },
mesh = {*Microbiota ; Humans ; *Software ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; },
abstract = {Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g. species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like gene set enrichment analysis are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, a taxon set enrichment analysis tool available as an R package, a web portal (https://shiny.taxsea.app), and a Python package. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) while also allowing users to incorporate custom sets such as taxonomic groupings. In silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from inflammatory bowel disease and type 2 diabetes metagenomic data, TaxSEA can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation, and advancing understanding of microbiome-host and environmental interactions.},
}
@article {pmid40254787,
year = {2025},
author = {Dame-Teixeira, N and Lynch, J and Yu, X and Cena, JA and Do, T},
title = {The Caries and Caries-Free Archaeome.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251329343},
doi = {10.1177/00220345251329343},
pmid = {40254787},
issn = {1544-0591},
abstract = {The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.},
}
@article {pmid40254701,
year = {2025},
author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K},
title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40254701},
issn = {1867-1314},
abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.},
}
@article {pmid40254251,
year = {2025},
author = {Chang, FM and Chen, YH and Hsu, PS and Wu, TH and Sung, IH and Wu, MC and Nai, YS},
title = {RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108341},
doi = {10.1016/j.jip.2025.108341},
pmid = {40254251},
issn = {1096-0805},
abstract = {The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by a worldwide spread ecto-parasite, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.},
}
@article {pmid40253770,
year = {2025},
author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J},
title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.},
journal = {International immunopharmacology},
volume = {156},
number = {},
pages = {114645},
doi = {10.1016/j.intimp.2025.114645},
pmid = {40253770},
issn = {1878-1705},
abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.<br><br>PURPOSE: This study aims to investigate the effects of BPRC on the gut microbiota and its metabolite SCFAs in T2DM rats.<br><br>METHODS: T2DM rat model was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), followed by a 4-week treatment with BPRC to observe its therapeutic effects. The impact of BPRC on the gut microbiota was studied through metagenomic sequencing. Quantitative analysis of SCFAs was conducted using GC-MS. Western blot and quantitative real-time PCR (qRT-PCR) were conducted to investigate the potential mechanisms of BPRC.<br><br>RESULTS: BPRC significantly improved insulin resistance in T2DM rats, downregulated levels of pancreatic cell apoptosis factors, and upregulated the abundance of Bacteroides uniformis, Bacteroides sp A1C1, Anaerostipes caccae, Alistipes finegoldii and Blautia sp.N6H1-15 in T2DM rats. Additionally, BPRC increased the levels of seven SCFAs in the intestines of T2DM rats. It activated intestinal TGR5, GPR41, GPR43, and GPR109a receptors, collectively upregulating GLP-1 protein expression, and exerted therapeutic effects on T2DM.<br><br>CONCLUSION: The results indicate that the synergistic mechanism of BPRC in treating T2DM is associated with modulating the gut microbiota, increasing SCFAs content in the intestines, and regulating intestinal GLP-1 production.},
}
@article {pmid40253436,
year = {2025},
author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y},
title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {39},
pmid = {40253436},
issn = {2524-6372},
support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; },
abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.},
}
@article {pmid40253169,
year = {2025},
author = {Aryal, A and Nwachukwu, ID and Aryee, ANA},
title = {Examining the impact of crops and foods biofortified with micronutrients on the gut microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {209},
number = {},
pages = {116189},
doi = {10.1016/j.foodres.2025.116189},
pmid = {40253169},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/physiology ; *Micronutrients ; Humans ; *Crops, Agricultural ; *Biofortification ; *Food, Fortified ; Animals ; },
abstract = {Micronutrient deficiencies (MNDs) impact more than three billion individuals worldwide, particularly those in impoverished and marginalized communities, leading to adverse long-term health consequences. Biofortification, which focusses on enhancing the nutrient density of food crops, presents a promising strategy to address this challenge. Recent studies involving both model organisms and human subjects have demonstrated that, beyond remedying common dietary insufficiencies, micronutrients can modulate the composition and functionality of the gut microbiome. The microbiota, in turn, utilize these micronutrients, facilitating digestion, synthesizing essential nutrients, and modulating immune responses, thereby establishing a bidirectional relationship known as the micronutrient-microbiome axis. Numerous studies have also documented significant variations in these interactions, highlighting the complex dynamics of the micronutrient-microbiome relationship. The composition and interactions of the microbiota have been investigated using various methodologies, including 16S rRNA gene sequencing, RT-PCR, metagenomics, and metabolomics. This review explores recent advancements in understanding the reciprocal relationship between micronutrient levels and the gut microbiome, emphasizing key findings that provide critical insights for the development of targeted dietary strategies aimed at alleviating MNDs and improving overall health.},
}
@article {pmid40252922,
year = {2025},
author = {Charya, AV and Jang, MK and Kong, H and Park, W and Tian, X and Keller, M and Phipps, K and Sanders, A and Shah, P and Mathew, J and Aryal, S and Berry, GJ and Marboe, C and Orens, JB and Nathan, SD and Agbor-Enoh, S},
title = {Donor-derived cell-free DNA is associated with the degree of immunosuppression in lung transplantation.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2025.04.011},
pmid = {40252922},
issn = {1600-6143},
abstract = {Donor-derived cell-free DNA is increasingly used in clinical practice to monitor lung transplant patients for acute rejection. However, its association with conventional approaches to monitor immunosuppression remains unclear. This multicenter observational cohort study examines the association of donor-derived cell free DNA with surrogate measures of immunosuppression. Serial plasma samples were collected for quantification of donor-derived cell-free DNA and anellovirus abundance via shotgun and metagenomic sequencing. Adjudication committees reviewed clinical data to define acute cellular and antibody-mediated rejection. The association between ddcfDNA, anellovirus abundance, and serum tacrolimus trough concentrations over the study period and during episodes of acute rejection were examined via linear mixed effects modeling. Donor-derived cell-free DNA demonstrated a significant inverse association with tacrolimus troughs (p=0.027) and anellovirus abundance (p<0.001) over time. Acute rejection episodes were associated with significantly decreased anellovirus abundance (median, 0.042 vs. 0.708, p<0.001) and higher ddcfDNA levels (1.49% vs. 0.26%, p<0.001) compared to stable control timepoints. However, tacrolimus levels were similar between acute rejection and controls (10.1 ng/ml vs 10.3 ng/ml, p = 0.13). Our findings suggest donor-derived cell-free DNA correlates with measures of immunosuppression in lung transplant patients. Additional studies are needed to assess the utility of donor-derived cell-free DNA to assess immunosuppression adequacy.},
}
@article {pmid40252793,
year = {2025},
author = {Yang, R and Guo, S and Huo, L and Yang, G and Tian, S},
title = {Impact of Watershed-Scale Land Restoration on Soil Microbial Communities and Their Functions: Insights from Metagenomic Analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121609},
doi = {10.1016/j.envres.2025.121609},
pmid = {40252793},
issn = {1096-0953},
abstract = {Land restoration in the gully regions of China's Loess Plateau has significantly altered soil conditions and farming practices, yet its impact on soil microbes remains unclear. This study applied metagenomic sequencing and correlation analysis to examine microbial community shifts and key genes involved in carbon, nitrogen, and phosphorus cycling. Results show increased biodiversity and microbial activity, especially downstream, enhancing carbon metabolism and ecosystem resilience. Phosphorus activation improved, with related gene abundance rising by 27.45%-52.57%, facilitating phosphorus availability. Nitrogen cycling showed enhanced nitrification and nitrogen fixation, with reduced denitrification, promoting nitrogen retention. Soil organic carbon, total nitrogen, ammonium nitrogen, and available phosphorus (AP), particularly AP, strongly influenced microbial dynamics. These findings highlight the positive role of land restoration in improving soil health and nutrient cycling, supporting sustainable agriculture.},
}
@article {pmid40252750,
year = {2025},
author = {Yang, M and Peng, L and Mu, M and Yang, F and Li, Z and Han, B and Zhang, K},
title = {Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126277},
doi = {10.1016/j.envpol.2025.126277},
pmid = {40252750},
issn = {1873-6424},
abstract = {Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89%) and Eisenia fetida (48.42%), whereas Euryarchaeota (36.71%) and Actinobacteria (39.42%) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.},
}
@article {pmid40252553,
year = {2025},
author = {Bariod, L and Fuentes, E and Millet, M and White, J and Jacquiod, S and Moreau, J and Monceau, K},
title = {Exposure to pesticides is correlated with gut microbiota alterations in a farmland raptor.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109436},
doi = {10.1016/j.envint.2025.109436},
pmid = {40252553},
issn = {1873-6750},
abstract = {The gut microbiota is crucial for host health and can be impacted by various environmental disruptions, yet the effects of multiple pesticide exposures on farmland organisms' microbiomes remain largely unexplored. We assessed microbiota changes in a wild apex predator exposed to multiple pesticides in agricultural landscapes. Pesticides, including acetochlor and quinoxyfen, which are supposed to be banned, were significantly positively correlated with certain key bacteria from Actinobacteria, Alphaproteobacteria and Gammaproteobacteria classes. Our results light up the potential collateral effect of pesticides on gut bacterial assemblages through unknown mechanisms. These effects could result in dysbiosis and the promotion of potential pathogens and/or the selection of bacteria that might allow the organism to detoxify the organism. Although formal metagenomic analyses would be required soon, these microbial shifts underline the broader ecological consequences of pesticide exposure, emphasising the need for integrated biodiversity conservation and ecosystem management to protect environmental and public health.},
}
@article {pmid40252419,
year = {2025},
author = {Ciuchcinski, K and Kaczorowska, AK and Biernacka, D and Dorawa, S and Kaczorowski, T and Park, Y and Piekarski, K and Stanowski, M and Ishikawa, T and Stokke, R and Steen, IH and Dziewit, L},
title = {Computational pipeline for sustainable enzyme discovery through (re)use of metagenomic data.},
journal = {Journal of environmental management},
volume = {382},
number = {},
pages = {125381},
doi = {10.1016/j.jenvman.2025.125381},
pmid = {40252419},
issn = {1095-8630},
abstract = {Enzymes derived from extremophilic organisms, also known as extremozymes, offer sustainable and efficient solutions for industrial applications. Valued for their resilience and low environmental impact, extremozymes have found use as catalysts in various processes, ranging from dairy production to pharmaceutical manufacturing. However, discovery of novel extremozymes is often hindered by challenges such as culturing difficulties, underrepresentation of extreme environments in reference databases, and limitations of traditional sequence-based screening methods. In this work, we present a computational pipeline designed to discover novel enzymes from metagenomic data derived from extreme environments. This pipeline represents a versatile and sustainable approach that promotes reuse and recycling of existing datasets and minimises the need for additional environmental sampling. In its core, the algorithm integrates both traditional bioinformatic techniques and recent advances in structural prediction, enabling rapid and accurate identification of enzymes. However, due to its design, the algorithm relies heavily on existing databases, which can limit its effectiveness in situations where reference data is scarce or when encountering novel protein families. As a proof-of-concept, we applied the pipeline to metagenomic data from deep-sea hydrothermal vents, with a focus on β-galactosidases. The pipeline identified 11 potential candidate proteins, out of which 10 showed in vitro activity. One of the selected enzymes, βGal_UW07, showed strong potential for industrial applications. The enzyme exhibited optimal activity at 70 °C and was exceptionally resistant to high pH and the presence of metal ions and reducing agents. Overall, our results indicate that the pipeline is highly accurate and can play a key role in sustainable bioprospecting, leveraging existing metagenomic datasets and minimising in situ interventions in pristine regions.},
}
@article {pmid40252413,
year = {2025},
author = {Okamura, T and Hasegawa, Y and Ohno, Y and Saijo, Y and Nakanishi, N and Honda, A and Hamaguchi, M and Takano, H and Fukui, M},
title = {Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet.},
journal = {Chemosphere},
volume = {379},
number = {},
pages = {144401},
doi = {10.1016/j.chemosphere.2025.144401},
pmid = {40252413},
issn = {1879-1298},
abstract = {The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.},
}
@article {pmid40252307,
year = {2025},
author = {Qian, L and Jiang, J and Zhang, Y and Huang, X and Che, Z and Chen, G and Liu, S},
title = {Sublethal exposure to boscalid induced respiratory abnormalities and gut microbiota dysbiosis in adult zebrafish.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {283},
number = {},
pages = {107370},
doi = {10.1016/j.aquatox.2025.107370},
pmid = {40252307},
issn = {1879-1514},
abstract = {Boscalid (BO), one of the frequently detected fungicides of succinate dehydrogenase inhibitor in water environments, has unknown effects on the respiratory function and gut health of aquatic organisms. Therefore, zebrafish were exposed to BO solutions (0.01-1.0 mg/L) for 21 days to assess its effects on zebrafish respiration and intestinal microbiota in this study. The results showed that exposure to 0.1 and 1.0 mg/L BO for 21 days resulted in zebrafish exhibiting aggregation of gill filaments, reduction of mucous cells, and significantly decreased opercular movement, linked to a marked decline in the activity of respiratory chain complex II. 16S rRNA gene sequencing revealed significant changes in the intestinal microbiota composition of zebrafish exposed to 1.0 mg/L BO. Specifically, the relative abundance of beneficial bacteria (Cetobacterium) was markedly reduced, while pathogenic bacteria (such as Ralstonia, Legionella, Acinetobacter, Escherichia/Shigella) associated with energy metabolism and immune pathways in zebrafish showed a significant increase in relative abundance. Accordingly, metagenomic functional prediction analysis further revealed the potential impact of BO-induced gut microbiota changes on energy metabolism and immune pathways in zebrafish. Furthermore, histopathological analysis of intestinal tissues revealed that exposure to BO resulted in necrosis and shedding of epithelial cells, as well as a decrease in goblet cell count, which exacerbated adverse effects on intestinal health. In conclusion, sublethal exposure to BO affects the respiratory function and intestinal health of zebrafish. Therefore, the impact of BO in aquatic environments on fish health warrants attention.},
}
@article {pmid40252261,
year = {2025},
author = {Li, B and Liang, C and Xu, B and Song, P and Liu, D and Zhang, J and Gu, H and Jiang, F and Gao, H and Cai, Z and Zhang, T},
title = {Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer.},
journal = {Microbiological research},
volume = {297},
number = {},
pages = {128182},
doi = {10.1016/j.micres.2025.128182},
pmid = {40252261},
issn = {1618-0623},
abstract = {Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.},
}
@article {pmid40251489,
year = {2025},
author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E},
title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {382},
pmid = {40251489},
issn = {1471-2164},
support = {INV-004891/GATES/Gates Foundation/United States ; },
mesh = {*Bacillus/genetics/isolation &amp; purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.<br><br>RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.<br><br>CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.},
}
@article {pmid40251030,
year = {2025},
author = {Chen, J and Zhang, S and Wang, M and Kang, G and Lu, L and Chang, N and Wang, N and Xie, Z and Liu, Y and Zhang, H and Shen, W},
title = {Investigating the Impact of Landfill Age and Season on the Occurrence and Dissemination of Antibiotic Resistance Genes in Leachate and the Underlying Mechanisms Using Metagenomics.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf091},
pmid = {40251030},
issn = {1365-2672},
abstract = {AIMS: Antibiotic resistance genes (ARGs) pose a critical public health concern, with landfill leachate serving as a significant environmental reservoir. While ARG dynamics in leachate have been investigated in various contexts, their occurrence and influence factors in semi-arid regions remain poorly understood. This study investigated the occurrence and influence factors of ARG profiles, their potential hosts, and underlying mechanisms driving their proliferation.<br><br>METHODS AND RESULTS: Comprehensive metagenomic analysis of leachate samples collected from landfills of varying landfill ages (5, 10, and 20 years) in Hohhot, Inner Mongolia-a representative semi-arid region of northern China-across three seasons (autumn, spring, and summer). Metagenomic analysis revealed distinct patterns in core ARG abundances modulated by both landfill age and seasonal variations. Notably, landfill age predominantly influenced tetracycline- and glycopeptide- ARGs, while seasonal fluctuations primarily affected glycopeptide- and multidrug- ARGs. Taxonomic analysis identified Pseudomonas aeruginosa and Pseudomonas fluorescens as the predominant resistant pathogens, with elevated prevalence during spring and winter compared to summer. Network analysis and metabolic pathway reconstruction demonstrated that landfill age maybe impacted ARG dissemination through modulation of carbohydrate and nitrogen metabolic pathways. This novel finding suggests a previously unrecognized mechanism linking waste decomposition stages to ARG proliferation.<br><br>CONCLUSIONS: Our study provides the first systematic characterization of ARG dynamics in semi-arid landfill leachate, offering crucial insights for developing targeted strategies to mitigate ARG dissemination in these distinct ecological contexts. These findings establish a theoretical framework for understanding ARG transmission in semi-arid environments while providing empirical evidence to inform environmental management practices.},
}
@article {pmid40251011,
year = {2025},
author = {Dawson, SJT and Shibu, P and Garnett, S and Newberry, F and Brook, TC and Tijani, T and Kujawska, M and Hall, LJ and McCartney, AL and Negus, D and Hoyles, L},
title = {Weberviruses are gut-associated phages that infect Klebsiella spp.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf043},
pmid = {40251011},
issn = {1574-6941},
abstract = {Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life and associated depolymerases. In this study we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n=258 from isolates, n=65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n=330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%) and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.},
}
@article {pmid40250773,
year = {2025},
author = {Wu, X and Li, Y and Li, P and Lu, G and Wu, J and Wang, Z and Wen, Q and Cui, B and Wang, J and Zhang, F},
title = {Structural variations in ulcerative colitis-associated E. coli reduce fructose utilization and aggravate inflammation under high fructose diet.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.03.039},
pmid = {40250773},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Structural variations (SVs) have significant effects on the microbial phenotypes. The underlying mechanism of functional changes caused by gut microbial SVs in the development of ulcerative colitis (UC) need further investigation.<br><br>METHODS: We performed long-read (ONT-based) and short-read (Illumina-based) metagenomic sequencing on stool samples from 93 UC patients and 100 healthy controls (HCs), and analyzed microbial SVs. A total of 648 Escherichia coli (E. coli) strains from fecal samples of UC patients (UC-strains) and HCs (HC-strains) were isolated. SV-associated scrK gene deletion was verified via whole-genome sequencing or targeted PCR. Then, representative UC-strains, HC-strains, and scrK-knockout E. coli were used for the in vitro and in vivo experiments to investigate the effects of specific SV in E. coli on fructose utilization ability and colitis.<br><br>RESULTS: E. coli in UC with the highest fold change had SVs-affected functional differences on fructose metabolism to that of HCs. The fructose utilization genes deletion was common in UC-strains, ostensibly reducing fructose utilization in vitro and leading to fructose-dependent aggravation of colitis in murine models. UC-strains and HC-strains induced comparable colitis under low fructose. However, high fructose exacerbated colitis severity exclusively in UC-strain-colonized mice, with elevated intestinal fructose residues, significant microbiome/metabolome changes, increased inflammation, and gut barrier disruption. These changes were mechanistically depended on the deletion of fructose utilization gene scrK.<br><br>CONCLUSIONS: SV-caused difference in fructose utilization and proinflammatory properties in E. coli from UC patients influence the development of UC, emphasizing the importance of fine-scale metagenomic studies in disease.},
}
@article {pmid40250459,
year = {2025},
author = {Munroe, ES and Spicer, A and Castellvi-Font, A and Zalucky, A and Dianti, J and Graham Linck, E and Talisa, V and Urner, M and Angus, DC and Baedorf-Kassis, E and Blette, B and Bos, LD and Buell, KG and Casey, JD and Calfee, CS and Del Sorbo, L and Estenssoro, E and Ferguson, ND and Giblon, R and Granholm, A and Harhay, MO and Heath, A and Hodgson, C and Houle, T and Jiang, C and Kramer, L and Lawler, PR and Leligdowicz, A and Li, F and Liu, K and Maiga, A and Maslove, D and McArthur, C and McAuley, DF and Serpa Neto, A and Oosthuysen, C and Perner, A and Prescott, HC and Rochwerg, B and Sahetya, S and Samoilenko, M and Schnitzer, ME and Seitz, KP and Shah, F and Shankar-Hari, M and Sinha, P and Slutsky, AS and Qian, ET and Webb, SA and Young, PJ and Zampieri, FG and Zarychanski, R and Fan, E and Semler, MW and Churpek, M and Goligher, EC and , and , },
title = {Evidence-based personalised medicine in critical care: a framework for quantifying and applying individualised treatment effects in patients who are critically ill.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(25)00054-2},
pmid = {40250459},
issn = {2213-2619},
abstract = {Clinicians aim to provide treatments that will result in the best outcome for each patient. Ideally, treatment decisions are based on evidence from randomised clinical trials. Randomised trials conventionally report an aggregated difference in outcomes between patients in each group, known as an average treatment effect. However, the actual effect of treatment on outcomes (treatment response) can vary considerably between individuals, and can differ substantially from the average treatment effect. This variation in response to treatment between patients-heterogeneity of treatment effect-is particularly important in critical care because common critical care syndromes (eg, sepsis and acute respiratory distress syndrome) are clinically and biologically heterogeneous. Statistical approaches have been developed to analyse heterogeneity of treatment effect and predict individualised treatment effects for each patient. In this Review, we outline a framework for deriving and validating individualised treatment effects and identify challenges to applying individualised treatment effect estimates to inform treatment decisions in clinical care.},
}
@article {pmid40250281,
year = {2025},
author = {Chen, Y and Hu, S and Hu, B and Li, Y and Chen, Z},
title = {Functional insights into microbial community dynamics and resilience in mycorrhizal associated constructed wetlands under pesticide stress.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138315},
doi = {10.1016/j.jhazmat.2025.138315},
pmid = {40250281},
issn = {1873-3336},
abstract = {Arbuscular mycorrhizal fungi (AMF) are critical mutualistic symbionts in most terrestrial ecosystems, where they facilitate nutrient acquisition, enhance plant resilience to environmental stressors, and shape the surrounding microbiome. However, its contributions (especially for microorganisms) to constructed wetlands (CWs) under pesticide stress remain poorly understood. This study investigated the effects of AMF on microbial community composition, diversity, metabolic pathways, and functional genes by metagenomics in CWs exposed to pesticides stress. Using comparative analyses of AMF-colonized and non-colonized CWs, we found that AMF enhanced overall microbial diversity, as evidenced by increases of 2.22 % (Chao1) and 2.83 % (observed species). Under fungicide stress, nitrogen-cycling microorganisms (e.g., Nitrososphaerota and Mucoromycota) increased in relative abundance, while carbon cycle-related microorganisms (e.g., Pseudomonadota and Bacteroidota) generally declined. AMF colonization improved microbial resilience, demonstrated by a 312 % rise in Rhizophagus abundance and significant increases in phosphorus-cycling microorganisms (e.g., Bradyrhizobium and Mesorhizobium). Functional gene analysis further revealed that AMF helped mitigate fungicide-induced reductions in genes related to nitrogen and carbon cycling, lowering the average decline rates to 4.02 % and 1.44 %, respectively, compared to higher rates in non-AMF treatments. In summary, these findings highlight the crucial role of AMF in enhancing pesticide stress resilience, maintaining microbial community stability, and improving the bioremediation capacity of CWs.},
}
@article {pmid40250270,
year = {2025},
author = {Yang, C and Xu, Y and Yu, T and Li, Y and Zeng, XC},
title = {Microbial reductive mobilization of As(V) in solid phase coupled with the oxidation of sulfur compounds: An overlooked biogeochemical reaction affecting the formation of arsenic-contaminated groundwater.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138234},
doi = {10.1016/j.jhazmat.2025.138234},
pmid = {40250270},
issn = {1873-3336},
abstract = {Dissimilatory As(V)-respiring prokaryotes (DARPs) are recognized as having a crucial role in the formation of arsenic-contaminated groundwater. DARPs use small-molecule organic acids as electron donor to directly reduce As(V) in solid phase to more mobile As(III). Therefore, DARPs are considered to be heterotrophic bacteria. However, these cannot explain why high concentrations of As(III) are produced in environments lacking soluble organic carbon. We thus propose that reduced sulfur compounds may also be utilized by DARPs and affect the DARPs-mediated arsenic mobilization. This study sought to confirm this hypothesis. Metagenomic investigations on the DARP population derived from As-contaminated soil indicated that approximately 84 % of DARP MAGs possess the enzymes potentially catalyzing the oxidation of S[2-], S[0], SO3[2-], or S2O3[2-]. Functional analysis of DARP population and a cultivable strain suggested that DARPs, in addition to small-molecule organic carbon, can effectively use sulfur compounds as electron donor to reduce As(V) to mobile As(III). Arsenic release experiments using DARP population and a cultivable DARP strain showed that DARPs indeed utilized sulfur compounds as the sole electron donors under autotrophic and anaerobic conditions to directly reduce adsorbed As(V) in the soils to mobile As(III). These findings provide new insights into the microbial mechanism responsible for the variation of As(III) concentrations in contaminated groundwater.},
}
@article {pmid40250268,
year = {2025},
author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC},
title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138285},
doi = {10.1016/j.jhazmat.2025.138285},
pmid = {40250268},
issn = {1873-3336},
abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.},
}
@article {pmid40250228,
year = {2025},
author = {Wang, H and Yang, Q and Wang, S},
title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179427},
doi = {10.1016/j.scitotenv.2025.179427},
pmid = {40250228},
issn = {1879-1026},
abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.},
}
@article {pmid40250042,
year = {2025},
author = {Menichini, D and Seta, F and Mastrolia, SA and Cetin, I and Carafa, A and Santagni, S and Foschi, C and Cerboneschi, M and Smeazzetto, S and Neri, I and Facchinetti, F},
title = {Probiotics in pregnancy and group B streptococcus colonization: A multicentric, randomized, placebo-controlled, double-blind study with a focus on vaginal microbioma.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {310},
number = {},
pages = {113976},
doi = {10.1016/j.ejogrb.2025.113976},
pmid = {40250042},
issn = {1872-7654},
abstract = {OBJECTIVE: To evaluate the feasibility and effects of the use of probiotics in pregnancy, starting in the third trimester, on rectovaginal colonization of group B streptococcus (GBS) in women at low obstetric risk.<br><br>METHODS: A multicentre, randomized, placebo-controlled, double-blind, parallel-group study was conducted in three tertiary hospitals in northern Italy and included low-risk pregnant women. The intervention consisted of oral administration of two capsules of probiotics or placebo from 30&#xa0;weeks of pregnancy until 37&#xa0;weeks of pregnancy. The primary outcome was GBS colonization, evaluated with rectovaginal swabs. In a subgroup, selected at random, changes in the vaginal microbiome after treatment administration were evaluated using 16S Metagenomic Sequencing Library Preparation sequencing and analysis.<br><br>RESULTS: In total, 267 pregnant women were randomized to receive probiotics (n&#xa0;=&#xa0;133) or placebo (n&#xa0;=&#xa0;134). The two groups were similar at baseline. After treatment, no differences were found in the rates of positive rectovaginal swabs (p&#xa0;=&#xa0;0.24) and antibiotic administration (p&#xa0;=&#xa0;0.27). Only one case of postpartum fever (>38&#xa0;&#xb0;C) was found in the placebo group. Labour and delivery outcomes and neonatal outcomes were similar in both groups. Analysis of the vaginal microbiota showed that the relative abundance of Lactobacillus spp. was not modified significantly by the probiotics, but the relative abundance of Gardnerella spp. decreased significantly (3.6&#xa0;&#xb1;&#xa0;7.9 vs 5.5&#xa0;&#xb1;&#xa0;10.2; p&#xa0;=&#xa0;0.03). Interestingly, the relative abundance of Lactobacillus spp. reduced significantly in women who subsequently presented with partial rupture of membranes (46.9&#xa0;&#xb1;&#xa0;43.6 vs 77.7&#xa0;&#xb1;&#xa0;24.9; p&#xa0;=&#xa0;0.02).<br><br>CONCLUSION: Although the clinical outcomes were unaffected, administration of probiotics led to favourable changes in vaginal microbiota. It remains to be established how this effect could be translated into clinical advantage.},
}
@article {pmid40249976,
year = {2025},
author = {Zhang, WG and Liang, S and Liao, Y and Ran, G and Ji, S and Gao, Y and Lei, Z},
title = {Insights into the impact of different phytoremediation strategies on antibiotic resistance genes at the metagenomic level in real scenarios.},
journal = {Ecotoxicology and environmental safety},
volume = {296},
number = {},
pages = {118211},
doi = {10.1016/j.ecoenv.2025.118211},
pmid = {40249976},
issn = {1090-2414},
abstract = {Engineered phytoremediation strategies provide cost effective options for eliminating antibiotics and antibiotic resistance genes (ARGs) from wastewater. However, there is a knowledge gap in understanding the impact of these phytoremediation strategies on the on the diversity and composition of ARGs as well as the key driving biotic and biological factors of ARGs at the metagenomic level in real scenarios. Through metagenomic sequencing, this study demonstrates that phytoremediation with Iris pseudacorus L., Myriophyllum verticillatum L., Eichhornia crassipes (Mart.) Solms and Oenanthe javanica (Bl. DC) significantly alters the pattern of antibiotic resistome. This study is the first to reveal, at the omics level, that phytoremediation enhances the diversity of ARGs (3.2 %∼11.6 % improvement), despite reducing their absolute abundances. Furthermore, this study highlights that plant varieties have a significant impact on the performance of phytoremediation in mitigating ARGs. The non-dominant bacterial taxa, specifically Verrucomicrobia, Planctomycetes, and Actinobacteria, play a crucial role in shaping the pattern of the antibiotic resistome during the wastewater treatment. The changes in the total organic carbon, total nitrogen and antibiotics robustly influence the environmental behaviors of antibiotic resistome and microbiome. In summary, this study gives insight into the impact of different phytoremediation strategies on mitigating ARGs at the omics level in real scenarios.},
}
@article {pmid40249811,
year = {2025},
author = {Huss, P and Kieft, K and Meger, A and Nishikawa, K and Anantharaman, K and Raman, S},
title = {Engineering bacteriophages through deep mining of metagenomic motifs.},
journal = {Science advances},
volume = {11},
number = {16},
pages = {eadt6432},
doi = {10.1126/sciadv.adt6432},
pmid = {40249811},
issn = {2375-2548},
mesh = {*Metagenomics/methods ; *Bacteriophage T7/genetics ; *Metagenome ; *Bacteriophages/genetics ; *Genetic Engineering ; },
abstract = {Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where these motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to find sequence motifs in metagenomic datasets to engineer phage activity. Meta-SIFT uses experimental deep mutational scanning data to create sequence profiles to mine metagenomes for functional motifs invisible to other searches. We experimentally tested ~17,000 Meta-SIFT-derived sequence motifs in the receptor binding protein of the T7 phage. The screen revealed thousands of T7 variants with novel host specificity with motifs sourced from distant families. Position, substitution, and location preferences dictated specificity across a panel of 20 hosts and conditions. To demonstrate therapeutic utility, we engineered active T7 variants against foodborne pathogen Escherichia coli O121. Meta-SIFT is a powerful tool to unlock the potential encoded in phage metagenomes to engineer bacteriophages.},
}
@article {pmid40249033,
year = {2025},
author = {Wei, Q and Chen, L and Yin, Y and Pai, M and Duan, H and Zeng, W and Hu, X and Xu, M and Li, S},
title = {Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70341},
doi = {10.1002/jmv.70341},
pmid = {40249033},
issn = {1096-9071},
support = {//This work was supported by the Chinese Society of Blood Transfusion Weigao Research Fund Project (CSBT-MWG-2020-02) and the Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Project (CAMS-2021-I2M-1-060)./ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *HIV Infections/microbiology/blood/drug therapy ; *Microbiota ; Metagenomics ; *Blood Donors ; *Bacteria/genetics/classification/isolation &amp; purification ; Male ; Adult ; Female ; Middle Aged ; Sequence Analysis, DNA ; *Blood/microbiology ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.},
}
@article {pmid40248366,
year = {2025},
author = {Lu, X and Lu, Q and Zhu, R and Sun, M and Chen, H and Ge, Z and Jiang, Y and Wang, Z and Zhang, L and Zhang, W and Dai, Z},
title = {Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582553},
pmid = {40248366},
issn = {2235-2988},
mesh = {Female ; Humans ; *Virome/genetics ; *Vagina/virology/microbiology ; *Metagenomics ; Phylogeny ; *Vaginitis/virology/microbiology ; Adult ; Microbiota ; Bacteriophages/genetics/classification ; *Viruses/classification/genetics/isolation &amp; purification ; Middle Aged ; Biodiversity ; Young Adult ; Bacteria/classification/genetics ; },
abstract = {INTRODUCTION: The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.<br><br>METHODS: We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.<br><br>RESULTS: DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.<br><br>DISCUSSION: These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.},
}
@article {pmid40247828,
year = {2025},
author = {Doorenspleet, K and Mailli, AA and van der Hoorn, BB and Beentjes, KK and De Backer, A and Derycke, S and Murk, AJ and Reiss, H and Nijland, R},
title = {Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19158},
pmid = {40247828},
issn = {2167-8359},
mesh = {*Biodiversity ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; North Sea ; Nanopores ; Belgium ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.},
}
@article {pmid40247824,
year = {2025},
author = {Chen, P and Yu, Q and Wang, C and Montoya, L and West, PT and Xu, L and Varoquaux, N and Cole, B and Hixson, KK and Kim, YM and Liu, L and Zhang, B and Zhang, J and Li, B and Purdom, E and Vogel, J and Jansson, C and Hutmacher, RB and Dahlberg, JA and Coleman-Derr, D and Lemaux, PG and Taylor, JW and Gao, C},
title = {Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70155},
pmid = {40247824},
issn = {1469-8137},
support = {32022002//National Natural Science Foundation of China/ ; 32101286//National Natural Science Foundation of China/ ; 32170129//National Natural Science Foundation of China/ ; 32322053//National Natural Science Foundation of China/ ; 2022YFC2303100//National Key Research and Development Program of China/ ; XDA28030401//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.},
}
@article {pmid40247698,
year = {2025},
author = {Zhao, J and Pachiadaki, M and Conrad, RE and Hatt, JK and Bristow, LA and Rodriguez-R, LM and Rossello-Mora, R and Stewart, FJ and Konstantinidis, KT},
title = {Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf072},
pmid = {40247698},
issn = {1751-7370},
abstract = {Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a recently developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spreading of adaptive mutations within the species (gene sweeps), further promoting the high intra-species diversity observed. Collectively, these results implicate rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species.},
}
@article {pmid40247632,
year = {2025},
author = {Lee, JS and Kao, DJ and Worledge, CS and Villamaria, ZF and Wang, RX and Welch, NM and Kostelecky, RE and Colgan, SP},
title = {E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2490211},
doi = {10.1080/19490976.2025.2490211},
pmid = {40247632},
issn = {1949-0984},
mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Wound Healing ; Gastrointestinal Microbiome ; Mice ; *Purines/metabolism ; *Colon/microbiology/metabolism/pathology ; *Butyrates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Colitis/chemically induced/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Male ; },
abstract = {The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.},
}
@article {pmid40246700,
year = {2025},
author = {Iguchi, H and Watanabe, A},
title = {Honey flavors formed via yeast fermentation in honey from Japanese honeybees.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf057},
pmid = {40246700},
issn = {1347-6947},
abstract = {Honey is formed from floral nectar through bee-derived substances, dehydration, and chemical reactions during storage in beehives. While bacteria and fungi inhabit honey and beehives, their roles in honey maturation remain unclear. In this study, we characterized the fermentation process of honey from Apis cerana japonica (Japanese honeybee) with respect to its microbial and flavor compound profiles. Metagenomic analysis revealed that the fungi in Japanese honeybee honey are dominated by Zygosaccharomyces siamensis, with minor members of Talaromyces, Oidiodendron, Starmerella, and Priceomyces. Fermentation of diluted raw honey increased the population of Z. siamensis. Inoculating honey with Z. siamensis produced aromatic compounds, including isoamyl alcohol, hotrienol, 2-phenylethanol, and 2-phenylethyl acetate, as well as the organic acid succinate. These results indicate that fermentation by Z. siamensis can generate favorable flavor compounds, offering the potential for enhancing honey's sensory qualities and applications in the food industry.},
}
@article {pmid40246602,
year = {2025},
author = {Zeng, S and Wang, S and Mu, D},
title = {Metagenomics for IgA-coated gut microbiota: from taxonomy to function.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.001},
pmid = {40246602},
issn = {1878-4380},
abstract = {Immunoglobulin A (IgA) establishes intricate interactions with human gut microbiota, thereby forming IgA-coated microbiota. This forum first explores state-of-the-art metagenomic techniques for characterizing IgA-coated microbiota. Thereafter, metagenomic insights into its taxonomic diversity and microbial genomic functions that mediate IgA coating are provided. Finally, clinical implications for human health are highlighted.},
}
@article {pmid40246210,
year = {2025},
author = {Wani, AK and Qadir, F and Elboughdiri, N and Rahayu, F and Saefudin, and Pranowo, D and Martasari, C and Kosmiatin, M and Suhara, C and Sudaryono, T and Prayogo, Y and Yadav, KK and Muzammil, K and Eltayeb, LB and Alreshidi, MA and Singh, R},
title = {Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108580},
doi = {10.1016/j.biotechadv.2025.108580},
pmid = {40246210},
issn = {1873-1899},
abstract = {Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.},
}
@article {pmid40245994,
year = {2025},
author = {Yang, R and Liu, Z and Liu, Y and Yang, Z and Zhang, Y and Lei, J and Wang, J and Zhang, A and Li, Z},
title = {High-throughput community and metagenomic elucidate systematic performance variation and functional transition mechanisms during morphological evolution of aerobic sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132550},
doi = {10.1016/j.biortech.2025.132550},
pmid = {40245994},
issn = {1873-2976},
abstract = {In this study, high-throughput sequencing and metagenomics were used to investigate the microbial succession and functional gene dynamics during aerobic sludge granulation from activated sludge (AS) to aerobic granular sludge (AGS) to algal-bacterial granular sludge (ABGS). It was found that the settleability and pollutant removal efficiency of the sludge system increased with the sludge morphology evolution. Extracellular polymeric substances (EPS) analysis showed a rise in protein from 2.1 to 17.4 mg/gSS during stage of AGS and polysaccharides from 3.3 to 5.9 mg/gSS during stage of ABGS. Microbial community analysis revealed that the sludge evolution reduced species richness but enriched functional bacteria for nitrogen/phosphorus removal, while increasing the complexity of community structure and close interactions between species. Key genes involved in the tricarboxylic acid cycle, nitrogen/phosphorus and EPS metabolism were also upregulated. This study revealed the continuity mechanism and stage dependence of the functional transition during sludge morphology evolution.},
}
@article {pmid40245993,
year = {2025},
author = {Zhang, J and Zhang, B and Duan, F and Xuan, Z and Sun, T and Lu, L},
title = {Metagenomic exploration of novel β-galactosidases for glycosylation engineering.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132546},
doi = {10.1016/j.biortech.2025.132546},
pmid = {40245993},
issn = {1873-2976},
abstract = {β-Galactosidases are important enzymatic tools for glycosylation, but their properties vary greatly with the source. Here, ten putative β-galactosidase genes, designated as bga1 to bga10, encoding proteins Bga1 to Bga10, were mined from an environmental metagenomic dataset comprising 119,152 sequences. Five of the encoded enzyme proteins exhibited less than 80% sequence similarity to known enzymes, but displayed conserved catalytic sites in their predicted three-dimensional models. After heterologous expression and characterization, two recombinant enzymes showed specific hydrolysis activity toward o-nitrophenyl-β-d-galactopyranoside. One of them, Bga4R, exhibited remarkable activity at pH 7.4 and 50℃, with excellent alkaline stability. Notably, Bga4R tolerated a wide range of acceptors for transglycosylation. It catalyzed galactosyl transfer to various monosaccharides and sugar alcohols, and enabling the synthesis of diverse glycosylated derivatives. This study identifies a novel GH 1 β-galactosidase as a powerful tool for glycosylation engineering, with promising potential for synthesizing galactosides valuable to food and pharmaceutical industries.},
}
@article {pmid40245807,
year = {2025},
author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C},
title = {New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation.},
journal = {Water research},
volume = {282},
number = {},
pages = {123607},
doi = {10.1016/j.watres.2025.123607},
pmid = {40245807},
issn = {1879-2448},
abstract = {Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.},
}
@article {pmid40245806,
year = {2025},
author = {Li, J and Zuo, X and Chen, Q and Lin, Y and Meng, F},
title = {Genome-resolved metagenomic analysis reveals a novel denitrifier with truncated nitrite reduction pathway from the genus SC-I-84.},
journal = {Water research},
volume = {282},
number = {},
pages = {123598},
doi = {10.1016/j.watres.2025.123598},
pmid = {40245806},
issn = {1879-2448},
abstract = {Understanding the genomic and ecological traits of partial denitrification (PD) bacteria is of high importance for developing wastewater treatment technologies. In this study, a PD-based bioreactor was operated, resulting in a mixed culture dominated by a potentially novel PD functional bacterium (SC-I-84). Progressively increased activity in both nitrate reduction and nitrite production were observed in the SC-I-84 enrichment system, whereas the nitrite reduction activity was always negligible. The phylogenetic analysis indicated that SC-I-84 was closely related to an uncultured beta-proteobacterium (99 %), whereas its denitrification functional genes (napA, napB, narV, and narY) exhibited evidence of co-evolution with chromosomal genes from the genus Cupriavidus, order Burkholderiales. In the genetic sketch of SC-I-84, only nitrate-reduction genes (nar and nap) were identified, whereas nitrite-reduction genes (nir) were absent. Notably, nitrate reduction genes were adjacent to carbon metabolism genes (sucB/C, mdh, idh) and a high abundance of tricarboxylic acid (TCA) cycling genes were found. This can promote the utilization efficiency of electron donors by nitrate reduction genes in SC-I-84, thus enhancing the denitrification activity. Furthermore, SC-I-84 positively cooperated with some bacteria that participate in nitrogen and carbon metabolism and other PD bacteria, but negatively interacted with full-denitrification bacteria. These results indicate that the enrichment of SC-I-84 restricted the growth of full-denitrification bacteria, aiding in the maintenance of a stable PD process. Taken together, the meta-genomic analysis of the novel PD functional bacterium is expected to enhance our understanding of PD processes and aid in the development of PD-based wastewater treatment processes.},
}
@article {pmid40245686,
year = {2025},
author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, &#xc1; and Muñoz, S and García-Cañas, V},
title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {262},
number = {},
pages = {116896},
doi = {10.1016/j.jpba.2025.116896},
pmid = {40245686},
issn = {1873-264X},
abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.},
}
@article {pmid40245533,
year = {2025},
author = {Zhao, J and Wang, Y and Zhang, D and Du, J and Gao, Y and Lu, MY and Guo, JY and Su, HT and Chen, XF and Wen, DH and Jia, SY and Xu, YC and Chen, J and Yang, QW},
title = {Uncovering the unseen: Metagenomic next-generation sequencing improves liver abscess diagnostics.},
journal = {Journal of infection and public health},
volume = {18},
number = {7},
pages = {102708},
doi = {10.1016/j.jiph.2025.102708},
pmid = {40245533},
issn = {1876-035X},
abstract = {BACKGROUND: This study retrospectively analyzed the metagenomic next-generation sequencing (mNGS) results and clinical data from patients with liver abscess (LA) to investigate the clinical value of mNGS in the diagnosis of LA.<br><br>METHODS: This retrospective observational study included patients with LA who were admitted to Peking Union Medical College Hospital (PUMCH) between April 2022 and July 2024. We comprehensively analyzed the final clinical etiological diagnosis, traditional pathogen detection through conventional microbiological testing (CMT), and mNGS results in terms of pathogen type and specimen turnaround time.<br><br>RESULTS: Among 60 patients with LA, 19 types of pathogens were identified. Using clinical etiological diagnosis as the standard, mNGS identified all pathogens, whereas CMT identified only 42.11&#x202f;% of pathogens. The true-positivity rate of mNGS (86.67&#x202f;%) was significantly higher than that of CMT (58.33&#x202f;%; P&#x202f;<&#x202f;0.001). The average specimen turnaround time for mNGS (57.66&#x202f;h) was shorter than that for CMT (86.54&#x202f;hours, P&#x202f;<&#x202f;0.001).<br><br>CONCLUSIONS: Compared with existing CMT, mNGS offers higher true-positive rates, broader pathogen coverage, and shorter specimen turnaround time. These advantages contribute to more accurate clinical diagnosis and treatment.},
}
@article {pmid40245502,
year = {2025},
author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT},
title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179353},
doi = {10.1016/j.scitotenv.2025.179353},
pmid = {40245502},
issn = {1879-1026},
abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.},
}
@article {pmid40244604,
year = {2025},
author = {Koyanagi, Y and Sajiki, AF and Yuki, K and Ushida, H and Kawano, K and Fujita, K and Shimizu, H and Okuda, D and Kosaka, M and Yamada, K and Suzumura, A and Kachi, S and Kaneko, H and Komatsu, H and Usui, Y and Goto, H and Nishiguchi, KM},
title = {Application of Metagenomic Long-Read Sequencing for the Diagnosis of Herpetic Uveitis.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {66},
number = {4},
pages = {50},
doi = {10.1167/iovs.66.4.50},
pmid = {40244604},
issn = {1552-5783},
mesh = {Humans ; *Aqueous Humor/virology ; Female ; Male ; *Uveitis/diagnosis/virology ; Middle Aged ; *Metagenomics/methods ; *DNA, Viral/analysis/genetics ; *Eye Infections, Viral/diagnosis/virology ; Adult ; Sensitivity and Specificity ; Aged ; Multiplex Polymerase Chain Reaction ; *Herpesviridae/genetics/isolation &amp; purification ; Young Adult ; },
abstract = {PURPOSE: To investigate the sensitivity and specificity of herpes virus detection by nanopore metagenomic analysis (NMA) compared with multiplex polymerase chain reaction (mPCR)-positive and -negative controls.<br><br>METHODS: This study included 43 patients with uveitis who had been screened for intraocular herpes virus infection using mPCR from aqueous humor samples. Aqueous humor samples stored after mPCR were subjected to whole-genome amplification, long-read sequencing, and analysis of the phylogenetic microorganism composition using a Flongle flow cell on the Oxford Nanopore MinION platform. For samples that tested positive with mPCR and negative with the Flongle flow cell, additional long-read sequencing was performed using a MinION flow cell, which enabled acquisition of more sequence data. The sensitivity and specificity of herpes virus detection by NMA were compared with the mPCR-positive and -negative controls.<br><br>RESULTS: NMA using a Flongle flow cell detected the pathogenic virus in 60.0% of those who tested positive by mPCR (12/20). Further analysis using the MinION flow cell successfully identified viral DNA fragments in three out of the eight initially undetected samples, yielding a collective sensitivity of 75.0% (15/20). All of the virus detected with the long-read sequencing were identical to those diagnosed by mPCR testing, and none of the samples that tested negative by mPCR revealed herpes viral DNA with the use of long-read sequencing.<br><br>CONCLUSIONS: For the detection of etiologic herpes virus DNA fragments, NMA revealed a reasonable sensitivity and high specificity. Our study highlights the potential of nanopore sequencing to facilitate further advances in uveitis diagnosis.},
}
@article {pmid40244481,
year = {2025},
author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R},
title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {248},
pmid = {40244481},
issn = {1432-0991},
support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; },
mesh = {Thailand ; *Bacteria/classification/genetics/isolation &amp; purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; },
abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.},
}
@article {pmid40244477,
year = {2025},
author = {Li, J and Zhang, Y and He, L},
title = {The role of urine microbiota in culture-negative patients with pyuria.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {227},
pmid = {40244477},
issn = {1433-8726},
mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; },
abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.<br><br>METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.<br><br>RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p&#x2009;=&#x2009;0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p&#x2009;=&#x2009;0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p&#x2009;=&#x2009;0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p&#x2009;=&#x2009;0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p&#x2009;<&#x2009;0.001].<br><br>CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.},
}
@article {pmid40244062,
year = {2025},
author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC},
title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf071},
pmid = {40244062},
issn = {1751-7370},
support = {COEVOPRO 802242//European Research Council Starting/ ; },
abstract = {Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.},
}
@article {pmid40243577,
year = {2025},
author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J},
title = {Potential Role of Malassezia restricta in Pterygium Development.},
journal = {International journal of molecular sciences},
volume = {26},
number = {7},
pages = {},
doi = {10.3390/ijms26072976},
pmid = {40243577},
issn = {1422-0067},
support = {IP-2020-02-8921//Croatian Science Foundation/ ; },
mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation &amp; purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; },
abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.},
}
@article {pmid40243351,
year = {2025},
author = {Li, Y and Liu, S and Han, P and Lei, J and Wang, H and Zhu, W and Dong, Z and Zhang, Y and Jiang, Z and Zheng, B and Rao, G and Yu, Z and Li, A},
title = {Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0259224},
doi = {10.1128/spectrum.02592-24},
pmid = {40243351},
issn = {2165-0497},
abstract = {UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generation sequencing (mNGS) for rapid antimicrobial susceptibility prediction (mNGS-based AST), which was tailored to five ESKAPEE bacteria: Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. However, the clinical utility remained unvalidated. Assuming that mNGS-based AST results were obtained during clinical management, we assessed its clinical utility using data from a previous observational cohort study of clinical mNGS applications. We collected the data from 114 patients infected with five ESKAPEE bacteria from 07/2021 to 03/2023 and incorporated the sequencing data into the model. We evaluated the performance and hypothetical impact of the method by comparing its results and therapy recommendations with those based on traditional culture-based AST. The primary outcome was the performance of mNGS-based AST (n = 113 strains). mNGS-based AST displayed an overall accuracy of 93.84% and shorter turnaround time (1.12 ± 0.33 days vs 2.81 ± 0.57 days for culture-based AST, t = -27.31, P < 0.05). The secondary outcomes included the proportion of patients who could benefit from mNGS-based AST. It could allow earlier and suitable antibacterial adjustments in 32.05% of culture-positive patients (25/78) and offer actionable antimicrobial susceptibility results in 16.67% of culture-negative cases (6/36). mNGS-based AST offers a promising approach for individualized antibacterial therapy.<br><br>IMPORTANCE: Metagenomic next-generation sequencing (mNGS)-based antimicrobial susceptibility prediction (AST) is a novel method for predicting the antimicrobial susceptibility of ESKAPEE bacteria using a machine learning approach and short-read sequencing data. Assuming that mNGS-based AST results were obtained during clinical management, it could significantly reduce turnaround time while maintaining a high level of accuracy, allowing for earlier therapeutic adjustments for patients. Furthermore, mNGS-based AST can be integrated with clinical mNGS to maximize the utility of short-read data without substantial cost increases. This study demonstrates the potential of mNGS-based AST for precise, individualized antibacterial selection and highlights its broader applicability in enhancing clinical antimicrobial use for various infections.},
}
@article {pmid40243342,
year = {2025},
author = {Gruninger, RJ and McCormack, ML and Chomistek, NC and Zaheer, R and McAllister, TA},
title = {Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0042325},
doi = {10.1128/spectrum.00423-25},
pmid = {40243342},
issn = {2165-0497},
abstract = {UNLABELLED: Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.<br><br>IMPORTANCE: Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.},
}
@article {pmid40243306,
year = {2025},
author = {Wang, Z and Sun, Y and Wang, H and Yun, J and Du, W},
title = {Metagenome-assembled genome of a novel Pseudoalteromonas species from South Mid-Atlantic Ridge deep-sea water suggests potential for chitin degradation.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0018925},
doi = {10.1128/mra.00189-25},
pmid = {40243306},
issn = {2576-098X},
abstract = {We report a high-quality metagenome-assembled genome (MAG) of a novel Pseudoalteromonas species recovered from deep-sea water of the South Mid-Atlantic Ridge. This MAG encodes key chitinase-related genes, suggesting potential involvement in chitin degradation and organic matter remineralization in the deep sea.},
}
@article {pmid40242593,
year = {2025},
author = {Sun, S and He, R and Chen, S and Ren, J and Ma, X and Yang, J},
title = {Odontogenic brain abscess caused by Porphyromonas gingivalis and Streptococcus constellatus: a case report and review article.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2485197},
pmid = {40242593},
issn = {2000-2297},
abstract = {BACKGROUND: Odontogenic brain abscess is a rare, but potentially fatal, central nervous system infection, with insidious onset and unclear etiology.<br><br>METHODS: This case reports a 70-year-old male patient who developed an odontogenic brain abscess secondary to periodontal infection and underwent neurological surgery. Extract pus during surgery for the metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: The mNGS of pus samples obtained from brain abscess aspiration identified the periodontal pathogens Porphyromonas gingivalis and Streptococcus constellatus. Consequently, he was referred to the department of stomatology for further examination and treatment.<br><br>CONCLUSIONS: Our study found that major periodontal pathogens including P. gingivalis and S. constellatus were essential in the development of odontogenic brain abscesses; thus, timely intervention and preventive measures are important for treatment.},
}
@article {pmid40242244,
year = {2025},
author = {Kang, Z and Zhang, R and Li, S and Wang, J and Huang, M and Li, W},
title = {Preliminary investigation of gut microbiota and associated metabolic pathways in the pathogenesis of primary central nervous system lymphoma.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1548146},
pmid = {40242244},
issn = {2234-943X},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) is a rare and highly aggressive form of non-Hodgkin lymphoma, primarily confined to the central nervous system. In recent years, growing evidence has indicated that dysbiosis of the gut microbiota is closely associated with the development of various malignancies. This study aims to systematically explore the potential role of gut microbiota and their metabolic pathways in the pathogenesis of PCNSL by integrating metagenomic and metabolomic approaches.<br><br>MATERIALS AND METHODS: A total of 33 PCNSL patients and 32 healthy controls were enrolled in this study, and fecal samples were collected from each participant. The fecal samples were analyzed using metagenomic and metabolomic techniques, followed by KEGG pathway enrichment analysis to investigate the biological pathways enriched by the differential gut microbiota and metabolites.<br><br>RESULTS: Significant differences were observed in the composition of gut microbiota and metabolites between PCNSL patients and healthy controls. In the gut microbiota of PCNSL patients, the abundance of the phylum Proteobacteria was markedly increased, while the Firmicutes/Bacteroidetes (F/B) ratio was significantly elevated. Metabolomic analysis revealed that the abundance of oleamide was significantly reduced in the PCNSL group, while the relative abundance of deoxycholic acid was significantly elevated. KEGG pathway analysis indicated that the differential gut microbiota and metabolites were primarily involved in key metabolic pathways such as nitrogen metabolism, phenylalanine metabolism, purine metabolism, and pyrimidine metabolism, with these pathways being more active in PCNSL patients.<br><br>CONCLUSION: This study is the first to systematically investigate the differences in gut microbiota and their metabolites between PCNSL patients and healthy individuals, highlighting the potential role of gut microbiota alterations in the pathogenesis of PCNSL.},
}
@article {pmid40241899,
year = {2025},
author = {Chen, L and Weng, W and Li, D and Xie, W and Lu, L and Li, S},
title = {Case Report: A clinically relevant isolation of Gardnerella leopoldii guided by morphological and molecular evidence from a urinary tract infection case.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1548067},
pmid = {40241899},
issn = {2296-858X},
abstract = {BACKGROUND: The genus Gardnerella is commonly found in the vaginal ecosystem and is considered a covert pathogen of the urinary tract. However, Gardnerella vaginalis had been the only recognized species of the genus Gardnerella for decades. Cases regarding the clinical relevance of Gardnerella leopoldii have rarely been reported, which is crucial for fully understanding the various species within the genus Gardnerella.<br><br>CASE PRESENTATION: A 72-year-old female patient was admitted to the hospital with gross hematuria and complaints of waist soreness. Physical examinations, including those of the head, chest, and abdomen, along with routine laboratory tests such as white blood cell (WBC) count and proportion, liver function, and renal function, yielded normal results. However, the patient also exhibited significantly elevated levels of serum C-reactive protein (CRP) and abnormal urinary test findings, which revealed positive results for occult blood and leukocyte esterase, and increased counts of erythrocyte and leukocyte. To further evaluate the urinary system, computerized tomography urography (CTU) was performed. The CTU results revealed multiple weakly enhanced foci in the right kidney and thickening of the right ureter, renal pelvis, calyces, and bladder walls. Based on the above findings, the initial diagnosis included hematuria, hydronephrosis, and urinary tract infection (UTI). To identify the causative pathogens, we employed a comprehensive approach that included microscopic morphology, Sanger sequencing, and metagenomic next-generation sequencing (mNGS). Finally, both Mycobacterium tuberculosis and G. leopoldii were identified as the co-infecting etiological agents responsible for the patient's urinary tract infection.<br><br>CONCLUSION: This case represents the first documented isolation of clinically relevant G. leopoldii, guided by morphological and molecular evidence from a clinical urine sample. It highlights the potential of mNGS as a promising tool for identifying previously unrecognized species and offers valuable insights to enhance the understanding of clinically relevant microorganisms.},
}
@article {pmid40241768,
year = {2025},
author = {Yao, XQ and Bao, H and La, NT and Jiang, GS and Zhai, PH and Liu, CB and Yu, L},
title = {Gut microbiota contribute to cold adaptation in mammals-primates and ungulates.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112245},
pmid = {40241768},
issn = {2589-0042},
abstract = {Gut microbiota play an influential role in how animals adapt to extreme environments. Two phylogenetically distant mammals, Yunnan snub-nosed monkey and reindeer both adapted to frigid environments. Metagenomic analyses revealed they developed similar cold adaptation strategies in response to food scarcity (enhanced fiber degradation and nitrogen balance maintenance), energy shortages (increased short-chain fatty acid [SCFA] synthesis), and a constant body temperature sustainment (stimulation of non-shivering thermogenesis [NST]). Moreover, they evolved distinct adaptation strategies to cope with different cold ecosystems. Yunnan snub-nosed monkey adapt to high-altitude hypoxia environment through enhancing ability to synthesize lactate and metabolize purine, while reindeer adapt to extreme cold environment through increasing blood flow, strengthening urea cycling, and enriching fat storage associated bacteria. Notably, reindeer microbiota uniquely enriched cholesterol-degrading bacteria, potentially mitigating cardiovascular risks from lipid storage. Our study expands the knowledge of how gut microbiome promotes cold adaptation through shared and specialized mechanisms shaped by different phylogenetic and ecological contexts.},
}
@article {pmid40241748,
year = {2025},
author = {Liu, T and Kress, AM and Debelius, J and Zhao, N and Smirnova, E and Bandyopadhyay, S and Bonham, K and Comstock, SS and Gill, S and Gern, JE and Koinis-Mitchell, D and Klepac-Ceraj, V and Lee-Sarwar, K and Litonjua, AA and McKee, K and McCauley, K and O'Connor, TG and Rosas-Salazar, C and Scheible, K and Stanford, JB and Moore, B and Jacobson, LP and Mueller, NT and , },
title = {Maternal vaginal and fecal microbiota in later pregnancy contribute to child fecal microbiota development in the ECHO cohort.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112211},
pmid = {40241748},
issn = {2589-0042},
abstract = {There is growing interest in the use of microbial-seeding interventions to mitigate the impacts of prenatal antibiotics, C-section, and lack of breastfeeding on mother-child microbe sharing. However, the relative importance of maternal vaginal vs. fecal microbiota in this process is unclear. Analyzing 16S rRNA sequences from five US birth cohorts, we found that maternal vaginal and fecal microbiota became more similar as pregnancy progressed, and both niches influenced the child's fecal microbiota. The relative contribution of maternal vaginal microbiota increased when vaginal sampling occurred later in gestation. As children aged from birth to 5 years, their fecal microbiota increasingly resembled their mother's fecal microbiota as compared to vaginal microbiota. Patterns of sharing appeared to differ by prenatal antibiotic use, birth mode (C-section vs. vaginal), and breastfeeding. Our findings enhance understanding of niche-specific mother-child microbe sharing and may inform microbial-seeding interventions. Metagenomic studies are needed to identify specific shared strains.},
}
@article {pmid40241728,
year = {2025},
author = {Xie, L and Wang, X and Wang, X and Liu, X},
title = {Changes in microbial community succession and volatile compounds during the natural fermentation of bangcai.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581378},
pmid = {40241728},
issn = {1664-302X},
abstract = {INTRODUCTION: Fermented bangcai (Brassica juncea var. crassicaulis) is a traditional Chinese food with unique flavor. However, the formation mechanism of flavor compounds related to the fermentation process of bangcai has not been thoroughly studied.<br><br>METHODS: Gas chromatography-ion mobility spectrometry technology combined with metagenomics was used to analyze the characteristic volatile flavor compounds and microbial community structure of bangcai before and after fermentation in this study.<br><br>RESULTS: A total of 91 types of volatile organic compounds were detected in this study. The pungent odor brought by allyl isothiocyanate, 1-butene isothiocyanate, and other substances in the raw materials was removed through fermentation. This process led to the formation of flavor substances such as propyl acetate, ethyl acetate, and 2-methyl-3-furanthiol, which imparted bangcai with flavors of flower and fruit, roast meat, and fried coffee. In addition, our study found that after air drying, bangcai mainly contained &#x3b3;-butyrolactone, nonanal and other flavor compounds, giving the bangcai products a richer floral and fruity flavor profile. Citrobacter, Lactobacillus, and Leuconostoc were the dominant bacteria in the fermentation process of bangcai. They were significantly related to the formation of differential flavor compounds such as &#x3b3;-butyrolactone, ethyl 2-methylpropanoat, and benzaldehyde-D.<br><br>DISCUSSION: These results provide a theoretical basis for improving the flavor quality of fermented vegetable products.},
}
@article {pmid40241696,
year = {2025},
author = {Yang, Z and Xie, Y and Zhu, Y and Lei, M and Chen, X and Jin, W and Fu, C and Yu, L},
title = {Unraveling the flavor formation process of mellow and thick-type ripened Pu-erh tea through non-targeted metabolomics and metagenomics.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102424},
pmid = {40241696},
issn = {2590-1575},
abstract = {Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes (P < 0.05). The contents of free amino acids, L-theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea, Aspergillus, Brachybacterium, and Staphylococcus. By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium. This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters (P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.},
}
@article {pmid40241220,
year = {2025},
author = {Yang, K and Li, G and Li, Q and Wang, W and Zhao, X and Shao, N and Qiu, H and Liu, J and Xu, L and Zhao, J},
title = {Distribution of gut microbiota across intestinal segments and their impact on human physiological and pathological processes.},
journal = {Cell &amp; bioscience},
volume = {15},
number = {1},
pages = {47},
pmid = {40241220},
issn = {2045-3701},
support = {82272812//National Natural Science Foundation of China/ ; 82360018//National Natural Science Foundation of China/ ; },
abstract = {In recent years, advancements in metagenomics, metabolomics, and single-cell sequencing have enhanced our understanding of the intricate relationships between gut microbiota and their hosts. Gut microbiota colonize humans from birth, with their initial composition significantly influenced by the mode of delivery and feeding method. During the transition from infancy to early childhood, exposure to a diverse diet and the maturation of the immune system lead to the gradual stabilization of gut microbiota's composition and distribution. Numerous studies have demonstrated that gut microbiota can influence a wide range of physiological functions and pathological processes by interacting with various tissues and organs through the gut-organ axis. Different intestinal segments exhibit unique physical and chemical conditions, which leads to the formation of vertical gradients along the intestinal tract: aerobes and facultative aerobes mainly live in the small intestine and anaerobic bacteria mainly live in the large intestine, and horizontal gradients: mucosa-associated microbiota and lumen-associated microbiota. In this review, we systematically summarize the distribution characteristics of gut microbiota across six intestinal segments: duodenum, jejunum, ileum, cecum, colon, and rectum. We also draw a conclusion that gut microbiota distributed in different intestinal segments affect the progression of different diseases. We hope to elucidate the role of microbiota at specific anatomic sites within the gut in precisely regulating the processes of particular diseases, thereby providing a solid foundation for developing novel diagnostic and therapeutic strategies for related diseases.},
}
@article {pmid40240641,
year = {2025},
author = {Muñoz-Rivera, MP and Martínez-Morales, F and Guzmán-Morales, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR},
title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40240641},
issn = {1618-1905},
abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.},
}
@article {pmid40240456,
year = {2025},
author = {Bahetjan, K and Yu-Xia, and Lin, S and Aili, N and Yang, H and Du, S},
title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13179},
pmid = {40240456},
issn = {2045-2322},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; },
abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.},
}
@article {pmid40240384,
year = {2025},
author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, J&#xc9;CT and Arruda, P and Dante, RA and Gerhardt, IR},
title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {636},
pmid = {40240384},
issn = {2052-4463},
support = {2022/08797-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (S&#xe3;o Paulo Research Foundation)/ ; 2022/08797-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (S&#xe3;o Paulo Research Foundation)/ ; },
mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.},
}
@article {pmid40240311,
year = {2025},
author = {Liu, D and Abdellah, YAY and Dou, T and Keiblinger, KM and Zhou, Z and Bhople, P and Jiang, J and Shi, X and Zhang, F and Yu, F and Xing, B},
title = {Livestock-Crop-Mushroom (LCM) Circular System: An Eco-Friendly Approach for Enhancing Plant Performance and Mitigating Microbiological Risks.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12517},
pmid = {40240311},
issn = {1520-5851},
abstract = {Mushroom production using agroforestry biowaste is a great green cycling agriculture alternative. Therefore, the current study explored the Livestock-Crop-Mushroom (LCM) circular production model, starting with co-composting of straw and cow manure as a'St' biofertilizer further used for mushroom cultivation that ultimately produced a'StM' biofertilizer. The two biofertilizers were tested for their impacts on plant growth and potential microbial risks. The results show significant growth of oats stimulated by biofertiliser use. Both'St' and'StM' increased plant biomass, while with the latter, the crude protein content (+5.1%) and root biomass were also higher. Reduced abundances of resistome genes (30%) and pathogens (25%) were observed during the oat growth. Further, metagenomics analysis also indicated a reduction in antibiotic-resistance genes by -20% in soils with oats treated by'St' and -46% in'StM' biofertilizer treatment. The'StM' had a three-fold stronger inhibitory effect on oat rhizosphere soil pathogens than'St'. Moreover, compared to'St','StM' suppressed pathogens in seeds and stems, with specific beneficial biomarker microbes in different plant parts. Overall, the antibiotic resistance gene related to oxytetracycline decreased more than three-fold in the LCM system. This study demonstrates the substantial potential and scalability of the LCM circular system within the agricultural domain.},
}
@article {pmid40239498,
year = {2025},
author = {Chen, M and Grégoire, DS and St-Germain, P and Berdugo-Clavijo, C and Hug, LA},
title = {Microbial diversity and capacity for arsenic biogeochemical cycling in aquifers associated with thermal mobilization.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179357},
doi = {10.1016/j.scitotenv.2025.179357},
pmid = {40239498},
issn = {1879-1026},
abstract = {Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic detoxification and metabolism, which include genes for efflux, methylation, and reduction/oxidation of As(V)/As(III). We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread among community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high‑arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.},
}
@article {pmid40238917,
year = {2025},
author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ},
title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.},
journal = {Science translational medicine},
volume = {17},
number = {794},
pages = {eadq8870},
doi = {10.1126/scitranslmed.adq8870},
pmid = {40238917},
issn = {1946-6242},
mesh = {Animals ; Humans ; *Operon/genetics ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology ; *Pyrimidines/toxicity ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; },
abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.},
}
@article {pmid40238748,
year = {2025},
author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C},
title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321389},
doi = {10.1371/journal.pone.0321389},
pmid = {40238748},
issn = {1932-6203},
mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; },
abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.},
}
@article {pmid40238740,
year = {2025},
author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X},
title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013069},
doi = {10.1371/journal.ppat.1013069},
pmid = {40238740},
issn = {1553-7374},
mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; },
abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.},
}
@article {pmid40238414,
year = {2025},
author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Agodi, A},
title = {Monitoring Antibiotic Resistance in Wastewater: Findings from Three Treatment Plants in Sicily, Italy.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {3},
pages = {},
doi = {10.3390/ijerph22030351},
pmid = {40238414},
issn = {1660-4601},
support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; },
mesh = {*Wastewater/microbiology ; Sicily ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) poses a global public health threat. Wastewater analysis provides valuable insights into antimicrobial resistance genes (ARGs), identifying sources and trends and evaluating AMR control measures. Between February 2022 and March 2023, pre-treatment urban wastewater samples were collected weekly from treatment plants in Pantano D'Arci, Siracusa, and Giarre (Sicily, Italy). Monthly composite DNA extracts were prepared by combining weekly subsamples from each site, yielding 42 composite samples-14 from each treatment plant. Real-time PCR analysis targeted specific ARGs, including blaSHV, erm(A), erm(B), blaOXA, blaNDM, blaVIM, blaTEM, and blaCTX-M. The preliminary findings revealed that blaERM-B, blaOXA, blaTEM, and blaCTX-M were present in all samples, with erm(B) (median value: 8.51; range: 1.67-30.93), blaSHV (0.78; 0.00-6.36), and blaTEM (0.72; 0.34-4.30) showing the highest relative abundance. These results underscore the importance of integrating ARG data with broader research to understand the persistence and proliferation mechanisms of ARGs in wastewater environments. Future studies should employ metagenomic analyses to profile resistomes in urban, hospital, agricultural, and farm wastewater. Comparing these profiles will help identify contamination pathways and inform the development of targeted ARG surveillance programs. Monitoring shifts in ARG abundance could signal cross-sectoral contamination, enabling more effective AMR control strategies.},
}
@article {pmid40238256,
year = {2025},
author = {Rueangsri, N and Roytrakul, S and Muangnoi, C and Tongkhao, K and Sae-Tan, S and Treesuwan, K and Sirivarasai, J},
title = {Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071148},
pmid = {40238256},
issn = {2304-8158},
support = {C02F660008//Mahidol University and the Office of National Higher Education Science Research and Innova-tion Policy Council through the Program Management Unit for Competitiveness, Thailand/ ; },
abstract = {Research in metagenomics and metaproteomics can reveal how microbiological interactions in fermented foods contribute to their health benefits. This study examined three types of fermented vegetables: a standard formulation, a probiotic formulation with Lacticaseibacillus rhamnosus GG, and a polyphenol formulation with vitexin from Mung bean seed coat. Measurements were taken at day 0 (after 36 h of fermentation at room temperature) and after 15 days. We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (Lactobacillus and Weissella) and species (Lacticaseibacillus rhamnosus and Levilactobacillus brevis) of lactic acid bacteria (LAB). All of these taxa demonstrated significant relative abundance between 0 and 15 days of fermentation in our metagenomic analysis. Our findings from principal component analysis and clustering analysis categorically distinguished protein expression patterns at various stages of fermentation. By comparing samples from day 0 to day 15, we identified proteins associated with DNA replication and repair mechanisms, including transcription elongation factor GreA, tRNA pseudouridine synthase B, and helicases. We also observed their roles in protein synthesis, which encompasses oxidoreductases and aspartokinase. Furthermore, we identified strong correlations of specific proteins across the three formulations with antioxidant markers. In conclusion, the results of this study decisively enhance our understanding of the role of the proteins related to specific LAB in fermented foods, highlighting their potential to improve texture, flavor, nutritional quality, and health benefits.},
}
@article {pmid40238219,
year = {2025},
author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G},
title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071082},
pmid = {40238219},
issn = {2304-8158},
abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.},
}
@article {pmid40238218,
year = {2025},
author = {Zhadyra, S and Tao, F and Xu, P},
title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071102},
pmid = {40238218},
issn = {2304-8158},
abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.},
}
@article {pmid40238191,
year = {2025},
author = {Ren, C and Zhao, M and Xue, T and Geng, T and Nie, X and Han, C and Wen, Y and Jia, L},
title = {Metagenomic and Physicochemical Analyses Reveal Microbial Community and Functional Differences Between Three Different Grades of Hongxin Low-Temperature Daqu.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071104},
pmid = {40238191},
issn = {2304-8158},
support = {202302140601016//Key R&amp;D Program of Shanxi Province/ ; },
abstract = {Hongxin (HX) is an indispensable Daqu in the production of light-flavor Baijiu (LFB). However, the classification method of HX is highly subjective, and the classification and functional differences in microorganisms in different grades of HX are still unclear. In this study, metagenomics and physiochemical analysis were used to compare three grades of HX (top, first, second) and clarify their brewing functions in LFB. The results showed that a total of 1556 genera and 5367 species were detected in all samples. Bacteria and fungi are the main microorganisms in HX, and the relative abundance of bacteria and fungi is above 4.5:1. Kroppenstedtia (11.43%), Leuconostoc (10.52%), Fructilactobacillus (9.00%) were the top three genera in HX. Although the microbial community composition of the three grades of HX is highly similar, each HX has a specific microbial community structure and macrogene functional characteristics, indicating that they have different brewing functions. The dominant microorganisms in top-grade HX and first-grade HX were mainly positively correlated with energy metabolism and lipid metabolism, while the dominant microorganisms in second-grade HX were mainly positively correlated with carbohydrate metabolism and amino acid metabolism. This study revealed the different fermentation effects of different grades of HX in LFB and provided suggestions for the scientific classification and quality control of HX.},
}
@article {pmid40238188,
year = {2025},
author = {Ugarcina Perovic, S and Ramji, V and Chong, H and Duan, Y and Maguire, F and Coelho, LP},
title = {argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf173},
pmid = {40238188},
issn = {1367-4811},
abstract = {SUMMARY: Currently available and frequently used tools for annotating antimicrobial resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challenging. The comparability of ARG annotation outputs can be improved by mapping gene names and their categories to a common controlled vocabulary such as the Antibiotic Resistance Ontology (ARO). We developed argNorm, a command line tool and Python library, to normalize all detected genes across 6 ARG annotation tools (8 databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.<br><br>argNorm is available as an open-source tool at: https://github.com/BigDataBiology/argNorm. It can also be downloaded as a PyPI package and is available on Bioconda and as an nf-core module.},
}
@article {pmid40237937,
year = {2025},
author = {Maimaris, J and Payne, J and Roa-Bautista, A and Breuer, J and Storey, N and Morfopoulou, S and Bamford, A and D'Arco, F and Gilmour, K and Aquilina, K and Hassell, J and Hacohen, Y and Silva, AHD and Merve, A and Jacques, TS and Rao, K and Chiesa, R and Amrolia, P and Silva, J and Braggins, H and Xu-Bayford, J and Goldblatt, D and Worth, A and Booth, C and Ip, W and Qasim, W and Kusters, M and Kaliakatsos, M and Brown, JR and Elfeky, R},
title = {Safety and Diagnostic Utility of Brain Biopsy and Metagenomics in Decision-Making for Patients with Inborn Errors of Immunity (IEI) and Unexplained Neurological Manifestations.},
journal = {Journal of clinical immunology},
volume = {45},
number = {1},
pages = {86},
pmid = {40237937},
issn = {1573-2592},
support = {GN-000707//Brain Tumour Charity/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Brain/pathology ; Male ; Biopsy ; Female ; Child, Preschool ; Infant ; Child ; Retrospective Studies ; *Nervous System Diseases/diagnosis/etiology ; Clinical Decision-Making ; Adolescent ; High-Throughput Nucleotide Sequencing ; },
abstract = {Unexplained neurological symptoms can pose a diagnostic challenge in patients with inborn errors of immunity (IEI) where the aetiology can be varied, and diverse pathologies may require contrasting treatments. Brain biopsy, the process of sampling brain tissue directly, has historically provided histological and microbiological information and can now be exploited for deep metagenomic next generation analysis (mNGS). We conducted a retrospective analysis of clinical and diagnostic data on paediatric patients with IEI who had a brain biopsy between 2010 and 2022 at a UK tertiary centre where 14 patients fulfilled our search criteria. We report on clinical characteristics, adverse events and the additional impact of mNGS of brain biopsies, where these were conducted. We found that brain biopsy enabled diagnostics with manageable complications in most cases, either by tissue or metagenomics analysis (n = 11/14, 79%). We found that mNGS analysis improved the diagnostic yield of brain biopsy in 29% of IEI cases (n = 4/14). Brain biopsy enabled a change in management in 71% of cases (n = 10/14). This series provides compelling evidence for the safe and purposeful use of brain biopsy in children with IEI.},
}
@article {pmid40237802,
year = {2025},
author = {Lei, W and Huang, R and Qu, L and Ma, K and Li, J},
title = {Exogenous Mogroside V Drove Microbial Carbohydrate Metabolism and Consequently Enhanced Fruity Aroma in Greengage Wine.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c10783},
pmid = {40237802},
issn = {1520-5118},
abstract = {The microbial community is essential for the formation of aroma development in high-acidity greengage wine fermentation. Recent observations also highlight positive effects of mogroside V (MG V) on microorganisms in fermented foods, but the underlying chemical and biological mechanisms remain inadequate. The results indicated differences in the physicochemical properties among greengage wines, particularly a 50% increase in the ethanol conversion rate. Concurrently, GC-MS and sensory analyses demonstrated that MG V augmented carbohydrate conversion into ethyl esters (twice as much as in the control group), exhibiting tropical fruit and floral aroma profiles. The perceived intensity of these aromatic compounds increased by over 30%, thereby enriching the overall aromatic harmony of the wine. Integrated analysis of KEGG pathways and CAZymes annotations demonstrated that the enhancement of ethyl ester formation by MG V depends on improvement of the transport of carbohydrates and MG V, as well as accelerating the flux of pyruvate to acetyl-CoA in yeast. In conclusion, our study presents a targeted strategy for the high-acidity fruit wine industry of modulating this metabolic node in yeast, thereby achieving a focused enhancement of tropical fruit aroma characteristics in fruit wines.},
}
@article {pmid40237492,
year = {2025},
author = {Hu, T and Meng, Y and Zhao, C and Sheng, D and Yang, S and Dai, J and Wei, T and Zhang, Y and Zhao, G and Liu, Y and Wang, Q and Zhang, L},
title = {Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0298424},
doi = {10.1128/spectrum.02984-24},
pmid = {40237492},
issn = {2165-0497},
abstract = {As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.},
}
@article {pmid40237489,
year = {2025},
author = {Rybicka, I and Kaźmierczak, Z},
title = {The human phageome: niche-specific distribution of bacteriophages and their clinical implications.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0178824},
doi = {10.1128/aem.01788-24},
pmid = {40237489},
issn = {1098-5336},
abstract = {Bacteriophages (phages) play a crucial role in shaping the composition and diversity of the human microbiome across various body niches. Recent advancements in high-throughput sequencing technologies have enabled comprehensive analysis of the human phageome in different body sites. This review comprehensively analyzes phage populations across major human body niches, examining their distribution and dynamics through recent metagenomic discoveries. We explore how phage-bacteria interactions within different body sites contribute to homeostasis and disease development. Emerging evidence demonstrates that phageome perturbations can serve as early indicators of various disorders, particularly in the gut microbiome. Understanding these complex microbial interactions offers promising opportunities for developing novel diagnostic markers and therapeutic approaches. However, the causal relationship between phages, bacteria, and disease development remains unclear. Further research is needed to elucidate the role of phages in human health and disease and to explore their potential as diagnostic or therapeutic tools. Understanding the intricate interactions between phages, bacteria, and the human host is crucial for unraveling the complexities of the human microbiome and its impact on health and disease.},
}
@article {pmid40237482,
year = {2025},
author = {Zhang, C and Bosma, TNP and Atashgahi, S and Smidt, H},
title = {Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150324},
doi = {10.1128/msystems.01503-24},
pmid = {40237482},
issn = {2379-5077},
abstract = {Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.},
}
@article {pmid40237336,
year = {2025},
author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR},
title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2493900},
doi = {10.1080/19490976.2025.2493900},
pmid = {40237336},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; },
abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.},
}
@article {pmid40236771,
year = {2025},
author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J},
title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70008},
pmid = {40236771},
issn = {2770-596X},
abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.},
}
@article {pmid40236770,
year = {2025},
author = {Zhang, C and Chen, Y and Duan, R and Zhang, Y and Zheng, H and Zhang, J and Zhang, T and Xu, J and Li, K and Pei, F and Duan, L},
title = {Preconception maternal gut dysbiosis affects enteric nervous system development and disease susceptibility in offspring via the GPR41-GDNF/RET/SOX10 signaling pathway.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70012},
pmid = {40236770},
issn = {2770-596X},
abstract = {Maternal health, specifically changes in the gut microbiota, can profoundly impact offspring health; however, our understanding of how gut microbiota alterations during the preconception period influence the offspring remains limited. In this study, we investigated the impact and mechanisms of preconception maternal gut dysbiosis on the development of the enteric nervous system (ENS) in mice. We found that preconception maternal exposure to antibiotics led to the abnormal development of the ENS in offspring, increasing their susceptibility to water avoidance stress at the adult stage. Metagenomic, targeted metabolomic, and transcriptomic analyses revealed that preconception antibiotic exposure disrupted the expression of genes crucial for embryonic ENS development by altering maternal gut microbiota composition. Multi-omics analysis combined with Limosilactobacillus reuteri and propionate gestational supplementation demonstrated that the maternal gut microbiota and metabolites may influence embryonic ENS development via the GPR41-GDNF/RET/SOX10 signaling pathway. Our findings highlight the critical importance of maintaining a healthy maternal gut microbiota before conception to support normal ENS development in offspring.},
}
@article {pmid40236767,
year = {2025},
author = {Huang, L and Wang, P and Liu, S and Deng, G and Qi, X and Sun, G and Gao, X and Zhang, L and Zhang, Y and Xiao, Y and Gao, T and Maitiabula, G and Wang, X},
title = {Gut microbiota-derived tryptophan metabolites improve total parenteral nutrition-associated infections by regulating Group 3 innate lymphoid cells.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70007},
pmid = {40236767},
issn = {2770-596X},
abstract = {Clinical nutritional support is recognized by Klinefner's Surgery as one of the four pivotal advancements in surgical practice during the 20th century. Surgeons regard clinical nutrition as a "life-saving" discipline, pivotal in preserving the lives of numerous critically ill patients and facilitating the success of many surgical procedures. Parenteral nutrition (PN) support serves as a crucial component of clinical nutritional therapy, while a range of complications associated with total parenteral nutrition (TPN) can significantly undermine the efficacy of patient treatment. Impaired intestinal homeostasis is strongly associated with the occurrence and progression of TPN-related infections, yet the underlying mechanisms remain poorly understood. In this study, RNA sequencing and single-cell RNA sequencing (scRNA-Seq) revealed that reduced secretion of interleukin-22 (IL-22) by intestinal Group 3 innate lymphoid cells (ILC3s) is a significant factor contributing to the onset of TPN-related infections. Additionally, through 16S ribosomal RNA (16S rRNA) gene sequencing of the gut microbiota from patients with chronic intestinal failure and metagenomic sequencing analysis of the gut microbiota from mice, we observed that TPN reduced the abundance of Lactobacillus murinus (L. murinus), while supplementation with L. murinus could promote IL-22 secretion by ILC3s. Mechanistically, L. murinus upregulates indole-3-carboxylic acid, which activates the nuclear receptor Rorγt to stimulate IL-22 secretion by ILC3s. This pathway strengthens gut barrier integrity and reduces infection susceptibility. Our findings enhance our understanding of the mechanisms driving the onset of TPN-related infections, highlighting the critical role of gut microbiota in maintaining immune homeostasis and improving clinical outcomes.},
}
@article {pmid40236616,
year = {2025},
author = {Lu, Y and Zhang, C and Wu, J and Xu, X and Lu, A and Huang, H and Chen, M},
title = {Explore the Application Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid in the Early Diagnosis of Pulmonary Tuberculosis.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1837-1845},
pmid = {40236616},
issn = {1178-6973},
abstract = {OBJECTIVE: Compare the diagnostic efficacy of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) with that of four traditional methods in the diagnosis of pulmonary tuberculosis (PTB), and explore the application value of BALF mNGS in the early diagnosis of PTB.<br><br>METHODS: A retrospective analysis was performed on 102 patients with suspected PTB in Wuming Hospital Affiliated with Guangxi Medical University from January 2021 to August 2024, among which 61 cases were PTB and 41 cases were non - PTB. Diagnostic performance metrics (sensitivity, specificity, positive/negative predictive value [PPV/NPV], accuracy) were calculated for BALF mNGS, sputum TB-DNA, sputum acid-fast bacilli (AFB) smear, BALF AFB smear, and BALF TB-DNA, using clinical diagnosis as the reference standard.<br><br>RESULTS: BALF mNGS demonstrated a sensitivity of 75.41% (46/61), specificity of 87.80% (36/41), PPV of 90.20% (46/51), NPV of 70.59% (36/51), and accuracy of 80.39% (82/102). Its accuracy was significantly higher than sputum-based methods (53.03-58.82%, P < 0.0125) and second only to BALF TB-DNA (84.13%, P > 0.0125). BALF mNGS exhibited superior sensitivity compared to sputum TB-DNA (38.00%), sputum AFB smear (41.67%), and BALF AFB smear (41.50%) (P < 0.0125). While specificity and PPV showed no significant differences among methods, BALF mNGS had a higher NPV than sputum-based assays (53.03-54.17%) but lower than BALF TB-DNA (82.53%, P < 0.0125). Both BALF mNGS (Kappa = 0.608, P < 0.001) and BALF TB-DNA (Kappa = 0.670, P < 0.001) showed strong concordance with clinical diagnosis.<br><br>CONCLUSION: BALF mNGS demonstrates high sensitivity and accuracy for PTB diagnosis, outperforming conventional sputum-based methods. Although BALF TB-DNA achieved the highest specificity and NPV, BALF mNGS serves as a robust supplementary tool, particularly for early-stage or paucibacillary PTB. Integration of these molecular techniques may optimize diagnostic workflows in high-TB-burden settings.},
}
@article {pmid40236150,
year = {2025},
author = {Bommana, S and Olagoke, S and Hu, Y and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, T and Dean, D},
title = {Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with Chlamydia trachomatis infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.02.646699},
pmid = {40236150},
issn = {2692-8205},
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes with Chlamydia trachomatis (Ct) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples from women who, overtime, had Ct persistence, clearance, or no infection to evaluate azithromycin-induced changes in microbial composition, function, and the resistome. Our results show a shift in composition and function that support Ct post-treatment with azithromycin resistance mutations in the Ct rplV gene and significant endocervical enrichment of azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis, the strains of which have moderate/high potential for biofilm formation. These findings highlight the unintended ecological consequences of azithromycin, including resistance gene propagation and microbiome shifts that support persistent/recurrent Ct, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}
@article {pmid40235649,
year = {2025},
author = {Mohamed, AYA and Gill, L and Monleon, A and Pronk, M and van Loosdrecht, M and Saikaly, PE and Ali, M},
title = {Genome-resolved metatranscriptomics unveils distinct microbial functionalities across aggregate sizes in aerobic granular sludge.},
journal = {Environmental science and ecotechnology},
volume = {25},
number = {},
pages = {100560},
pmid = {40235649},
issn = {2666-4984},
abstract = {Microbial aggregates of different sizes in aerobic granular sludge (AGS) systems have been shown to exhibit distinct microbial community compositions. However, studies comparing the microbial activities of different-sized aggregates in AGS systems remain limited. In this study, genome-resolved metatranscriptomics was used to investigate microbial activity patterns within differently sized aggregates in a full-scale AGS plant. Our analysis revealed a weak correlation between the relative abundance of metagenome-assembled genomes (MAGs) and their transcriptomic activity, indicating that microbial abundance does not directly correspond to metabolic activity within the system. Flocculent sludge (FL; <0.2 mm) predominantly featured active nitrifiers and fermentative polyphosphate-accumulating organisms (PAOs) from Candidatus Phosphoribacter, while small granules (SG; 0.2-1.0 mm) and large granules (LG; >1.0 mm) hosted more metabolically active PAOs affiliated with Ca. Accumulibacter. Differential gene expression analysis further supported these findings, demonstrating significantly higher expression levels of key phosphorus uptake genes associated with Ca. Accumulibacter in granular sludge (SG and LG) compared to flocculent sludge. Conversely, Ca. Phosphoribacter showed higher expression of these genes in the FL fraction. This study highlights distinct functional roles and metabolic activities of crucial microbial communities depending on aggregate size within AGS systems, offering new insights into optimizing wastewater treatment processes.},
}
@article {pmid40234711,
year = {2025},
author = {Wu, M and Liu, X and Musat, F and Guo, J},
title = {Microbial oxidation of short-chain gaseous alkanes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40234711},
issn = {2058-5276},
abstract = {Short-chain gaseous alkanes (SCGAs), including ethane, propane and butane, are major components of natural gas and their atmospheric emissions impact global air quality and tropospheric chemistry. Many microbial taxa can degrade SCGAs aerobically and anaerobically to CO2, acting as the major biological sink of these compounds and reducing their negative impacts on climate. Environmental metagenomics and cultivation efforts have expanded our understanding of SCGA-oxidizing microorganisms. In this Review, we discuss recent discoveries in the diversity, physiology and metabolism of aerobic and anaerobic SCGA-oxidizing microorganisms, highlight their climate implications and discuss how knowledge of these processes can help develop biotechnologies for environmental remediation and value-added chemical production.},
}
@article {pmid40234093,
year = {2025},
author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ},
title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {4},
pages = {},
doi = {10.1136/jitc-2025-011706},
pmid = {40234093},
issn = {2051-1426},
mesh = {Humans ; *Melanoma/drug therapy/pathology/mortality ; Female ; Male ; *Azetidines/therapeutic use/pharmacology ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Neoadjuvant Therapy/methods ; *Piperidines/pharmacology/therapeutic use ; *Vemurafenib/pharmacology/therapeutic use ; Aged ; Neoplasm Staging ; Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; *Skin Neoplasms/drug therapy ; },
abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.<br><br>METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.<br><br>RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.<br><br>CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab&#xb1;vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.<br><br>TRIAL REGISTRATION NUMBER: NCT03554083.},
}
@article {pmid40233994,
year = {2025},
author = {Jenkins, R and Samec, M and Arment, C and Warrington, KJ and Davis, JM and Koster, MJ},
title = {Use of Metagenomic Microbial Plasma Cell-Free DNA Next-Generation Sequencing Assay in Outpatient Rheumatology Practice.},
journal = {The Journal of rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.3899/jrheum.2024-1211},
pmid = {40233994},
issn = {1499-2752},
abstract = {OBJECTIVE: To assess the utility of a metagenomic microbial plasma cell-free DNA next-generation sequencing assay (Karius TestTM; KT) in the evaluation of patients in an outpatient rheumatology practice.<br><br>METHODS: All patients with a KT ordered and obtained by a rheumatology provider in the outpatient setting from 1 January 2020 through 31 December 2022 were retrospectively identified. Demographic, clinical, laboratory, radiologic, histopathology, and microbial studies were abstracted. Indication for KT testing was categorized. KT results were defined based on positive result and clinical relevance regarding the symptoms under investigation at the time of the rheumatologic investigation. Review of cases three months after KT was undertaken to determine clinical outcome.<br><br>RESULTS: 150 patients with a KT were included (52.7% female, mean age 52 years). The reason for KT was evaluation of atypical presentation of rheumatic disease (80.0%), assessing flare versus infection in patient on immunosuppression (16.7%), and fever of unknown origin (3.3%). 24 (16.0%) KTs were positive, six of which were considered clinically relevant and altered the final diagnosis and treatment. Of the 126 negative KTs, 5 (4.0%) were found to have a clinically relevant infection by conventional testing methodologies.<br><br>CONCLUSION: In this large retrospective cohort study, the most frequent reason for KT utilization was an atypical presentation of rheumatic disease. Twenty-five percent of positive KTs altered the final diagnosis and treatment, whereas a false-negative rate of 4.0% was observed. KT has utility in the outpatient rheumatology assessment. Further delineation of which patients are best suited for KT testing remains to be defined.},
}
@article {pmid40233938,
year = {2025},
author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM},
title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.},
journal = {Journal of applied microbiology},
volume = {136},
number = {4},
pages = {},
doi = {10.1093/jambio/lxaf076},
pmid = {40233938},
issn = {1365-2672},
support = {80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; },
mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation &amp; purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; },
abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.<br><br>METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.<br><br>CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.},
}
@article {pmid40037519,
year = {2025},
author = {Jawale, N and Shenberger, JS and Rodriguez, RJ and Shetty, AK and Garg, PM},
title = {The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis.},
journal = {American journal of perinatology},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2549-6551},
pmid = {40037519},
issn = {1098-8785},
support = {U54GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428//NIGMS of the NIH/ ; },
abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..},
}
@article {pmid40233768,
year = {2025},
author = {Tinker, KA and Anthony, W and Brandi, M and Flett, S and Bagwell, CE and Smallwood, C and Davis, R and Gulliver, D},
title = {Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70076},
doi = {10.1111/1758-2229.70076},
pmid = {40233768},
issn = {1758-2229},
support = {//U.S. Department of Energy's (DOE) Office of Fossil Energy and Carbon Management's Hydrogen with Carbon Management Program and executed through the National Energy Technology Laboratory (NETL) Research &amp; Innovation Center's Natural Gas Decarbonization and Hydrogen Technologies Multi-Year Research Plan/ ; },
mesh = {*Hydrogen/metabolism ; *Groundwater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Illinois ; Methane/metabolism ; Microbiota ; Metagenomics ; },
abstract = {Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.},
}
@article {pmid40233618,
year = {2025},
author = {Fan, C and Hou, D and Zhang, L and Li, C and Chen, L and Zhang, P and Wu, Y and Zou, J},
title = {Bioaugmentation using HN-AD consortia for high salinity wastewater treatment: Synergistic effects of halotolerant bacteria and nitrogen removal bacteria.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125355},
doi = {10.1016/j.jenvman.2025.125355},
pmid = {40233618},
issn = {1095-8630},
abstract = {Bioaugmentation shows promise in enhancing nitrogen removal efficiency of high-salt wastewater, yet the impact of microbial associations on ecosystem function and community stability remains unclear. This study innovatively introduced a novel heterotrophic nitrification-aerobic denitrification bacterial consortium to improve the performance of SBR reactor for removing nitrogen from saline wastewater. The results revealed that the bioaugmented reactor (R2) exhibited superior removal performance, achieving maximum removal efficiencies of 87.8 % for COD and 97.8 % for NH4[+]-N. Moreover, proper salinity (2 % and 4 %) promoted the secretion of EPS and ectoine, further enhancing the resistance and stability of bacterial consortia. 16S rRNA gene sequencing and metagenomics analysis revealed the key denitrifying bacteria Pseudomonas and salt-tolerant bacteria Halomonas were successfully coexistence and the relative abundances of crucial genes (napB, nirS, norB, norC and nosZ) were increased obviously, which were benefit for the excellent nitrogen removal performance in R2. These findings elucidate microbial interactions in response to salinity in bioaugmentation, providing a valuable reference for the efficient treatment of high-saline wastewater.},
}
@article {pmid40233040,
year = {2025},
author = {Pomej, K and Frick, A and Scheiner, B and Balcar, L and Pajancic, L and Klotz, A and Kreuter, A and Lampichler, K and Regnat, K and Zinober, K and Trauner, M and Tamandl, D and Gasche, C and Pinter, M},
title = {Study protocol: Fecal Microbiota Transplant combined with Atezolizumab/Bevacizumab in Patients with Hepatocellular Carcinoma who failed to achieve or maintain objective response to Atezolizumab/Bevacizumab - the FAB-HCC pilot study.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321189},
doi = {10.1371/journal.pone.0321189},
pmid = {40233040},
issn = {1932-6203},
mesh = {Humans ; *Liver Neoplasms/therapy/drug therapy ; *Carcinoma, Hepatocellular/therapy/drug therapy ; Pilot Projects ; *Fecal Microbiota Transplantation/methods ; *Bevacizumab/therapeutic use/administration &amp; dosage ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration &amp; dosage ; Male ; Female ; Gastrointestinal Microbiome ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: The gut microbiota is often altered in chronic liver diseases and hepatocellular carcinoma (HCC), and increasing evidence suggests that it may influence response to cancer immunotherapy. Strategies to modulate the gut microbiome (i.e., fecal microbiota transplant (FMT)) may help to improve efficacy of immune checkpoint inhibitors (ICIs) or even overcome resistance to ICIs. Here, we describe the design and rationale of FAB-HCC, a single-center, single-arm, phase II pilot study to assess safety, feasibility, and efficacy of FMT from patients with HCC who responded to PD-(L)1-based immunotherapy or from healthy donors to patients with HCC who failed to achieve or maintain a response to atezolizumab plus bevacizumab.<br><br>METHODS: In this single-center, single-arm, phase II pilot study (ClinicalTrials.gov identifier: NCT05750030), we plan to include 12 patients with advanced HCC who failed to achieve or maintain a response to atezolizumab/bevacizumab. Patients will receive a single FMT via colonoscopy from donors with HCC who responded to PD-(L)1-based immunotherapy or from healthy individuals, followed by atezolizumab/bevacizumab every 3 weeks. The primary endpoint is safety, measured by incidence and severity of treatment-related adverse events. The main secondary endpoint is efficacy, as assessed by best radiological response according to RECISTv1.1 and mRECIST. Additional exploratory endpoints include data on the effect of FMT on recipient gut microbiota, as well as metagenomic analysis of stool samples, analyses of circulating immune cells and serum and stool proteomic, metabolomic and lipidomic signatures.<br><br>DISCUSSION: The results of this study will help to define the potential of FMT as add-on intervention in the systemic treatment of advanced HCC, with the potential to improve efficacy of immunotherapy or even overcome resistance.<br><br>TRIAL REGISTRATION: EudraCT Number: 2022-000234-42 Clinical trial registry &amp; ID: ClinicalTrials.gov identifier: NCT05750030 (Registration date: 16.01.2023).},
}
@article {pmid40232948,
year = {2025},
author = {Leech, SM and Barrett, HL and Dorey, ES and Mullins, T and Laurie, J and Nitert, MD},
title = {Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001385},
pmid = {40232948},
issn = {2057-5858},
mesh = {Humans ; Female ; Pregnancy ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/genetics ; Adult ; *Diabetes, Gestational/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.},
}
@article {pmid40232107,
year = {2025},
author = {Ravizza, T and Volpedo, G and Riva, A and Striano, P and Vezzani, A},
title = {Intestinal microbiome alterations in pediatric epilepsy: Implications for seizures and therapeutic approaches.},
journal = {Epilepsia open},
volume = {},
number = {},
pages = {},
doi = {10.1002/epi4.70037},
pmid = {40232107},
issn = {2470-9239},
support = {PE0000006/DN.1553//National Recovery and Resilience Plan (NRRP)/ ; //AICE-FIRE/ ; },
abstract = {The intestinal microbiome plays a pivotal role in maintaining host health through its involvement in gastrointestinal, immune, and central nervous system (CNS) functions. Recent evidence underscores the bidirectional communication between the microbiota, the gut, and the brain and the impact of this axis on neurological diseases, including epilepsy. In pediatric patients, alterations in gut microbiota composition-called intestinal dysbiosis-have been linked to seizure susceptibility. Preclinical models revealed that gut dysbiosis may exacerbate seizures, while microbiome-targeted therapies, including fecal microbiota transplantation, pre/pro-biotics, and ketogenic diets, show promise in reducing seizures. Focusing on clinical and preclinical studies, this review examines the role of the gut microbiota in pediatric epilepsy with the aim of exploring its implications for seizure control and management of epilepsy. We also discuss mechanisms that may underlie mutual gut-brain communication and emerging therapeutic strategies targeting the gut microbiome as a novel approach to improve outcomes in pediatric epilepsy. PLAIN LANGUAGE SUMMARY: Reciprocal communication between the brain and the gut appears to be dysfunctional in pediatric epilepsy. The composition of bacteria in the intestine -known as microbiota- and the gastrointestinal functions are altered in children with drug-resistant epilepsy and animal models of pediatric epilepsies. Microbiota-targeted interventions, such as ketogenic diets, pre-/post-biotics administration, and fecal microbiota transplantation, improve both gastrointestinal dysfunctions and seizures in pediatric epilepsy. These findings suggest that the gut and its microbiota represent potential therapeutic targets for reducing drug-resistant seizures in pediatric epilepsy.},
}
@article {pmid40232020,
year = {2025},
author = {Zhang, X and Chi, H and Peng, D and Jiang, M and Wang, C and Zhang, H and Kang, W and Li, L},
title = {Integrated Metagenomic and LC-MS/MS Analysis Reveals the Biogenic Amine-Producing Strains of Two Typical Chinese Traditional Fish Products: Fermented Mandarin Fish (Siniperca chuatsi) and Semi-Dried Yellow Croaker (Larimichthys crocea).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14061016},
pmid = {40232020},
issn = {2304-8158},
support = {2022TD02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; },
abstract = {Two typical fish products-fermented mandarin fish and semi-dried yellow croaker-are associated with biogenic amines (BAs), which are harmful to human health. The objective of this study was to investigate the bacterial ecology of the two fish products and to determine their capacity for producing BAs. Putrescine and cadaverine were major BAs detected in the fish products. Concentrations of BAs were significantly corrected with microbial count (p < 0.05). BA-producing isolates (33) in the two fish products were all multiple BA producers. Several of them, including Lactobacillus sakei, Bacillus cereus and Hafnia alvei isolated from fermented mandarin fish, as well as Shewanella baltica, Aeromonas veronii, and Photobacterium phosphoreum isolated from semi-dried yellow croaker, showed remarkable BA-producing capacity. Hafnia alvei produced the greatest abundance of putrescine, cadaverine, tyramine and 2-phenylethylamine. Lactobacillus sakei mainly produced tryptamine and putrescine. Photobacterium phosphoreum showed the strongest histamine-producing capacity.},
}
@article {pmid40231916,
year = {2025},
author = {A'yuni, Q and Mok, K and Nakphaichit, M and Jangchud, K and Pirak, T},
title = {Thai Cannabis sativa Leaves as a Functional Ingredient for Quality Improvement and Lactic Acid Bacterial Growth Enhancement in Kombucha.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14060942},
pmid = {40231916},
issn = {2304-8158},
support = {FF(KU)25.66//Fundamental fund of Kasetsart University/ ; //Kasetsart's Agro-Industry Scholarship from Department of Product Development, Faculty of Agro-Industry, Kasetsart University/ ; },
abstract = {Kombucha is a well-known fermented drink that gained interest due to its gut health benefits. However, it has a harsh taste of acetic acid and is hard to consume. Thai Cannabis leaves (Cannabis sativa sp. Hang Kra Rog Phu phan ST1) contain high protein and phytochemicals which can improve the growth of lactic acid bacteria (LAB) and enhance the organoleptic quality of the Kombucha. This study revealed the effect of infusing assam green tea leaves with cannabis leaves on the fermentation rate, microbial communities, volatile compounds, and overall quality and taste of the kombucha. The high protein content (23.10%) of Cannabis leaves was found. Phytonutrients and phytochemicals found in the leaves promotes LAB growth, which resulted in the higher number of LAB in the treatment with cannabis leaves. At the end of fermentation (day 7), the highest LAB count (5.53 log CFU mL[-1]) was presented in kombucha infused with 30% cannabis leaves. Kombucha with better quality, higher pH, and less acidity was obtained in a dose manner. The change in microbial communities was detected using metagenomic analysis. The prominence of Dekkera and Komagataeibacter, with low abundance of Zygosaccharomyces and Weissella were identified. These microorganisms improved flavor by lessening strong fermented odor and harsh acidic taste. From volatile compounds, HS-SPME-GCMS revealed that kombucha infused with 30% cannabis leaves possessed less acetic acid, ethanol, and carbon dioxide and gave a better odor and taste. Hence, cannabis leaves was the novel substrate for kombucha fermentation by enhancing LAB growth and improving the overall qualities.},
}
@article {pmid40231684,
year = {2025},
author = {Glenna, S and Birkeland, EE and Orr, RJ and Gilfillan, GD and Dalland, M and Økstad, OA and Voie, &#xd8;A and Rounge, TB},
title = {Skin bacterial community dynamics of hands and forearms before and after military field exercise.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0295324},
doi = {10.1128/spectrum.02953-24},
pmid = {40231684},
issn = {2165-0497},
abstract = {The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.},
}
@article {pmid40230845,
year = {2025},
author = {Gao, Q and Li, Z and Geng, J and Han, B and Yang, T and Feng, S and Zhao, L and Teng, Y and Li, Y and Zhao, R and Zhang, W and Wang, Y and Wang, Y},
title = {The type of pathogen is associated with organ failure and legacy dysfunction in patients with sepsis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1541634},
pmid = {40230845},
issn = {1664-3224},
mesh = {Humans ; *Sepsis/mortality/microbiology/complications ; Male ; Female ; *Multiple Organ Failure/mortality/microbiology/etiology ; Middle Aged ; Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Retrospective Studies ; },
abstract = {INTRODUCTION: Is there a difference in pathogen infection among sepsis patients with different organ dysfunction and Post-sepsis persistent organ dysfunction? Is this related to survival? It is currently unclear.<br><br>METHODS: This study reviewed 1982 sepsis patients between December 2019 and September 2023, and included 619 patients after removing patients with missing data. Of these, 332 were tested for metagenomic next-generation sequencing (mNGS). First, the pathogens distribution was assessed in all NGS-positive patients, followed by patients with different organ dysfunction (excluding those who died during hospitalization). Lastly, the survival analysis was conducted on patients infected with different pathogens.<br><br>RESULTS: The results showed that the mortality rate in our cohort was 27.63% in patients with sepsis, and patients with Respiratory, Liver, Circulatory, Hematologic, Neurological, and Renal dysfunction had poor survival. And patients with post-sepsis persistent organ dysfunction after sepsis have worse survival rates. In addition, we found the infection rates of Legionella and Betapapillomavirus were higher in patients with liver dysfunction. The infection rates of Mastadenovirus, Enterococcus, and Candida were higher in patients with neurological dysfunction. The infection rates of Candida were higher in patients with renal dysfunction and hematologic dysfunction. The infection rates of Moraxella were higher in patients with circulatory dysfunction. The infection rates of Enterococcus, Pneumocystis, and Acinetobacter were higher in patients with Post-sepsis cardiac dysfunction.The infection rates of Enterococcus, Acinetobacter, and Morganella were higher in patients with Post-sepsis liver dysfunction. The infection rates of Enterococcus, Acinetobacter, and Staphylococcus were higher in patients with Post-sepsis respiratory dysfunction. The infection rates of Enterococcus, Candida, Pneumocystis, Staphylococcus, and Listeria were higher in patients with Post-sepsis renal dysfunction. In addition, we found that patients with Escherichia infection in sepsis had the lowest survival rate. The survival rate of patients with Enterococcus infection combined with post-sepsis persistent respiratory dysfunction is also worse.<br><br>DISCUSSION: In conclusion, there are differences in the types and proportions of pathogens infected in patients with different organ dysfunction and Post-sepsis persistent organ dysfunction. The combination of Escherichia infection and Enterococcus infection with post-sepsis persistent respiratory dysfunction can affect the survival of patients. We should strengthen the management of sepsis patients, especially those with Post-sepsis persistent organ dysfunction.},
}
@article {pmid40230330,
year = {2025},
author = {Cui, T and Kushmaro, A and Barak, H and Poehlein, A and Daniel, R and Mägert, HJ},
title = {Enhanced discovery of bacterial laccase-like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70037},
pmid = {40230330},
issn = {2211-5463},
abstract = {Laccases belong to the superfamily of multicopper oxidases (MCO), a group of enzymes with the ability to reduce oxygen to water in a reaction without producing harmful byproducts. Laccase activity is influenced by many factors, such as structure; the number, location and binding status of copper ions; and the substrate-binding status. A large number of sequences that have not been experimentally characterized yet have been annotated as laccases. However, the biological functions of the characterized MCOs are considered to vary, and the substrate spectrum overlaps with that of other MCOs. Here, we identified 34 putative bacterial laccase sequences from metagenome data for industrial wastewater. We used machine-learning tools to screen enzymes with laccase activity by combining the T1 copper-binding capacity, the overall copper-binding capacity and the substrate-binding capacity. We also used the software comparisons to remove sequences with large discrepancies between different software applications. Three-dimensional structures of identified enzymes were predicted using alphafold, the positions of metal ions within the proteins were predicted by metal3d and autodock-vina, and their docking with ABTS [i.e. 2,2'-azinobis(3‑ethylbenzo-6‑thiazolinesulfonic acid)] as a substrate was predicted by rosetta and autodock-vina. Based on the docking results, we selected 10 high-scoring proteins, two low-scoring proteins and one composite protein for expression using the pET-21d (+) vector. In line with our predictions, all selected high-scoring proteins exhibited activity towards ABTS. Overall, we describe a method for discovering and designing novel bacterial laccase-like multicopper oxidases, offering increased possibilities for the degradation of various harmful components derived from environmental pollution.},
}
@article {pmid40230307,
year = {2025},
author = {Liu, B and He, N and Li, H and Yang, Z and Lin, Y and Wu, X and Zhang, H and Zhang, Z and Zhang, Z and Tian, Y and Wu, Z and Zou, Y and Peng, J and Li, S},
title = {3-Fucosyllactose Prevents Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota-Derived Pantothenate in Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00079},
pmid = {40230307},
issn = {1520-5118},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health threat. Human milk oligosaccharides (HMOs) exhibit prebiotic properties that may alleviate NAFLD progression. Herein, our study demonstrates that 3-fucosyllactose (3-FL), a distinctive and crucial HMO, significantly attenuates body weight gain, enhances hepatic lipid metabolism, and reduces inflammation in a high-fat diet (HFD)-induced NAFLD mouse model. These findings suggest its potential as a dietary supplement for preventing and alleviating NAFLD progression. Subsequently, fecal metagenomic and nontargeted metabolomics analyses revealed that 3-FL treatment significantly alleviated HFD-induced gut microbiota dysbiosis, with a specific enhancement of the pantothenate (vitamin B5) metabolic pathways. Our targeted metabolite analysis further revealed a significant increase in both hepatic and fecal pantothenate concentrations, which contributed to the enhancement of the coenzyme A (CoA)-mediated lipid metabolism pathway. Furthermore, the subsequent population cohort analyses revealed a significant correlation between serum pantothenate levels and the progression of NAFLD, thereby reinforcing its candidacy as a noninvasive diagnostic biomarker. These findings show that 3-FL acts as an effective prebiotic to alleviate NAFLD symptoms, in part by enhancing the gut microbiota-mediated pantothenate/CoA metabolic pathway.},
}
@article {pmid40230133,
year = {2025},
author = {Chen, HD and Gao, S and Wang, LJ and Zhao, B and Lu, MQ and Song, YM and Cui, JS and Zhang, LL},
title = {[Spatial and Temporal Differences and Influencing Factors of Mobile Genetic Elements in Urban and Suburban River Sediments in Shijiazhuang City].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {4},
pages = {2250-2262},
doi = {10.13227/j.hjkx.202403034},
pmid = {40230133},
issn = {0250-3301},
mesh = {*Rivers ; China ; *Geologic Sediments/microbiology ; *Interspersed Repetitive Sequences/genetics ; Cities ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Spatio-Temporal Analysis ; },
abstract = {With the widespread use of antibiotics in medicine and agriculture, the spread of antibiotic resistance genes （ARGs） in the environment has become a serious threat to ecological balance and human health, particularly for its role in facilitating the emergence of multidrug-resistant pathogens. The study of riverine environments as a major transmission route for ARGs and closely related mobile genetic elements （MGEs） is of great importance. MGEs exacerbate the spread of resistance genes by facilitating the horizontal transfer of ARGs in bacterial populations. Although studies have been conducted to explore the interactions between MGEs and ARGs, there is still a relative lack of research on the spatial and temporal differences in the distribution of MGEs in rivers and their drivers. This study selected two rural rivers （with a total of six sampling points） and three urban rivers （with a total of nine sampling points） within Shijiazhuang as research subjects, and sediment samples were collected in December 2020 and April 2021. By employing metagenomic sequencing technology, this study comprehensively compared and analyzed the spatiotemporal distribution characteristics and influencing factors of MGEs in the sediment of urban and rural rivers. The results showed that： ① In December, 1 738 types of MGEs （60572 RPKM） and 1 604 types of MGEs （26916 RPKM） were detected in urban and rural rivers, respectively. In April, 1 790 types of MGEs （74354 RPKM） and 1 631 types of MGEs （32062 RPKM） were detected in urban and rural rivers, respectively. ② The types and abundance of MGEs in urban rivers were greater than those in rural rivers, and the types and abundance of MGEs in April were greater than those in December. ③ ISPa38, IS26, and tnpA were the most significantly different typical MGEs among the rivers in urban and suburban Shijiazhuang. ④ PCoA and NMDS analyses showed significant spatiotemporal differences in MGEs between urban and rural rivers. ⑤ Correlation analysis and co-occurrence results indicated that the abundance of MGEs in urban rivers was significantly positively correlated with antibiotic concentration, industrial enterprises, sewage treatment plants, total population, livestock farming, and aquaculture. In suburban rivers, the abundance of MGEs was mainly significantly positively correlated with antibiotic concentration, livestock farming, aquaculture, and total population. Overall, by comparing the spatiotemporal heterogeneity of MGEs in urban and rural rivers and identifying the main driving factors of MGEs in urban and suburban rivers, this study provides data support for subsequent risk management and control of antibiotic resistance in different rivers.},
}
@article {pmid40229213,
year = {2025},
author = {Hoops, SL and Moutsoglou, D and Vaughn, BP and Khoruts, A and Knights, D},
title = {Metagenomic source tracking after microbiota transplant therapy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2487840},
doi = {10.1080/19490976.2025.2487840},
pmid = {40229213},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Colitis, Ulcerative/therapy/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Bayes Theorem ; Feces/microbiology ; },
abstract = {Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.},
}
@article {pmid40228816,
year = {2025},
author = {Chen, J and Liu, X and Bai, Y and Tang, X and Xue, K and Zhu, Z and Liu, W and Wang, J and Wang, C and Qiao, H and Dang, E and Yin, W and Wang, G and Shao, S},
title = {Tonsillar Microbiota Alterations Contribute to Immune Responses in Psoriasis by Skewing Aged Neutrophils.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf134},
pmid = {40228816},
issn = {1365-2133},
abstract = {BACKGROUND: The interplay between microbiota and the onset of immune-mediated diseases is increasingly coming to light. However, the role of tonsillar microbiota in cutaneous inflammation remains largely unknown.<br><br>OBJECTIVE: We aimed to determine how tonsillar microbiota influence skin inflammation in psoriasis and to uncover the underlying molecular mechanisms.<br><br>METHODS: Tonsillar microbiota samples were collected from 24 healthy controls and 28 psoriasis patients. Microbial community composition was analyzed using 16S rRNA sequencing and metagenomic sequencing. Serum levels of short-chain fatty acids (SCFAs) were measured via liquid chromatography-mass spectrometry in 10 healthy controls and 14 psoriasis patients. Peripheral blood neutrophils from both groups were then exposed to a representative microbial metabolite, and key pro-inflammatory markers were evaluated using functional immune assays.<br><br>RESULTS: We found significant alterations in the diversity and composition of the tonsillar microbial community in psoriasis group, with an increased prevalence of Bacteroidales and a decreased prevalence of Burkholderiales, Micrococcales, and Pasteurellales relative to healthy controls. Notably, a marked reduction in Rothia mucilaginosa correlated inversely with systemic inflammation (neutrophil-to-lymphocyte ratio) and disease severity (psoriasis area and severity index). Metagenomic analysis revealed disruptions in pathways critical for SCFAs production, including propanoate, pyruvate, and butanoate metabolism, which was supported by significantly lower serum SCFAs levels in psoriasis patients. Functional assays demonstrated that SCFAs inhibited neutrophil aging, pro-inflammatory cytokine secretion, and neutrophil extracellular traps (NETs) formation.<br><br>CONCLUSION: Our findings reveal that changes in tonsillar microbiota and their metabolic outputs contribute to psoriasis by modulating immune responses, highlighting potential clinical implications.},
}
@article {pmid40228693,
year = {2025},
author = {Ma, JY and Liu, JH and Chen, CZ and Zhang, YZ and Guo, ZS and Song, MP and Jiang, F and Chai, ZT and Li, Z and Lv, SX and Zhen, YJ and Wang, L and Liang, ZL and Jiang, ZY},
title = {Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121559},
doi = {10.1016/j.envres.2025.121559},
pmid = {40228693},
issn = {1096-0953},
abstract = {The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.},
}
@article {pmid40228470,
year = {2025},
author = {Zhang, Y and Ye, Y and Fang, M and Xiang, Y and Chen, J and Tang, X and Yang, Z and Qian, Q},
title = {Biogas production enhancement from anaerobic digestion with magnetic biochar: Insights into the functional microbes and DIET.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125347},
doi = {10.1016/j.jenvman.2025.125347},
pmid = {40228470},
issn = {1095-8630},
abstract = {The application of magnetic biochar in anaerobic digestion (AD) has gained increasing attention. However, the underlying mechanisms remain insufficiently understood. This study systematically investigated the effects of magnetic biochar on functional microbial communities involved in methanogenesis and elucidated its role in promoting direct interspecies electron transfer (DIET) within AD systems. The addition of 40 mg g[-1] TSadded of magnetic biochar significantly enhanced methane production by 42.21 %, reaching 223.08 mL g[-1] TS with highest organic matter degradation efficiency. Microbial community analysis showed that magnetic biochar significantly enriched microorganisms associated with hydrolysis, acidogenesis, and methanogenesis, as well as electroactive microorganisms' abundance such as Geobacter spp., Syntrophus spp., P. aestuarii, and M. harundinacea, providing direct evidence for the DIET process of AD with magnetic biochar. Furthermore, the abundance of key genes involved in the DIET, including pilA, Fpo, and the genes encoded outer-membrane c-type cytochromes, was respectively upregulated by 44.49 %, 22.04 %, and 37.6 % in the presence of magnetic biochar. These findings suggest that magnetic biochar enhances the production of conductive pili and cytochrome c, facilitating extracellular electron transfer between syntrophic microorganisms. This accelerated electron transfer promotes CO2 reduction to CH4, ultimately improving methane production efficiency in the AD system. Moreover, the enhancement of hydrogenotrophic methanogenesis was particularly pronounced with magnetic biochar, further contributing to the improved AD performance. This study provides novel mechanistic insights into biochar-mediated DIET, offering a theoretical basis for optimizing biochar applications in AD.},
}
@article {pmid40226917,
year = {2025},
author = {Lai, Q and Yao, S and Zha, Y and Zhang, H and Zhang, H and Ye, Y and Zhang, Y and Bai, H and Ning, K},
title = {Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.},
journal = {Nucleic acids research},
volume = {53},
number = {7},
pages = {},
doi = {10.1093/nar/gkaf305},
pmid = {40226917},
issn = {1362-4962},
support = {2021YFA0910500//National Key R&amp;D Program of China/ ; 32071465//National Natural Science Foundation of China/ ; },
mesh = {*Multigene Family ; *Biosynthetic Pathways/genetics ; *Neural Networks, Computer ; *Genome, Microbial ; Phylogeny ; Metagenome ; Secondary Metabolism/genetics ; Genome, Bacterial ; },
abstract = {Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet's capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.},
}
@article {pmid40226542,
year = {2025},
author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B},
title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19260},
pmid = {40226542},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation &amp; purification ; Firmicutes/genetics/isolation &amp; purification ; Sympatry ; Bacteroidetes/genetics/isolation &amp; purification ; },
abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.},
}
@article {pmid40226095,
year = {2025},
author = {Ho, JY and Koh, XQ and Kang, DY and Low, A and Hu, D and Haryono, MAS and Williams, RBH and Case, RJ and Boucher, YF},
title = {Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1437936},
pmid = {40226095},
issn = {1664-302X},
abstract = {Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41G[T] as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813[TS] (=BAABNI000000000.1[TS]) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891[T] outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.},
}
@article {pmid40225905,
year = {2025},
author = {Lambisia, AW and Mwita Morobe, J and Moraa, E and Mwarumba, S and K N Korir, F and Seif Athman, R and Kiptui, R and Mbee, M and Mugo, N and Amoth, P and Muange, P and J Houldcroft, C and Barasa, E and Mwangangi, J and Githinji, G and C Holmes, E and Isabella Ochola-Oyier, L and N Agoti, C},
title = {Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {28},
pmid = {40225905},
issn = {2398-502X},
abstract = {BACKGROUND: In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as "red eye" disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.<br><br>METHODS: Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.<br><br>RESULTS: Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV.<br><br>CONCLUSION: The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.},
}
@article {pmid40225898,
year = {2025},
author = {Liu, H and Wang, H and Sun, J and Yang, T and Mo, Z and Huang, H and Pan, Y},
title = {High-Altitude Open-Pit Coal Mining has Changed the Sulfur Cycle and Ecological Network of Plant Rhizosphere Microorganisms.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71183},
pmid = {40225898},
issn = {2045-7758},
abstract = {Ecological restoration of mining sites has a considerable effect on microbial community dynamics; however, its impact on sulfur cycling is unclear. This study explored the changes in functional genes related to sulfur cycling and microbial diversity during different stages of succession following the ecological restoration of a mining site in a cold arid area. A total of three succession stages were selected-natural, secondary, and artificial. The expression of sulfur cycle-related genes and associated microbial drivers was investigated using metagenomics and network analysis. The dominant bacteria in the secondary succession were found to be r-strategy-adopting Proteobacteria and Cyanobacteria. Natural succession primarily comprised Aspergillus and Thermus, whereas artificial succession comprised Proteobacteria, Chlorophyta, and Actinobacteria. Mining disturbances were determined to significantly reduce the abundance of sulfur-cycling archaea. Secondary succession was primarily influenced by soil total phosphorus in the sulfur-cycle gene network. The key bacteria and archaea involved in the sulfur cycle were found to be Bradyrhizobium and Nitrosopumilus, respectively. The abundance of Streptomyces was significantly higher in natural succession than in artificial or secondary succession. Burkholderia, which has biological control and bioremediation effects, was abundant during artificial succession. These results provide a theoretical basis for restoring the sulfur cycle and promoting a positive succession of ecosystems in mining areas.},
}
@article {pmid40225105,
year = {2025},
author = {He, W and Wang, S and Xiong, X and Dai, W},
title = {[18]F-FDG PET/CT Imaging of Talaromyces marneffei Infection with Bone Destruction in an HIV-Negative Patient: Case Report and Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1745-1752},
pmid = {40225105},
issn = {1178-6973},
abstract = {BACKGROUND: Talaromycosis is an opportunistic fungal infection caused by Talaromyces marneffei (T. marneffei), commonly occurs in HIV-positive individuals. While less common, it can also affect HIV-negative individuals. We reported a T. marneffei infection in an HIV-negative patient, whose imaging findings and diagnostic process offer valuable clinical insights.<br><br>CASE PRESENTATION: An HIV-negative male adult patient with an intermittent cough for more than two years and worsened for more than one month. Enhanced CT scan indicated lung cancer with rib and lymph nodes metastasis. The lower respiratory tract and bronchial lavage fluid culture of the patient were negative. He received two bronchoscopies, two biopsies and two metagenomic next-generation sequencing (mNGS) tests, which failed to find the malignant cell but sequentially identified the presence of Pasteurella multocida and the Epstein-Barr virus. His condition did not improve after anti-infective treatment for 2weeks. An 18-fluorodeoxy glucose ([18]F-FDG) PET/CT scan revealed increased radioactivity in right supraclavicular lymph node, left lung and the right tenth rib. Ultimately, a biopsy at the hypermetabolic lesion of left lung, and a third mNGS test confirmed the presence of Talaromyces marneffei. Subsequently, the patient started antifungal therapy with amphotericin B and itraconazole and showed a favorable response.<br><br>CONCLUSION: We reviewed all reported PET/CT findings of T. marneffei infection patients, suggesting that fungus T. marneffei should be considered in patients identified as infection and exhibited bone destruction and also highlight the role of PET/CT in guiding the biopsy site.},
}
@article {pmid40224142,
year = {2025},
author = {Caille, A and Connan, C and Lyon Belgy, N and Borezée, E and Cherbuy, C and Meunier, N and Meslier, V},
title = {Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103268},
pmid = {40224142},
issn = {2215-0161},
abstract = {Recent advances in the study of the gut microbiota has pointed to its under-utilized source of potentially beneficial bacteria, known as next generation probiotics, offering a promising avenue to restore or compensate impaired gut microbiota toward a healthy state. Aside from the difficulties to achieve in-lab adequate culture conditions, the use of beneficial bacterial isolates is also limited by their bioavailability in the donor itself. In the iTARGET study, we positively selected donors based on their diet enriched in fiber, that has been shown to increase the prevalence of bacterial species associated with health. The iTARGET study is a monocenter, prospective, observational study of adults with healthy lifestyle and high daily fiber consumption. We aim to recruit individuals in two phases, the first one for all individuals that will permit the identification of carriers for bacteria of interest and the second phase for a subset of individuals to allow for culture and isolation of previously identified potentially beneficial bacteria. Our primary outcome is the isolation and culture of at least one potentially beneficial isolate. The secondary outcomes comprised the high throughput metagenomic profiles of the intestinal microbiota and the characterization of the cultured isolates. The study was approved by the French Research Ethics Committees (Comité de Protection des Personnes Sud-Est I) under the National reference ID 2023-A01677-38. Study findings and results will be published in peer-reviewed Open Access journals. (Trial registration number on ClinicalTrials.gov: NCT06166810).},
}
@article {pmid40223813,
year = {2025},
author = {Alp-Baltakesmez, D and Ertürkmen, P and Bulantekin, &#xd6;},
title = {Diversity and Functional Roles of Microorganisms in Anatolian Black Pine Cone Vinegar Fermentation.},
journal = {Food science &amp; nutrition},
volume = {13},
number = {4},
pages = {e70155},
pmid = {40223813},
issn = {2048-7177},
abstract = {The parts of some pine species are a rich source of bioactive compounds that can be used in various food products. The current work, the physicochemical, bioactive, antimicrobial, sensory, and aromatic properties of traditional vinegar produced from Anatolian Black Pine Cones from different provinces of Turkey were determined, as well as the cultivable microbial diversity and metagenomic analysis. The total phenolic content of the vinegars ranged from 163.88 to 174.79 mg GAE/L. Antioxidant activity, measured via DPPH and ABTS assays, varied among the samples. CnB vinegar, made from Burdur province cones, stood out for its bioactive compounds, including terpenes, acetic acid, ascorbic acid, and the highest α-terpineol content (3.13%). CnB also exhibited the strongest antimicrobial activity, with the largest inhibition zone (44.91 mm) against E. coli type A, while CnM showed the lowest activity. Sensory evaluations favored CnB for its balanced flavor, while CnV was criticized for excessive sharpness, and CnM was deemed too mild. The bacterial microbiome of CnB was predominantly composed of acetic acid bacteria, with an average concentration of 7.36 log CFU/mL in the enumeration of culturable microorganisms. The dominant bacterial taxa at the phyla level included Proteobacteria (72.296%), Firmicutes (22.062%), Bacteroidota (3.665%), followed by Acetobacteraceae (71.47%), Clostridia (13.187%), Bacilli (5.066%), Bacteroidetes (3.665%), and C. negativicutes (3.737%) at the phylum level. The fungal microbiome was mainly represented by Ascomycota (78.717%) and Eukaryota Incertae sedis (15.840%). The findings demonstrate that pine cone vinegar can be employed in a multitude of applications, including food preservation and health promotion.},
}
@article {pmid40223739,
year = {2025},
author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A},
title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
doi = {10.4103/sjg.sjg_24_25},
pmid = {40223739},
issn = {1998-4049},
abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.<br><br>METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-na&#xef;ve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.<br><br>RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4, uncultured_crAssphage, Staphylococcus_phage_SPbeta-like, Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.<br><br>CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment na&#xef;ve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.},
}
@article {pmid40223703,
year = {2025},
author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H},
title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00306},
pmid = {40223703},
issn = {1520-5851},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.},
}
@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}
@article {pmid40223231,
year = {2025},
author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S},
title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2489154},
doi = {10.1080/21505594.2025.2489154},
pmid = {40223231},
issn = {2150-5608},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; },
abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.},
}
@article {pmid40223096,
year = {2025},
author = {Yang, Z and Zhou, Y and Lin, J and Wang, X and Huang, C and Gao, J and Wang, G and Yang, B and Liu, G and Duan, H and Cui, J and Zhao, J and Luo, W and Cheng, S and Liu, Y},
title = {Identification and characterization of pigeon adenovirus 1 as an emerging pathogen in pigeons from Northern and Northwest China.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {266},
pmid = {40223096},
issn = {1746-6148},
support = {BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; },
mesh = {Animals ; *Columbidae/virology ; China/epidemiology ; *Adenoviridae Infections/veterinary/virology/epidemiology/pathology ; *Bird Diseases/virology/epidemiology/pathology ; *Aviadenovirus/genetics/isolation &amp; purification ; Phylogeny ; Genome, Viral ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; },
abstract = {BACKGROUND: In 2022, a new infectious disease characterized by severe acute hepatitis, sudden death, and high mortality among breeding pigeons, was reported in China.<br><br>RESULTS: In naturally infected pigeons, key necropsy findings comprised hepatic swelling with patchy hemorrhage and pericardial effusion. Histopathological examination further revealed degeneration, necrosis, and basophilic intranuclear inclusion bodies affecting hepatocytes, cardiomyocytes, and vascular endothelial cells. Transmission electron microscopy revealed a typical icosahedral virus structure and crystal-like arrangement of viral particles in the nucleus. Metagenomic next-generation sequencing (mNGS) of pericardial effusion samples revealed the presence of pigeon adenovirus. Sequencing analysis of the hexon and fiber-2 genes suggested that it constituted pigeon adenovirus 1 (PiAdV-1). The complete genome of CH/BJ/1/2022 was determined to be 48,071 nucleotides in length, with a 10-amino acid deletion in the fiber-2 gene at residues 627-636 and a 95-animo acid insertion in the 100&#xa0;K gene at residue 75. The same disease was reproduced in pigeons by experimental infection.<br><br>CONCLUSION: Collectively, our analyses confirmed that the etiological agent was PiAdV-1, an emerging pathogen that causes severe acute hepatitis and high mortality in pigeons. This virus merits close attention because it could be catastrophic for the pigeon industry.},
}
@article {pmid40222673,
year = {2025},
author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL},
title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26395},
pmid = {40222673},
issn = {1525-3198},
abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.},
}
@article {pmid40222492,
year = {2025},
author = {Xia, Y and Chen, X and Jiang, X and Shen, J},
title = {Enhanced denitrification under saline Conditions: Glycine betaine as a key osmoprotectant.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132517},
doi = {10.1016/j.biortech.2025.132517},
pmid = {40222492},
issn = {1873-2976},
abstract = {Biological denitrification is significantly inhibited by salinity, which adversely affects microbial activity and reduces efficiency. This study aimed to evaluate the impact of salinity on denitrification performance and assess the potential of glycine betaine (GB) as an osmotic pressure regulator and protective agent. Results indicated that under the optimal conditions, including an influent nitrate concentration of 51.03 mg L[-1], C/N ratio of 5.42, pH value of 8.95, and salinity of 1.05 %, the nitrate removal efficiency was predicted to reach 100 %. However, a sharp decline (56.09 ± 4.52 %) in nitrate removal efficiency occurred when salinity increased from 0 % to 3 % within the initial 6 h. This inhibition was mitigated by adding 25 mg L[-1] GB, which enhanced nitrate removal efficiency by 2.19 times. GB promoted the secretion of extracellular polymeric substances (EPS), especially polymeric protein, a critical contributor to salinity resistance. Metagenomics analysis revealed that GB improved denitrification process by upregulating key genes involved in nitrogen and carbon metabolism. Furthermore, the relative abundance of Na[+] transporter genes, K[+] transporter genes, and GB absorption and synthesis genes rose with GB addition, underscoring the indispensable role of GB in alleviating osmotic stress and accelerating microbial metabolism. These findings emphasize the detrimental effects of salinity on denitrification and demonstrate the potential of GB as an osmoprotectant, enabling efficient nitrogen removal under saline conditions.},
}
@article {pmid40222473,
year = {2025},
author = {Jing, K and Li, Y and Li, Y and Meng, Q and Guan, Q},
title = {The treated wastewater enhances the biodegradation of sulfonamide antibiotics in biofilm-sediment downstream of the receiving river outlet.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121600},
doi = {10.1016/j.envres.2025.121600},
pmid = {40222473},
issn = {1096-0953},
abstract = {Although the treated wastewater meets the discharge standards, it can still become a potential transmitted stressor that affects aquatic organisms in receiving rivers. Biofilms and sediments as the main solid-phase substances in natural aquatic environments can biodegrade micropollutants. However, most of the current studies have selected a single solid-phase material, and there are relatively few studies that comprehensively consider the effect of treated wastewater on the dissipation of micropollutants in a composite biofilm-sediment system. Therefore, this study investigated the dissipation pathways of six sulfonamide antibiotics (SAs) in biofilm-sediment and the effect of treated wastewater on SAs dissipation. The results showed that biodegradation was the main pathway for SAs dissipation in biofilm-sediment. The input of treated wastewater increased the abundance of dominant degradation bacteria Burkholderiales and Pseudomonadale, thereby improving the biodegradation rate of SAs (approximately 1.5 times higher than upstream degradation rate). These genera could also be further integrated into downstream communities to continuously mediate the biodegradation of SAs. Through mass spectrometry and metagenomic sequencing analysis, it was found that the common degradation pathways of SAs in biofilm-sediment affected by treated wastewater are acetylation, formylation, hydroxylation, and bond cleavage. Acetyltransferase played an important role in the biodegradation of SAs. In addition, the enrichment of antibiotic resistant genes during biodegradation increased the risk of their spread in the aquatic environment. These findings provide new insights into the fate of antibiotics in aquatic environments and the impact of treated wastewater on downstream bacterial communities.},
}
@article {pmid40222470,
year = {2025},
author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z},
title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121602},
doi = {10.1016/j.envres.2025.121602},
pmid = {40222470},
issn = {1096-0953},
abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2%) was higher than ammonia-oxidizing bacteria (AOB, 12.0%), but lower than ammonia-oxidizing archaea (AOA, 64.8%). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.},
}
@article {pmid40222255,
year = {2025},
author = {Bobrovska, S and Newcomer, E and Gottlieb, M and McSorley, VE and Kittner, A and Hayden, MK and Green, S and Barbian, HJ},
title = {Hospital air sampling enables surveillance of respiratory virus infections and genomes.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179346},
doi = {10.1016/j.scitotenv.2025.179346},
pmid = {40222255},
issn = {1879-1026},
abstract = {There is an urgent need for early detection and comprehensive surveillance of respiratory pathogens. Environmental surveillance may be key to timely responses for newly emerging pathogens and infections that are unreported or underreported. Here, we employed air sampling in a large urban hospital. Air samples (n = 358) were collected weekly at five locations, including two in the emergency department, two in hospital common areas and one in a storage room, for two respiratory virus seasons (November 2022 to June 2024). Air samples were tested for eight respiratory pathogens by qPCR, including RNA and DNA viruses and a bacterium. Air samples had an average of four detected pathogens per sample and 97 % samples contained SARS-CoV-2. Air sample pathogen positivity and quantity were strongly correlated with clinical surveillance for four seasonal respiratory pathogens: influenza A and B, respiratory syncytial virus, and human metapneumovirus. Targeted amplicon sequencing of SARS-CoV-2 showed that lineages detected in air samples reflected those in contemporaneous regional clinical specimens. Metagenomic sequencing with viral capture enrichment detected myriad human pathogens, including respiratory-associated viruses with recovery of full viral genomes. Detection of viral pathogens correlated well between virus capture sequencing and qPCR. Overall, this suggests air sampling can be an agile and effective tool for pathogen early warning, surveillance and genome characterization.},
}
@article {pmid40222247,
year = {2025},
author = {Suzuki, M and Hayashi, T and Takahashi, K and Nozaki, K and Kasuya, KI},
title = {Exploring biodegradation limits of n-alkanes as polyethylene models using multi-omics approaches.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179365},
doi = {10.1016/j.scitotenv.2025.179365},
pmid = {40222247},
issn = {1879-1026},
abstract = {Polyethylene (PE) is widely regarded as non-biodegradable in natural environments, despite reports suggesting partial biotic degradation. Using multi-omics analysis, this study investigated the biodegradation mechanisms of n-alkanes-structural analogs of PE-to determine the threshold carbon number in PE that allows for environmental biodegradation. n-Alkanes with 6-40 carbons (C6-C40) were biodegraded in the soil, whereas C44 and PE were not. 16S rRNA gene amplicon sequence analysis identified distinct microbial communities associated with non-degradable compounds (PEs and C44) and biodegradable alkanes (C6-C40). Notably, the microbial community composition for C40 differed from those associated with biodegradable alkanes below C36. Multi-omics analysis identified the genera Aeromicrobium, Nocardia, Nocardioides, Rhodococcus, Acinetobacter, and Fontimonas as key degraders of n-alkanes at C36 and below, utilizing alkane hydroxylases such as alkane monooxygenase (AlkB), LC-alkane monooxygenase from Acinetobacter (AlmA), and cytochrome P450 (CYP153). Conversely, the biodegradation of C40 was facilitated by taxa, including the order Acidimicrobiales and the genera, Acidovorax, Sphingorhabdus, Prosthecobacter, and Roseimicrobium using AlmA and CYP153-type hydroxylases. This difference in key degraders and alkane hydroxylases may explain the reduced biodegradability of n-alkanes above C40, including PE.},
}
@article {pmid40222078,
year = {2025},
author = {Xu, A and Gao, D and Wu, WM and Gong, X and Liang, H},
title = {Enhanced denitrification using iron modified biochar under low carbon source condition: Modulating community assembly, allocating carbon metabolism and facilitating electron transfer.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125354},
doi = {10.1016/j.jenvman.2025.125354},
pmid = {40222078},
issn = {1095-8630},
abstract = {Biochar can modulate microbial community structure to enhance denitrification but the activity is still restricted by the availability of electron transfer (ETS) under metabolic imbalance conditions. Here we developed iron (Ⅲ) modified biochar (FeBC) to substantially mitigate this electron limitation, enhance ETS and accelerate denitrification reaction via intracellular metabolism and community interaction. The results demonstrated that FeBC could significantly improve the denitrification performance, the nitrate removal rate was significantly increased by 30 % at C/N ratio of 3 (W/W) with little nitrite and nitrous oxide accumulation, attributing to the enhanced activities of the ETS and denitrifying reductases and complex microbial interactions via increased abundance of microorganisms involved in carbon and nitrogen transformations. Biochemical quantification and electrochemical analysis, revealed that FeBC activated the acceleration of the ETS process. Comparative metagenome analyses indicated that upregulating key enzymes in the tricarboxylic acid cycle was the potential respiratory enzyme associated with FeBC-mediated ETS. NADH/NAD[+] circulation stimulate the startup of carbon metabolism. This energy-linked mechanism could provide ATP for denitrification. This study revealed the functional roles of FeBC in mediating ETS and regulating the bacterial community to achieve enhanced denitrification.},
}
@article {pmid40221653,
year = {2025},
author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ},
title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {26},
pmid = {40221653},
issn = {2730-6844},
mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth &amp; development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.<br><br>DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil&#xae; DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.},
}
@article {pmid40221647,
year = {2025},
author = {Zhang, N and Dou, H and Guo, P and Sun, J and Zhang, F and Chen, T and Gao, C and Wang, Z},
title = {Concurrent invasive disseminated Nocardia farcinica and Candida infections in a patient undergoing long-term glucocorticoid therapy for autoimmune thrombocytopenia: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {520},
pmid = {40221647},
issn = {1471-2334},
support = {gxgnfx2022035//Domestic Visiting Training Program for Outstanding Young Backbone Teachers/ ; 2023SYKFZ05//Open project of Anhui Biochemical Drug Engineering Technology Research Center in 2023/ ; },
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/microbiology/complications ; Middle Aged ; *Nocardia/isolation &amp; purification ; *Candidiasis/drug therapy/diagnosis/microbiology/complications ; *Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications ; *Glucocorticoids/therapeutic use/adverse effects ; Antifungal Agents/therapeutic use ; Candida albicans/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology ; Prednisone/therapeutic use/adverse effects ; Immunocompromised Host ; },
abstract = {BACKGROUND: Nocardia farcinica is a virulent organism known for its high resistance to many antibiotics and its ability to cause disseminated life-threatening infections, particularly in immunocompromised patients or those undergoing organ transplantation. Candida albicans can cause disseminated candidiasis with a mortality rate ranging from 30% to 60%. Cases involving concurrent disseminated N. farcinica and C. albicans, particularly in patients with autoimmune thrombocytopenia, are extremely rare. The presence of two disseminated pathogens complicates both diagnosis and treatment, creating substantial challenges for healthcare providers.<br><br>CASE PRESENTATION: A 50-year-old woman who had a history of autoimmune thrombocytopenia and was being treated with prednisone (60&#xa0;mg qd). She presented with a 40-day history of high-grade fevers (40&#x2103;), cough, headache, and multiple abscesses in the skin structure. N. farcinica was found in her skin structure, cerebrospinal fluid, and blood, and C. albicans was cultured in cerebrospinal fluid, sputum, and urine. She was diagnosed with disseminated nocardiosis and disseminated candidiasis. The patient received a prolonged course of multiple anti-bacterial and anti-fungal medications and eventually recovered.<br><br>CONCLUSIONS: Due to the atypical clinical presentations, the diagnosis of concurrent invasive disseminated N. farcinica and C. albicans infections might be delayed. A variety of diagnostic testing, including metagenomics next-generation sequencing, can help to identify the pathogen rapidly. Drug susceptibility test can guide the selection and adjustment of antibiotics, which should be in companion with surgical interventions to save lives in affected patients.},
}
@article {pmid40221512,
year = {2025},
author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y},
title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12568},
pmid = {40221512},
issn = {2045-2322},
support = {82104236//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; },
abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.},
}
@article {pmid40221485,
year = {2025},
author = {Wu, Q and Gao, J and Sa, B and Cong, H and Deng, W and Zhang, Y and Zhong, X and Zhang, J and Wang, L and Liu, H and Yan, Y and Zhang, Y and Liu, D and Yan, W},
title = {Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {612},
pmid = {40221485},
issn = {2052-4463},
support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42293292//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Prochlorococcus/genetics ; *Synechococcus/genetics ; *Genome, Bacterial ; Nanopore Sequencing ; *Genome, Viral ; Metagenome ; Pacific Ocean ; Indian Ocean ; Seawater/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Prochlorococcus and Synechococcus are key contributors to marine primary production and play essential roles in global biogeochemical cycles. Despite the ecological importance of these two picocyanobacterial genera, current genomic datasets still lack comprehensive representation of under-sampled ocean regions, associated bacteria and viruses. To address this gap, we used a combination of second- and third-generation sequencing technologies to assemble comprehensive genomic data from 105 Picocyanobacterial enrichment cultures isolated from the Indian Ocean, the South China Sea, and the western Pacific Ocean. This dataset includes 55 Prochlorococcus and 50 Synechococcus genomes with high completeness (>98%) and low contamination (<2%), along with 308 non-redundant associated bacterial genomes derived from 1,457 medium- and high-quality non-cyanobacteria metagenome-assembled genomes (MAGs, completeness ≥50% and contamination ≤10%). Additionally, 2,113 non-redundant viral operational taxonomic units (vOTUs) were derived from a total of 7632 qualified viral contigs. This dataset provides a valuable resource for improving our understanding of the complex interactions among Prochlorococcus, Synechococcus, and their associated bacteria and viruses in marine ecosystems, offering a foundation to study their ecological roles and evolutionary dynamics.},
}
@article {pmid40221450,
year = {2025},
author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW},
title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {57},
pmid = {40221450},
issn = {2055-5008},
support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.},
}
@article {pmid40220806,
year = {2025},
author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q},
title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {142983},
doi = {10.1016/j.ijbiomac.2025.142983},
pmid = {40220806},
issn = {1879-0003},
abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.},
}
@article {pmid40220770,
year = {2025},
author = {Venkatesan, P},
title = {UK launch metagenomic pathogen surveillance programme.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101143},
doi = {10.1016/j.lanmic.2025.101143},
pmid = {40220770},
issn = {2666-5247},
}
@article {pmid40220715,
year = {2025},
author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X},
title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105686},
doi = {10.1016/j.ebiom.2025.105686},
pmid = {40220715},
issn = {2352-3964},
abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.<br><br>METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.<br><br>FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.<br><br>INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.<br><br>FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).},
}
@article {pmid40220662,
year = {2025},
author = {Yuan, Q and Ng, C and Goh, SG and Khor, WC and Ong, GHM and Aung, KT and Gin, KY},
title = {Evaluation of public health impact risks associated with bacterial antimicrobial resistome in tropical coastal environments.},
journal = {Water research},
volume = {282},
number = {},
pages = {123621},
doi = {10.1016/j.watres.2025.123621},
pmid = {40220662},
issn = {1879-2448},
abstract = {This study investigated antimicrobial resistance genes (ARGs) and microbial communities in Singapore's tropical coastal environments, comparing natural marine waters with aquaculture sites using metagenomic analysis. Results show consistently low ARG levels in natural ecosystems, whereas aquaculture sites exhibit elevated ARG concentrations, particularly those relevant to human pathogens, with considerably temporal fluctuations likely driven by human activities and seasonal factors. Additionally, aquaculture sites were found to host mobile genetic elements (MGEs) that may facilitate ARG spread, identifying aquaculture as a key reservoir of resistance genes with potential public health implications. These findings underscore distinct prevalence of ARG between natural and managed marine environments and highlight the need for continued surveillance to monitor ARG dynamics in coastal areas. By elucidating the potential for ARGs to transfer from aquaculture environments to the human food chain, this research emphasizes the importance of sustainable aquaculture practices and proactive ARG management strategies to mitigate antimicrobial resistance risks posed by tropical coastal ecosystem.},
}
@article {pmid40220550,
year = {2025},
author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E},
title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.},
journal = {Archives of oral biology},
volume = {175},
number = {},
pages = {106251},
doi = {10.1016/j.archoralbio.2025.106251},
pmid = {40220550},
issn = {1879-1506},
abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.<br><br>DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.<br><br>RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.<br><br>CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.},
}
@article {pmid40220395,
year = {2025},
author = {Zhu, Y and Zhang, X and Tao, W and Yang, S and Qi, H and Zhou, Q and Su, W and Zhang, Y and Dong, Y and Gan, Y and Lei, C and Zhang, A},
title = {Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138221},
doi = {10.1016/j.jhazmat.2025.138221},
pmid = {40220395},
issn = {1873-3336},
abstract = {The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.},
}
@article {pmid40219113,
year = {2025},
author = {Vinskienė, J and Tamošiūnė, I and Andriūnaitė, E and Gelvonauskienė, D and Rugienius, R and Hakim, MF and Stanys, V and Buzaitė, O and Baniulis, D},
title = {Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071045},
pmid = {40219113},
issn = {2223-7747},
support = {S-MIP-22-54//Lietuvos Mokslo Taryba/ ; },
abstract = {In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.},
}
@article {pmid40219101,
year = {2025},
author = {Fouad, N and El-Zayat, EM and Amr, D and El-Khishin, DA and Abd-Elhalim, HM and Hafez, A and Radwan, KH and Hamwieh, A and Tadesse, W},
title = {Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071033},
pmid = {40219101},
issn = {2223-7747},
abstract = {Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.},
}
@article {pmid40218354,
year = {2025},
author = {Zhu, F and Ma, J and Xue, M and Xu, W and Liu, W and Zhou, Y and Liu, M and Fan, Y},
title = {Seasonal and Regional Dynamics of the Intestinal Microbiota in Schizothorax nukiangensis from the Nujiang River.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070961},
pmid = {40218354},
issn = {2076-2615},
support = {2023TD46, 2023TD09//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (CAFS)/ ; },
abstract = {The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected samples of S. nukiangensis across different seasons and regions within the Nujiang River to comprehensively elucidate the diversity and composition of its intestinal microbiota using metagenomic technology. The results indicated that Firmicutes and Proteobacteria predominated at the phylum level, while Priestia, Bacillus, and Aeromonas were the most abundant genera identified. Notably, the relative abundance of these microorganisms varied significantly across different seasons and regions. From autumn through spring and into summer, the predominant microorganisms shifted from Firmicutes to Proteobacteria. Biomarker analysis revealed that Firmicutes (including the class bacilli and the genera Priestia and Bacillus) exhibited a higher relative abundance within the upstream group, where categories related to amino acid metabolism and carbohydrate metabolism were significantly enriched. Conversely, Proteobacteria (including several potential pathogens, such as Saezia, Pantoea, Lelliotia, and Aeromonas genera) showed an increased relative abundance within downstream groups, where disease-related categories exhibited significant enrichment. Our findings significantly enhance our understanding of how S. nukiangensis adapts to its environment, providing valuable data support for the conservation of S. nukiangensis and for ecological security assessment of the Nujiang River.},
}
@article {pmid40218343,
year = {2025},
author = {Ajmi, N and Duman, M and Coskun, B and Esen, C and Sonmez, O and Tasci, G and Coskuner-Weber, O and Ay, H and Yoyen-Ermis, D and Yibar, A and Desbois, AP and Saticioglu, IB},
title = {Unraveling Genomic and Pathogenic Features of Aeromonas ichthyocola sp. nov., Aeromonas mytilicola sp. nov., and Aeromonas mytilicola subsp. aquatica subsp. nov.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070948},
pmid = {40218343},
issn = {2076-2615},
support = {TGA-2024-1797 and 124Z735//The Research Fund of Bursa Uludag University and T&#xdc;B&#x130;TAK/ ; },
abstract = {The Gram-negative genus Aeromonas contains diverse bacterial species that are prevalent in aquatic environments. This present study describes three novel Aeromonas strains: A. ichthyocola sp. nov. A-5[T] and A. mytilicola subsp. aquatica subsp. nov. A-8[T] isolated from rainbow trout (Oncorhynchus mykiss), and A. mytilicola sp. nov. A-7[T] isolated from mussels (Mytilus galloprovincialis), respectively. Genomic analyses revealed that strains A-5[T] and A-7[T] shared the highest 16S rRNA gene sequence similarity with A. rivipollensis P2G1[T] (99.7% and 99.8%, respectively), while strain A-8[T] exhibited 99.7% identity with A. media RM[T]. Together with morphological, physiological, and biochemical data, genome-based analyses provided additional evidence for species differentiation. Digital DNA-DNA hybridization (dDDH; 56.8-65.9%) and average nucleotide identity (ANI; 94.2-95.7%) values fell below the species delineation thresholds, confirming that these isolates represent distinct taxa. Pathogenicity assays using greater wax moth (Galleria mellonella) larvae demonstrated strain-specific virulence profiles. Further genomic analyses identified biosynthetic gene clusters for nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), which often have roles in secondary metabolite production. Ecological analyses, based on genomic comparisons and metagenomic database searches, revealed the adaptability of the strains to diverse habitats, including freshwater, wastewater, and activated sludge. Based on the genetic and phenotypic data, the novel taxa Aeromonas ichthyocola sp. nov. A-5ᵀ (LMG 33534ᵀ = DSM 117488ᵀ), Aeromonas mytilicola sp. nov. A-7ᵀ (LMG 33536ᵀ = DSM 117490ᵀ), and Aeromonas mytilicola subsp. aquatica subsp. nov. A-8ᵀ (LMG 33537ᵀ = DSM 117493ᵀ) are proposed.},
}
@article {pmid40217586,
year = {2025},
author = {Komoróczy, B and Váncsa, S and Váradi, A and Hegyi, P and Vágási, V and Baradács, I and Szabó, A and Nyirády, P and Benkő, Z and Ács, N},
title = {Optimal Aspirin Dosage for the Prevention of Preeclampsia and Other Adverse Pregnancy Outcomes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072134},
pmid = {40217586},
issn = {2077-0383},
abstract = {Background/Objectives: This systematic review and meta-analysis aimed to determine the effectiveness of different aspirin dosages in preventing preeclampsia and its effect on other pregnancy-associated conditions. Methods: A comprehensive search of three databases (Pubmed, Embase, and Cochrane Library) was conducted for randomized controlled trials without time interval criteria, comparing aspirin at various doses with placebo or no specific preeclampsia prophylaxis. Eligible randomized controlled trials (RCTs) examined pregnant women receiving aspirin at any dose and time during their pregnancy, while the control group received a placebo, or placebo and a different dose of aspirin, or no specific preeclampsia prevention. No exclusion criteria were established regarding the population, study size, study site, or length of aspirin prophylaxis. Studies examining additional preventive medication (such as low-molecular-weight heparin) compared to aspirin without a placebo group were excluded. For all outcomes, the risk ratios (RRs) and mean differences (MDs) with 95% confidence intervals (CIs) were calculated. Meta-regression was performed to examine the relation between aspirin dosage and preeclampsia. Results: Based on the analysis of 31 studies involving 28,318 pregnancies and 20 studies involving 26,551 pregnancies, the early initiation of aspirin significantly reduced the overall incidence of preeclampsia (RR = 0.63, CI: 0.47-0.84) and perinatal death risk (RR = 0.82, CI: 0.72-0.93), respectively. Based on our meta-regression model, we could not establish a dose-dependent correlation between aspirin dosage and the risk of preeclampsia. Conclusions: Early-initiated aspirin prophylaxis is effective in preventing preeclampsia, without raising the incidence of placental abruption or increasing the amount of peripartum bleeding. No specific dose was superior to others; thus, further research should explore higher doses and focus on preterm preeclampsia, maternal-fetal complications, and bleeding.},
}
@article {pmid40217292,
year = {2025},
author = {Diop, K and Mbaye, B and Nili, S and Filin, A and Benlaifaoui, M and Malo, J and Renaud, AS and Belkaid, W and Hunter, S and Messaoudene, M and Lee, KA and Elkrief, A and Routy, B},
title = {Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {21},
pmid = {40217292},
issn = {1757-4749},
abstract = {BACKGROUND: The gut microbiome represents a novel biomarker for melanoma and non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Gut microbiome metagenomics profiling studies of patients treated with immunotherapy identified bacteria associated with ICI efficacy, while others have been linked to resistance. However, limitations of metagenomics sequencing, such as complex bioinformatic processing requirements, necessity of a threshold for positive detection, and the inability to detect live organisms, have hindered our ability to fully characterize the gut microbiome. Therefore, combining metagenomics with high-throughput culture-based techniques (culturomics) represents an ideal strategy to fully characterize microbiome composition to more robustly position the microbiome as a biomarker of response to ICI.<br><br>METHODS: We performed culturomics using fecal samples from 22 patients from two academic centres in Canada and the United Kingdom with NSCLC and cutaneous melanoma treated with ICI (cancer group), comparing their microbiome composition to that of 7 healthy volunteers (HV), along with matching shotgun metagenomics sequencing.<br><br>RESULTS: For culturomics results, 221 distinct species were isolated. Among these 221 distinct species, 182 were identified in the cancer group and 110 in the HV group. In the HV group, the mean species richness was higher compared to the cancer group (34 vs. 18, respectively, p&#x2009;=&#x2009;0.002). Beta diversity revealed separate clusters between groups (p&#x2009;=&#x2009;0.004). Bifidobacterium spp. and Bacteroides spp. were enriched in HV, while cancer patients showed an overrepresentation of Enterocloster species, as well as Veillonella parvula. Next, comparing cancer patients' clinical outcomes to ICI, we observed that among the 20 most abundant bacteria present in non-responder patients, 2 belonged to the genus Enterocloster, along with an enrichment of Hungatella hathewayi and Cutibacterium acnes. In contrast, responders to ICI exhibited a predominance of Bacteroides spp. In NSCLC patients, metagenomics analysis revealed that of the 154 bacteria species isolated through culturomics, 61/154 (39%) were also identified by metagenomics sequencing. Importantly, 94 individual species were uniquely detected by culturomics.<br><br>CONCLUSION: These findings highlight that culturomics and metagenomics can serve as complementary tools to characterize the microbiome in patients with cancer. This integrated approach uncovers specific microbiome signatures that differentiate HV from cancer patients, and identifies specific species associated with therapy response and resistance.},
}
@article {pmid40216789,
year = {2025},
author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG},
title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3469},
pmid = {40216789},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; },
abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.},
}
@article {pmid40216686,
year = {2025},
author = {Fan, Q and Zhang, Y and Lian, J and Liang, D and Yu, J and Liu, X and Zhang, N},
title = {Screening and community succession and functional prediction of high-efficiency degradation microbial communities for rice straw at low-temperature.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {20},
pmid = {40216686},
issn = {1433-4909},
support = {2023YFD2100803//National Key R&amp;D Programme Project of China/ ; },
mesh = {*Oryza/microbiology/metabolism ; *Microbiota ; *Cold Temperature ; Lignin/metabolism ; },
abstract = {Traditional straw return relies on microbial degradation, but cold winters delay it, risking crops. Therefore, a microbial community adapted to rice straw degradation in cold regions was constructed by restrictive consecutively sub-cultured under low-temperature limitations. The capabilities of the microbial community, such as adaptability, stability, and degradation power, were evaluated by analyzing straw degradation features, Characterization experiments and lignocellulose enzyme activities across multiple generations. 16S amplicon sequencing was used to monitor the changes in its structure over generations. Metagenomic sequencing uses CAZy and KEGG to classify gene functions. The results showed that the highest degradation efficiencies and enzyme activities were observed in the E and F generations, dominated by Proteobacteria, Bacteroidetes, and Fungi The stable microbial community was designated as LJ-7. Metagenomic analysis showed that functional genes of LJ-7 were mainly concentrated in glycoside hydrolase (GHs) and glycosyl transferase (GTs) related genes which contained many fiber and lignin-degrading enzyme genes. It is speculated that microbial enzymes degrade straw by breaking down its complex structure into monosaccharides or metabolizing quinone compounds for energy. This experiment successfully screened a microbial community capable of degrading rice straw at low temperatures, thus offering novel research insights and pathways for straw degradation in cold conditions.},
}
@article {pmid40216167,
year = {2025},
author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW},
title = {Investigating the bidirectional interactions between senotherepeutic agents and human gut microbiota.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107098},
doi = {10.1016/j.ejps.2025.107098},
pmid = {40216167},
issn = {1879-0720},
abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.},
}
@article {pmid40216056,
year = {2025},
author = {Liu, S and Li, J and Zhang, Z and Tuo, J and Zhang, Q and Zhou, J and Liu, P and Zhang, XX},
title = {Exploring phylogenetic diversity of antibiotic resistance genes in activated sludge: A host and genomic location perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121588},
doi = {10.1016/j.envres.2025.121588},
pmid = {40216056},
issn = {1096-0953},
abstract = {Antibiotic resistance has emerged as a significant global public health issue. The environmental behaviors of antibiotic resistance genes (ARGs), such as their persistence and horizontal transfer, have been extensively investigated. However, the genetic diversity characteristics of ARGs remain underexplored, which limits a comprehensive analysis of their roles in the environment. In this study, we examined the genetic diversity of ARGs in activated sludge from 44 wastewater treatment plants in five countries. Most ARGs detected in activated sludge possessed multiple variants, with a median of 48. The number of variants of gd-ARGs varied among different resistance mechanisms and ARG types. The number of potential variants of ARGs was strongly correlated with host diversity. Pseudomonas spp. and Klebsiella pneumoniae, identified as pathogenic bacteria, harbored multiple ARGs and had the most variants. Most ARG subtypes on plasmids and chromosomes showed divergent evolution. Molecular docking of AdeH proteins revealed that genomic location affects tetracycline binding energy. The findings underscore the intricate interplay between genetic variation and environmental adaptation in ARGs, offering a novel perspective on the spread of antibiotic resistance.},
}
@article {pmid40215877,
year = {2025},
author = {Saeed, M and Al-Khalaifah, H and Al-Nasser, A and Al-Surrayai, T},
title = {Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105130},
doi = {10.1016/j.psj.2025.105130},
pmid = {40215877},
issn = {1525-3171},
abstract = {The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.},
}
@article {pmid40215446,
year = {2025},
author = {Allioni, GA and de Souza, GSM and Labello, JH and Torres, GSA and da Costa, DL and Casal, YR and Duarte-Neto, AN and Dorlass, EG and Amgarten, D and Malta, FM and Doi, AM and Peres Fernandes, GB and Rebello Pinho, JR and Vieira, GT and Castro, LH and Guedes, BF},
title = {Chronic Dengue Virus Encephalitis: A Case Study and Metagenomic Analysis.},
journal = {Neurology(R) neuroimmunology &amp; neuroinflammation},
volume = {12},
number = {3},
pages = {e200394},
doi = {10.1212/NXI.0000000000200394},
pmid = {40215446},
issn = {2332-7812},
mesh = {Humans ; Male ; *Dengue/complications/diagnosis ; Young Adult ; Metagenomics ; *Dengue Virus/genetics ; *Encephalitis, Viral/virology/pathology/diagnosis/complications ; Chronic Disease ; },
abstract = {BACKGROUND AND OBJECTIVES: Dengue virus (DENV) infection can cause acute encephalitis. Chronic encephalitis with progressive dementia is rarely reported.<br><br>METHODS: We present a case of chronic encephalitis with rapidly progressive dementia, in which a potential DENV brain infection was identified with brain tissue metagenomic next-generation sequencing. Brain pathology and molecular diagnosis are also presented.<br><br>RESULTS: A 20-year-old man from SP, Brazil, presented with rapidly progressive dementia, speech apraxia, and apathy in June 2022. By January 2023, cognitive testing showed severe global impairment (MMSE score of 18/30). MRI revealed white matter abnormalities and atrophy; CSF analysis disclosed a mild lymphocytic pleocytosis, mildly elevated protein levels, and positive CSF oligoclonal bands. Despite extensive testing ruling out common infectious and inflammatory causes, the patient's condition worsened with executive dysfunction, language impairment, tremors, and myoclonus. In August 2023, a brain biopsy and next-generation sequencing identified DENV-1 genotype V, linked to Brazilian sequences from 2000 to 2022.<br><br>DISCUSSION: This case highlights a challenging instance of encephalitis with unknown etiology, where metagenomic analysis detected DENV-1 RNA in brain tissue, suggesting a possible cause.},
}
@article {pmid40215391,
year = {2025},
author = {Gómez, &#xc1; and Rodríguez-Largo, A and Pérez, E and García Freire, S and Hundehege, C and Berberich, E and Luján, L and Cortés, D},
title = {Clinicopathological progression and molecular characterization of intestinal dilatation syndrome in commercial brown layers.},
journal = {Veterinary pathology},
volume = {},
number = {},
pages = {3009858251331106},
doi = {10.1177/03009858251331106},
pmid = {40215391},
issn = {1544-2217},
abstract = {Intestinal dilatation syndrome (IDS) is a poorly described condition affecting layers and breeder hens globally. Its prevalence is increasing, particularly in free-range systems, but the cause remains unknown. This retrospective study examined 35 hens from 3 flocks: free-range flock A (n = 20) and enriched-caged flock B (n = 5), both affected by IDS, and enriched-caged flock C (n = 10), with no history of IDS. Clinicopathological studies were performed on these hens, and metagenomic analysis was conducted on the proventriculus and jejunum of hens from flock A (n = 2) and flock C (n = 2). Based on clinical signs and lesions, 3 progressive stages of IDS were identified. In the first stage, although hens were without clinical signs, proventricular dilatation and lymphoplasmacytic and heterophilic jejunitis and duodenitis were observed. The second stage was marked by cachexia, pale and small combs and wattles, and severe egg production drop. Jejunal dilatation was observed, with microscopic evidence of necrotic, lymphoplasmacytic and heterophilic jejunitis; ganglioneuritis; and mineralization of the jejunal nervous plexuses and subserosal ganglia. In the third stage, spontaneous death occurred due to jejunal volvulus and vascular involvement. Affected hens (stage 2) also exhibited elevated cloacal temperatures (>0.9°C) and marked heterophilia. Metagenomic analysis identified sequences consistent with Megrivirus C in IDS-affected hens and a disruption of the gut microbiota, with increased abundance of Fusobacterium mortiferum and Megamonas funiformis. In conclusion, this study describes in detail the clinicopathological progression of the IDS and suggests that Megrivirus C, in combination with opportunistic intestinal bacteria, could play a role in the pathogenesis of this disease.},
}
@article {pmid40214404,
year = {2025},
author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, M&#xd8; and Rudi, K},
title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12464},
pmid = {40214404},
issn = {1520-5851},
abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.},
}
@article {pmid40214102,
year = {2025},
author = {Cernooka, E and Zrelovs, N and Kazaks, A},
title = {C-terminal anchor endolysins-proposing a third class of tailed bacteriophage endolysins.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70042},
pmid = {40214102},
issn = {1873-3468},
support = {lzp-2021/1-0050//Latvijas Zin&#x101;tnes Padome/ ; },
abstract = {Endolysins-enzymes produced by tailed bacteriophages to degrade bacterial cell walls-have traditionally been classified as canonical or signal-anchor-release (SAR) endolysins. However, analysis of expanding viral (meta)genomic data has revealed a third class, which we designate as C-terminal anchor (CTA) endolysins. These enzymes feature an N-terminal enzymatic domain, a C-terminal transmembrane domain, and typically lack signal sequences, distinguishing them from SAR endolysins. CTA endolysins span all known enzymatic activities and exhibit diverse architectures, though most have a single transmembrane helix and an N-out, C-in topology, consistent with periplasmic activity. While their functional mechanisms remain to be elucidated, our findings suggest that CTA endolysins are nearly as prevalent as SAR endolysins and represent a distinct, previously unrecognized branch of the endolysin world.},
}
@article {pmid40213331,
year = {2025},
author = {Wang, X and Zhao, Z and Zhao, F and Li, Y and Liang, Y and Zhou, R and Shen, S and Yu, J and Liu, W and Menghe, B},
title = {Dual-omics strategy for selecting optimal fermentation strains in traditional koumiss production.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102407},
pmid = {40213331},
issn = {2590-1575},
abstract = {Koumiss is a fermented mare's milk beverage with a long history. However, due to the current lack of specialized starters, the product quality is unstable. Therefore, we used dual-omics combined with pure culture technology to screen out strains with excellent fermentation performance for koumiss. The results showed that: (1) The dominant species in koumiss were mainly Lactobacillus and Lactococcus, and metabolites such as arachidonic acid and ascorbic acid were significantly enriched in koumiss. (2) There was a significant correlation between specific microbial species and metabolites. (3) Through preliminary screening using experiments such as milk-based curdling experiments and acid resistance tests, and then rescreening through fermentation tests, five strains with excellent fermentation characteristics were screened out. They are Lacticaseibacillus paracasei SXM-5, Lactobacillus kefianofaciens MGE42-8, Lactobacillus helveticus CFS12-11-1, Saccharomyces cerevisiae PFD-2, and Kluyveromyces marxianus PYM-1. The screened strains supply microbial resources for koumiss products and boost the development of milk beverages.},
}
@article {pmid40212922,
year = {2025},
author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H},
title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71221},
pmid = {40212922},
issn = {2045-7758},
abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.},
}
@article {pmid40212663,
year = {2025},
author = {Natasha, A and Pye, SE and Park, K and Rajoriya, S and Yang, I and Park, J and Pangestu, HS and Kim, J and Oh, Y and López, CB and Song, JW and Kim, WK},
title = {Detection and characterization of Langya virus in Crocidura lasiura (the Ussuri white-toothed shrew), Republic of Korea.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {101017},
pmid = {40212663},
issn = {2352-7714},
abstract = {Langya virus (LayV) is the only documented zoonotic agent within the shrew borne Parahenipavirus genus. Other Parahenipavirus species, including Gamak virus and Daeryeong virus, have been discovered in the Republic of Korea, highlighting the prevalence of this genus in the region. We retrospectively analyzed metagenomic next-generation sequencing of two Crocidura lasiura (the Ussuri white-toothed shrew) kidney samples from 2017, followed by paramyxovirus screening of 24 kidney samples from the same species collected in 2023. The LayV positivity rate was 12.5 % (3 of 24). Amplicon-based sequencing was subsequently developed to obtain the complete viral sequences. Five complete genomes of Langya virus Korea (LayV KOR) were identified: two from 2017 samples and three from 2023 samples. LayV KOR exhibited approximately 80 % and 95.5 % homology at the nucleotide and amino acid levels, respectively. Phylogenetic analysis underscored the close relationship between LayV KOR and LayV from China. This study represents the first detection of LayV complete sequences in shrews outside of China.},
}
@article {pmid40212081,
year = {2024},
author = {Tuerhongjiang, G and Guo, M and Qiao, X and Liu, J and Xi, W and Wei, Y and Liu, P and Lou, B and Wang, C and Sun, L and Yuan, X and Liu, H and Xiong, Y and Ma, Y and Li, H and Zhou, B and Li, L and Yuan, Z and Wu, Y and She, J},
title = {Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.},
journal = {Small science},
volume = {4},
number = {9},
pages = {2300337},
pmid = {40212081},
issn = {2688-4046},
abstract = {AIMS: Heart failure (HF) is associated with profound changes in cardiac metabolism. At present, there is still a lack of relevant research to explore the key microbiome and their metabolites affecting the progression of HF. Herein, the interaction of gut microbiota and circulating free fatty acid (FFA) in HF patients and mice is investigated.<br><br>METHODS AND RESULTS: In HF patients, by applying metagenomics analysis and targeted FFA metabolomics, enriched abundance of Clostridium sporogenes (C.sp) in early and late stage of HF patients, which negatively correlated to saturated free fatty acid (SFA) levels, is identified. KEGG analysis further indicates microbiota gene enrichment in FFA degradation in early HF, and decreased gene expression in FFA synthesis in late HF. In HF mice (C57BL/6J) induced by isoproterenol (ISO), impaired intestinal permeability is observed, and decreased fecal C.sp and increased SFA are further validated. At last, by supplementing C.sp to ISO-induced HF mice, the cardiac function, fibrosis, and myocardial size are partially rescued, together with decreased circulating SFA levels.<br><br>CONCLUSIONS: Clostridium abundance is increased in HF, compensating cardiac function deterioration via downregulation of circulating SFA levels. The results demonstrate that the gut microbiota-SFA axis plays an important role in HF protection, which may provide a strategic advantage for the probiotic therapy development in HF.},
}
@article {pmid40211978,
year = {2025},
author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ},
title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf149},
pmid = {40211978},
issn = {1477-4054},
support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China Project/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //Westlake University Industries of the Future Research Funding/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Models, Genetic ; Metagenome ; Algorithms ; },
abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.},
}
@article {pmid40211688,
year = {2025},
author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX},
title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17751},
doi = {10.1111/mec.17751},
pmid = {40211688},
issn = {1365-294X},
support = {2021YFD1400900//National Key R&amp;D Program of China/ ; },
abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.},
}
@article {pmid40211685,
year = {2025},
author = {Kim, JW and Choi, EC and Lee, KJ},
title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.},
journal = {Osong public health and research perspectives},
volume = {},
number = {},
pages = {},
doi = {10.24171/j.phrp.2024.0319},
pmid = {40211685},
issn = {2210-9099},
abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.<br><br>METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.<br><br>RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.<br><br>CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.},
}
@article {pmid40211121,
year = {2025},
author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, &#xc9; and Pombo, GDV and Santana, MHA},
title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {359},
pmid = {40211121},
issn = {1471-2164},
support = {2021/03265-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/12105-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).<br><br>RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.<br><br>CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40210868,
year = {2025},
author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA},
title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3434},
pmid = {40210868},
issn = {2041-1723},
support = {1R01DK140854//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; },
abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.},
}
@article {pmid40210629,
year = {2025},
author = {Park, JW and Yun, YE and Cho, JA and Yoon, SI and In, SA and Park, EJ and Kim, MS},
title = {Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3427},
pmid = {40210629},
issn = {2041-1723},
support = {2020R1A5A8017671//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009664//National Research Foundation of Korea (NRF)/ ; 2018R1D1A3B07050366//National Research Foundation of Korea (NRF)/ ; 2021R1F1A1064222//National Research Foundation of Korea (NRF)/ ; },
mesh = {Humans ; *Virome/genetics ; *Vegetables/virology ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Plant Leaves/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; },
abstract = {Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 10[7] viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.},
}
@article {pmid40210439,
year = {2025},
author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS},
title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279543.124},
pmid = {40210439},
issn = {1549-5469},
abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.},
}
@article {pmid40210403,
year = {2025},
author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH},
title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.},
journal = {Food microbiology},
volume = {130},
number = {},
pages = {104780},
doi = {10.1016/j.fm.2025.104780},
pmid = {40210403},
issn = {1095-9998},
mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fungi/classification/genetics/isolation &amp; purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; },
abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.},
}
@article {pmid40210162,
year = {2025},
author = {Gao, X and Yuan, S and Li, X and Xing, W},
title = {Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126213},
doi = {10.1016/j.envpol.2025.126213},
pmid = {40210162},
issn = {1873-6424},
abstract = {Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5% w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1,301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.},
}
@article {pmid40210157,
year = {2025},
author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY},
title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126209},
doi = {10.1016/j.envpol.2025.126209},
pmid = {40210157},
issn = {1873-6424},
abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58%) and Acidobacteria (6.04%) were identified as the dominant phyla and Thiobacillus (1.84%) and Lysobacter (0.99%) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r>0.7, p<0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p<0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.},
}
@article {pmid40209695,
year = {2025},
author = {Yamane, T and Masaoka, T and Ishii, C and Masuoka, H and Suda, W and Kurokawa, S and Kishimoto, T and Mikami, Y and Fukuda, S and Kanai, T},
title = {Factors contributing to the efficacy of fecal microbiota transplantation for diarrhea-dominant functional bowel disorders.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-22},
doi = {10.1159/000545183},
pmid = {40209695},
issn = {1421-9867},
abstract = {INTRODUCTION: In cases of effective fecal microbiota transplantation (FMT) for irritable bowel syndrome (IBS), donor feces have been observed to be enriched in Bifidobacterium spp., and FMT for functional bowel disease improved psychiatric symptoms. Although intestinal dysbiosis has received attention as one of the pathophysiologies of IBS, the efficacy of FMT for IBS has not yet been established. In this study, we performed a post-hoc analysis of the efficacy of FMT, focusing on metabolites in donor feces.<br><br>METHODS: FMT was performed in 12 patients, 8 with refractory diarrhea-predominant IBS and 4 with functional diarrhea (FDr), who were refractory to medical therapy. The donors were family members within the second degree of kinship and were different for each transplant. Fecal characteristics were evaluated before and 12 weeks after transplantation using the Bristol stool scale (BS). BS scores of 3-5 at 12 weeks after transplantation were considered indicative of responders, while BS scores of 6 and 7 were indicative of non-responders. Metagenomic and metabolomic analyses of all 12 donor fecal samples were performed to compare the responder and non-responder groups.<br><br>RESULTS: Before transplantation, all 12 patients had BS scores of 6-7, but 12 weeks after transplantation, 6 were in the responder group and 6 were in the non-responder group. Metagenomic analysis showed that effective donor feces contained significantly higher levels of Prevotella than ineffective donor feces. Metabolomic analysis showed that effective donor feces contained significantly higher levels of propionate and butyrate and significantly lower lactate levels than ineffective donor feces.<br><br>CONCLUSION: Propionate-, butyrate-, or Prevotella-rich donor feces may contribute to successful FMT in patients with diarrhea-dominant functional gastrointestinal disorders.},
}
@article {pmid40209677,
year = {2025},
author = {Lin, Y and Lau, HC and Liu, C and Ding, X and Sun, Y and Rong, J and Zhang, X and Wang, L and Yuan, K and Miao, Y and Wu, WK and Wong, SH and Sung, JJ and Yu, J},
title = {Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {4},
pages = {589-601.e3},
doi = {10.1016/j.chom.2025.03.012},
pmid = {40209677},
issn = {1934-6069},
mesh = {Humans ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Gastrointestinal Microbiome ; Cohort Studies ; Metagenome ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Aged ; Fusobacterium nucleatum/isolation &amp; purification ; Biomarkers, Tumor ; ROC Curve ; },
abstract = {Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.},
}
@article {pmid40209409,
year = {2025},
author = {Cheng, Y and Zheng, X and Jiang, Y and Xiao, Q and Luo, Q and Ding, Y},
title = {Key genes and microbial ecological clusters involved in organophosphate ester degradation in agricultural fields of a typical watershed in southwest China.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138076},
doi = {10.1016/j.jhazmat.2025.138076},
pmid = {40209409},
issn = {1873-3336},
abstract = {Organophosphate esters (OPEs) are widely used as flame retardants and plasticizers, and they have raised global concern due to their persistence, bioaccumulation, and potential toxicity. However, OPE contamination characteristics and microbial degradation mechanisms in agricultural soils remain poorly understood. This study investigated agricultural soils from the riparian zone of the Anning River Basin in southwest China. The concentrations of 12 OPEs were determined using gas chromatography-tandem mass spectrometry. The results revealed that the total OPE concentration was moderate, with triethyl phosphate being the most abundant compound. Metagenomic techniques and Bayesian linear regression analysis were employed in combination with the Kyoto Encyclopedia of Genes and Genomes database to identify potential degradation pathways for triethyl phosphate and tris (2-chloroethyl) phosphate. The phoA, phoB, phoD, and glpQ genes, which encode phosphatases, catalyze ester bond cleavage, thereby facilitating the degradation of OPEs. Further microbial interaction network analysis identified core OPE-degrading microorganisms, including Pimelobacter simplex, Nocardioides sp. JS614, Nocardioides daphniae, and Methylocystis heyeri. Additionally, neutral community models indicated that environmental selection drives microbial community structure. In conclusion, this study provides an in-depth understanding of OPE contamination and its microbial degradation mechanisms in agricultural soils, offering theoretical insights for pollution management and remediation strategies.},
}
@article {pmid40209382,
year = {2025},
author = {Su, C and Kang, J and Liu, S and Li, C},
title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144192},
doi = {10.1016/j.foodchem.2025.144192},
pmid = {40209382},
issn = {1873-7072},
abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.},
}
@article {pmid40209373,
year = {2025},
author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J},
title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144178},
doi = {10.1016/j.foodchem.2025.144178},
pmid = {40209373},
issn = {1873-7072},
abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.},
}
@article {pmid40209228,
year = {2025},
author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ},
title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10888},
pmid = {40209228},
issn = {1520-5851},
abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.},
}
@article {pmid40208400,
year = {2025},
author = {Bourgon, N and Padioleau, I and Guibon, J and Fourgeaud, J and Lermine, A and Meurice, G and Guilleminot, T and Bussieres, L and Leruez-Ville, M and Dupont, JM and Ville, Y},
title = {Metagenomic analysis of NIPT raw data suggests high negative predictive value for congenital cytomegalovirus infection screening.},
journal = {Ultrasound in obstetrics &amp; gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/uog.29221},
pmid = {40208400},
issn = {1469-0705},
}
@article {pmid40207985,
year = {2025},
author = {Zhang, Q and Wang, Q and Zhang, F and Li, X and Sun, Y and Wang, L and Zhang, Z},
title = {Diagnostic value of metagenomic next-generation sequencing in patients with osteoarticular infections: a prospective study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0106424},
doi = {10.1128/spectrum.01064-24},
pmid = {40207985},
issn = {2165-0497},
abstract = {Due to the limits of traditional microbiological methods and the complexity of osteoarthritis pathogens, only a few pathogens can be detected. We evaluated metagenomic next-generation sequencing (mNGS) for detecting pathogens in osteoarthritis infection samples. We prospectively included 150 patients with osteoarthritis infection who visited the Orthopedics Department of Shandong Provincial Public Health Center from 2023 to 2024, including 124 cases of primary osteoarthritis (POI) and 26 cases of invasive osteoarthritis (IOI). The most common pathogenic bacteria were Mycobacterium tuberculosis complex, Staphylococcus aureus, and Brucella melitensis. mNGS (75.33%) significantly improved the detection of pathogens in osteoarticular infections compared to conventional tests (CT) methods (36.67%). mNGS could detect a wider spectrum of pathogens compared to CT methods, especially for mixed and rare pathogens. The treatment strategies for patients with osteoarthritis infection could be adjusted based on the results obtained from mNGS testing. Furthermore, the abundance of M. tuberculosis complex, B. melitensis, and Staphylococcus epidermidis was significantly correlated with clinical indicators.IMPORTANCEIdentifying the microorganisms responsible for osteoarthritis infection could help with early diagnosis and treatment. In this study, we compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and CT methods in patients with osteoarthritis infection and found that mNGS had a higher microbial detection rate and a broader spectrum of pathogens (especially for mixed pathogens). This study demonstrates that mNGS is an ideal tool for detecting pathogens in patients with osteoarticular infections.},
}
@article {pmid40207938,
year = {2025},
author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ},
title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.},
journal = {mBio},
volume = {},
number = {},
pages = {e0069925},
doi = {10.1128/mbio.00699-25},
pmid = {40207938},
issn = {2150-7511},
abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.<br><br>IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.},
}
@article {pmid40207877,
year = {2025},
author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W},
title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70336},
doi = {10.1002/jmv.70336},
pmid = {40207877},
issn = {1096-9071},
support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; },
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation &amp; purification ; Adult ; Aged ; Longitudinal Studies ; },
abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.},
}
@article {pmid40207279,
year = {2025},
author = {Teng, NM and Malfettone, A and Dalby, MJ and Kiu, R and Seki, D and Robinson, T and Gion, M and Bermejo, B and Pérez-García, JM and Prat, A and Vázquez, RM and Llombart-Cussac, A and Curigliano, G and Schmid, P and Barroso-Sousa, R and Mancino, M and Shimizu, E and Rodríguez-Morató, J and Mina, L and Hall, LJ and Robinson, SD and Cortés, J},
title = {Profiling the gut and oral microbiota of hormone receptor-positive, HER2-negative metastatic breast cancer patients receiving pembrolizumab and eribulin.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {4},
pmid = {40207279},
issn = {2771-5965},
abstract = {Aim: Changes in host-associated microbial communities (i.e., the microbiota) may modulate responses to checkpoint blockade immunotherapy. In the KELLY phase II study (NCT03222856), we previously demonstrated that pembrolizumab [anti-programmed cell death protein 1 (PD-1)] combined with eribulin (plus microtubule-targeting chemotherapy) showed encouraging antitumor activity in patients with hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (mBC) who had received prior treatments. Methods: A total of 58 fecal and 67 saliva samples were prospectively collected from a subset of 28 patients at baseline (BL), after three treatment cycles, and end of treatment. Shotgun metagenomics, 16S rRNA gene amplicon sequencing, and bioinformatics and statistical approaches were used to characterize fecal and oral microbiota profiles. Results: Treatment caused no substantial perturbations in gut or oral microbiota, suggesting minimal drug-related microbial toxicity. Bacteroides and Faecalibacterium were the dominant gut microbiota genera, while Prevotella and Streptococcus were present in both oral and gut samples, highlighting potential gut-oral microbial interactions. Additionally, clinical benefit (CB) appeared to be associated with gut-associated Bacteroides fragilis (B. fragilis) and a BL oral abundance of Streptococcus ≥ 30%. Notably, B. fragilis NCTC 9343 supernatant induced dose-dependent lactate dehydrogenase (LDH) release from the MCF-7 (HR-positive/HER2-negative) BC cell line. Conclusion: These findings suggest that specific gut and oral microbiota may modulate the effectiveness of combinatory anti-BC therapies, potentially through the action of microbial metabolites.},
}
@article {pmid40207161,
year = {2025},
author = {Helmi, NR},
title = {Exploring the diversity and antimicrobial potential of actinomycetes isolated from different environments in Saudi Arabia: a systematic review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568899},
pmid = {40207161},
issn = {1664-302X},
abstract = {The increasing prevalence of antimicrobial resistance (AMR) presents a significant global health challenge, underscoring the urgent need for novel antimicrobial agents. Actinomycetes, particularly Streptomyces species, are well known for synthesizing bioactive compounds with antibacterial, antifungal, and antiviral properties. This review explores the diversity and antimicrobial potential of actinomycetes from Saudi Arabia's unique ecosystems, including terrestrial (soil, rhizosphere), aquatic (marine, freshwater), extreme (deserts, caves, hot springs, mountains, and mangroves), and other unique environments. The adaptation of these microorganisms to harsh environmental conditions has driven the evolution of unique strains with enhanced biosynthetic capacities. Several studies have demonstrated their antimicrobial efficacy against multidrug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Pseudomonas aeruginosa, and Candida albicans. However, challenges in actinomycete research persist, including difficulties in culturing rare strains, limited genomic characterization, and high production costs. Recent advancements, such as genome mining, metagenomics, AI-driven bioinformatics, and CRISPR-based gene activation, offer promising avenues for unlocking novel antimicrobial compounds. Additionally, synthetic biology, advanced fermentation technologies, and nanotechnology-based drug delivery systems are enhancing the industrial scalability of actinomycete-derived antibiotics. Beyond antimicrobials, actinomycete-derived compounds show potential applications in oncology, immunotherapy, and agriculture. Alternative therapeutic strategies, including quorum sensing inhibitors, phage therapy, and combination therapies, are being explored to combat AMR. Cutting-edge analytical techniques, such as mass spectrometry, liquid chromatography, and nuclear magnetic resonance spectroscopy (NMR), are essential for structural elucidation and mechanism characterization of new bioactive compounds. To harness Saudi Arabia's microbial biodiversity effectively, interdisciplinary collaborations between microbiologists, biotechnologists, and pharmaceutical industries are crucial. Sustainable bioprospecting and advanced bioprocessing strategies will facilitate the translation of actinomycete-derived bioactive compounds into clinically viable therapeutics. Expanding research efforts into underexplored Saudi ecosystems can lead to groundbreaking discoveries in antibiotic development and beyond.},
}
@article {pmid40207154,
year = {2025},
author = {Ahn, JS and Han, EJ and Chung, HJ},
title = {Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533580},
pmid = {40207154},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous research on the gut microbiome has primarily focused on fecal microbiota, raising concerns about whether fecal samples accurately represent the entire intestinal microbiota. Studies have shown that microbial communities across the gastrointestinal (GI) tract are more diverse than those in feces, suggesting that microbial composition may vary depending on the sampling method. Additionally, analyzing the broader diversity of microbial communities in the GI tract may enhance the identification of potentially beneficial microbiota.<br><br>METHODS: In this study, we compare gut microbiome datasets obtained from fecal samples and GI samples (collected by pooling luminal contents and mucosal scrapings from the stomach to the end of the colon) of 6-month-old mice using 16S rRNA sequencing. We further investigate the associations between gut microbiota and motor, cognitive, and emotional functions in mice, examining differences between the two sample types. To assess these variations, we apply DESeq2 analysis to identify microbial species enriched in high-functioning groups and evaluate how their selection may differ depending on the sampling approach.<br><br>RESULTS: Our findings reveal notable differences in microbial composition between fecal and GI samples, suggesting that sampling methods may influence the identification of beneficial bacteria.<br><br>DISCUSSION: These results highlight the importance of selecting an appropriate sampling approach in microbiome research to ensure a comprehensive understanding of gut microbiota-host interactions.},
}
@article {pmid40207150,
year = {2025},
author = {Zhao, C and Yang, Y and Zhao, P and Bai, L},
title = {Comparative analysis of the fecal microbiota in Père David's deer and five other captive deer species.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1547348},
pmid = {40207150},
issn = {1664-302X},
abstract = {INTRODUCTION: Gut microbes are essential for host nutrition, immunity, and development. Various factors influence the composition and function of the gut microbial community. However, there is limited knowledge regarding the comparison of gut microbiota across different deer species, particularly those in the World Deer Park of Baotou (Inner Mongolia, China).<br><br>METHODS: This study utilized 16S rRNA gene amplicon sequencing to analyze the fecal microbiota and potential microbial function in P&#xe8;re David's Deer (Elaphurus davidianus), Sika deer (Cervus nippon), American Wapiti (Cervus canadensis), Red Deer (Cervuselaphus), Fallow Deer (Dama dama), and Reindeer (Rangifer tarandus).<br><br>RESULTS AND DISCUSSION: The findings indicated no significant differences in alpha diversity, yet there was a noteworthy distinction in beta diversity among the six deer groups. At the phylum level, the predominant bacteria in the deer populations were Firmicutes, Bacteroidetes, and Proteobacteria. At the genus level, 54 core bacterial microbiota were identified. The top four genera in AW, FD, PD, and SD were Ruminococcaceae UCG-005, Rikenellaceae RC9 gut group, RuminococcaceaeUCG-010 and Christensenellaceae R-7 group. The results of the neutral model revealed that neutral processes predominantly governed the gut microbiota community assembly in different deer species, particularly in P&#xe8;re David's deer. PICRUSt2 predictions showed significant enrichment of fecal bacterial functions related to fatty acid, lipid, metabolic regulator, and amino acid biosynthesis. This comparative analysis sheds light on the microbial community structure, community assembly, and potential functions, offering improved insights into the management and conservation of deer species, especially P&#xe8;re David's deer. Future research might focus on exploring metagenomic functions and dynamics in wild settings or across different seasons using metagenomics or metatranscriptomics.},
}
@article {pmid40206877,
year = {2025},
author = {Shi, M and Qin, T and Pu, Z and Yang, Z and Lim, KJ and Yang, M and Wang, Z},
title = {Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1473473},
pmid = {40206877},
issn = {1664-462X},
abstract = {INTRODUCTION: Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant.<br><br>METHODS: Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress.<br><br>RESULTS AND DISCUSSION: We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.},
}
@article {pmid40206699,
year = {2025},
author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS},
title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.},
journal = {Polar biology},
volume = {48},
number = {2},
pages = {62},
pmid = {40206699},
issn = {0722-4060},
abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.},
}
@article {pmid40206488,
year = {2025},
author = {He, J and Chen, Y and Jiang, Z and Li, F and Zhu, M and Xu, Z and Wang, M and Tang, M and Wu, Y and Li, Y},
title = {Diagnostic value of metagenomic next-generation sequencing in detecting Pneumocystis jirovecii pneumonia in HIV-infected patients.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1567484},
pmid = {40206488},
issn = {2296-858X},
abstract = {INTRODUCTION: Accurate diagnosis of Pneumocystis jirovecii pneumonia (PJP) in HIV patients remains challenging. This study compares metagenomic next-generation sequencing (mNGS) with PCR, GMS staining, and serum β-D-glucan (BG) assays for PJP detection and co-infection identification.<br><br>METHODS: BALF samples from 34 HIV-positive PJP patients and 50 non-PJP controls were analyzed. Diagnostic performance metrics (sensitivity, specificity, NPV, AUC) and co-pathogen profiles were evaluated for mNGS versus conventional methods.<br><br>RESULTS: mNGS and PCR both achieved 100% sensitivity. mNGS showed higher specificity (91.3% vs. 88%) and AUC (0.898 vs. 0.940 for PCR). Co-infections were detected in 67.6% of PJP cases by mNGS, including cytomegalovirus (41.2%), Epstein-Barr virus (29.4%), and non-tuberculous mycobacteria (14.7%). GMS and BG assays exhibited lower sensitivity (64.7% and 76.5%, respectively).<br><br>DISCUSSION: mNGS offers superior specificity, accuracy, and co-infection detection compared to traditional methods. Its high NPV (100%) supports clinical utility in ruling out PJP. While resource-intensive, mNGS is a promising first-line diagnostic tool for HIV-associated PJP, particularly in polymicrobial infection settings.},
}
@article {pmid40206430,
year = {2025},
author = {Zhou, Z and Sun, L and Zhou, W and Gao, W and Yuan, X and Zhou, H and Ren, Y and Li, B and Wu, Y and She, J},
title = {Probiotic Bifidobacterium reduces serum TMAO in unstable angina patients via the gut to liver to heart axis.},
journal = {Liver research (Beijing, China)},
volume = {9},
number = {1},
pages = {57-65},
pmid = {40206430},
issn = {2542-5684},
abstract = {BACKGROUND AND AIMS: Studies indicate that the gut microbiota and its metabolites are involved in the progression of cardiovascular diseases, and enterohepatic circulation plays an important role in this progression. This study aims to identify potential probiotics for the treatment of unstable angina (UA) and elucidate their mechanisms of action.<br><br>METHODS: Initially, the gut microbiota from patients with UA and control was analyzed. To directly assess the effects of Bifidobacterium supplementation, 10 patients with UA were enrolled and administered Bifidobacterium (630&#xa0;mg per intake twice a day for 1 month). The fecal metagenome, serum trimethylamine N-oxide (TMAO) levels, and other laboratory parameters were evaluated before and after Bifidobacterium supplementation.<br><br>RESULTS: After supplementing with Bifidobacterium for 1&#xa0;month, there were statistically significant differences (P&#xa0;<&#xa0;0.05) in TMAO, aspartate aminotransferase, total cholesterol, and low-density lipoprotein compared to before. Additionally, the abundance of Bifidobacterium longum increased significantly, although the overall abundance of Bifidobacterium did not reach statistical significance. The gut microbiota, metabolites, and gut-liver axis are involved in the progression of UA, and potential mechanisms should be further studied.<br><br>CONCLUSIONS: Metagenomic analysis demonstrated a reduced abundance of Bifidobacterium in patients with UA. Supplementation with Bifidobacterium restored gut dysbiosis and decreased circulating TMAO levels in patients with UA. This study provides evidence that Bifidobacterium may exert cardiovascular-protective effects through the gut-liver-heart axis.<br><br>CLINICAL TRIAL NUMBER: ChiCTR2400093946.},
}
@article {pmid40205852,
year = {2025},
author = {Nowicki, M and Mroczek, M and Mukhedkar, D and Bała, P and Nikolai Pimenoff, V and Arroyo Mühr, LS},
title = {HPV-KITE: sequence analysis software for rapid HPV genotype detection.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf155},
pmid = {40205852},
issn = {1477-4054},
mesh = {Humans ; Genotype ; Algorithms ; *Software ; *Papillomaviridae/genetics/classification ; *Papillomavirus Infections/virology/diagnosis ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Human papillomaviruses (HPVs) are among the most diverse viral families that infect humans. Fortunately, only a small number of closely related HPV types affect human health, most notably by causing nearly all cervical cancers, as well as some oral and other anogenital cancers, particularly when infections with high-risk HPV types become persistent. Numerous viral polymerase chain reaction-based diagnostic methods as well as sequencing protocols have been developed for accurate, rapid, and efficient HPV genotyping. However, due to the large number of closely related HPV genotypes and the abundance of nonviral DNA in human derived biological samples, it can be challenging to correctly detect HPV genotypes using high throughput deep sequencing. Here, we introduce a novel HPV detection algorithm, HPV-KITE (HPV K-mer Index Tversky Estimator), which leverages k-mer data analysis and utilizes Tversky indexing for DNA and RNA sequence data. This method offers a rapid and sensitive alternative for detecting HPV from both metagenomic and transcriptomic datasets. We assessed HPV-KITE using three previously analyzed HPV infection-related datasets, comprising a total of 1430 sequenced human samples. For benchmarking, we compared our method's performance with standard HPV sequencing analysis algorithms, including general sequence-based mapping, and k-mer-based classification methods. Parallelization demonstrated fast processing times achieved through shingling, and scalability analysis revealed optimal performance when employing multiple nodes. Our results showed that HPV-KITE is one of the fastest, most accurate, and easiest ways to detect HPV genotypes from virtually any next-generation sequencing data. Moreover, the method is also highly scalable and available to be optimized for any microorganism other than HPV.},
}
@article {pmid40205718,
year = {2025},
author = {Zhang, H and Yang, M and Ying, W and Hou, J and Zhou, Q and Sun, B and Wang, Y and Hui, X and Liu, L and Yao, H and Sun, J and Wang, W and Wang, X},
title = {Invasive fungal disease in a large cohort of hospitalized children with inborn errors of immunity in China.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {4},
pages = {e70074},
doi = {10.1111/pai.70074},
pmid = {40205718},
issn = {1399-3038},
support = {ZD2021CY001//the Shanghai Municipal Science and Technology Major Project/ ; },
mesh = {Humans ; China/epidemiology ; Male ; Female ; Retrospective Studies ; *Invasive Fungal Infections/epidemiology/drug therapy ; Child, Preschool ; Child ; Infant ; Prevalence ; *Immunologic Deficiency Syndromes/epidemiology/complications ; Adolescent ; Hospitalization ; Infant, Newborn ; },
abstract = {BACKGROUND: Invasive fungal disease (IFD) is a common complication observed in inborn errors of immunodeficiency (IEI) patients, and little is known about the overall prevalence of IFD in IEI patients. We aimed to summarize the fungal spectrum and outcomes of IFDs in a Chinese cohort of hospitalized patients with IEI.<br><br>METHODS: In this retrospective study, 607 IEI patients hospitalized from January 2018 to June 2022 were included. Demographic, clinical, and fungal infection data and IEI patient characteristics were collected and analyzed according to the IEI classification.<br><br>RESULTS: One hundred and two IEI patients were diagnosed with proven or probable IFD. The overall prevalence of IFD was 17% (102/607). There were 29 different genotypes, among which CYBB (25%), CD40LG (9%), and RAG1 (7%) mutations were the most common. Most IFD infections (87/102) were caused by one fungus. Invasive Aspergillus, Pneumocystis jirovecii pneumonia, and Penicillium infections were more commonly observed in patients with congenital defects in phagocytes, immunodeficiencies affecting cellular and humoral immunity, and defects in innate immunity, respectively. Most IFDs observed in IEI patients were single-site infections, most of which were lung infections (74%). Seventeen patients were diagnosed with disseminated IFDs, nine of which were caused by Penicillium. All patients received antifungal treatments. Eight patients (8%) died within 3&#x2009;months of IFD diagnosis.<br><br>CONCLUSIONS: IFD occurrence suggests the presence of immunity impairment. The IFD fungal profile may indicate different types of IEI. Early recognition of immunodeficiency and optimal timing of antifungal therapy can reduce fatality in IEI patients.},
}
@article {pmid40205678,
year = {2025},
author = {He, Y and Zhao, G and Ouyang, X and Wang, S and Chen, Y and Li, C and He, Y and Gao, J and Han, S and Zhao, J and Wang, J and Wang, C},
title = {Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489072},
doi = {10.1080/19490976.2025.2489072},
pmid = {40205678},
issn = {1949-0984},
mesh = {Animals ; Mice ; Gastrointestinal Microbiome/drug effects/radiation effects ; *Creatine/metabolism/pharmacology/administration &amp; dosage ; *Ferroptosis/drug effects/radiation effects ; Mice, Inbred C57BL ; Male ; *Intestines/radiation effects/microbiology ; *Radiation-Protective Agents/metabolism/administration &amp; dosage ; Radiation, Ionizing ; Feces/microbiology ; Enterocytes/radiation effects/metabolism ; },
abstract = {Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.},
}
@article {pmid40205588,
year = {2025},
author = {Li, M and Wang, Z and Ma, Z and Wang, Y and Jia, H and Zhang, L and Chen, P and Mao, Y and Yang, Z},
title = {Metagenomic analysis reveals microbial drivers of heat resistance in dairy cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {35},
pmid = {40205588},
issn = {2524-4671},
support = {2022YFF1001200//National Key Research and Development Program of China/ ; },
abstract = {Heat stress poses a significant challenge to dairy cattle, leading to adverse physiological effects, reduced milk yield, impaired reproduction performance and economic losses. This study investigates the role of the rumen microbiome in mediating heat resistance in dairy cows. Using the entropy-weighted TOPSIS method, we classified 120 dairy cows into heat-resistant (HR) and heat-sensitive (HS) groups based on physiological and biochemical markers, including rectal temperature (RT), respiratory rate (RR), salivation index (SI) and serum levels of potassium ion (K[+]), heat shock protein 70 (HSP70) and cortisol. Metagenomic sequencing of rumen fluid samples revealed distinct microbial compositions and functional profiles between the two groups. HR cows exhibited a more cohesive and functionally stable microbiome, dominated by taxa such as Ruminococcus flavefaciens and Succiniclasticum, which are key players in fiber degradation and short-chain fatty acid production. Functional analysis highlighted the enrichment of the pentose phosphate pathway (PPP) in HR cows, suggesting a metabolic adaptation that enhances oxidative stress management. In contrast, HS cows showed increased activity in the tricarboxylic acid (TCA) cycle, pyruvate metabolism and other energy-intensive pathways, indicating a higher metabolic burden under heat stress. These findings underscore the critical role of the rumen microbiome in modulating heat resistance and suggest potential microbiome-based strategies for improving dairy cattle resilience to climate change.},
}
@article {pmid40205543,
year = {2025},
author = {Zou, Z and Zhao, W and Chen, Y and Liu, Z and He, G and Zhang, H},
title = {Extracorporeal membrane oxygenation in the treatment of critical Pneumocystis jirovecii pneumonia in a child with Langerhans cell histiocytosis: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {492},
pmid = {40205543},
issn = {1471-2334},
mesh = {Humans ; *Extracorporeal Membrane Oxygenation/methods ; Female ; *Pneumonia, Pneumocystis/therapy/complications/microbiology ; Child, Preschool ; *Pneumocystis carinii/genetics/isolation &amp; purification ; *Histiocytosis, Langerhans-Cell/complications/drug therapy ; Treatment Outcome ; },
abstract = {BACKGROUND: Children with Langerhans cell histiocytosis (LCH) are particularly susceptible to infections such as Pneumocystis jirovecii pneumonia (PJP) due to the immunosuppressive effects of chemotherapy, which can progress to acute respiratory distress syndrome (ARDS) and respiratory failure. The use of Extracorporeal Membrane Oxygenation (ECMO) to manage hypoxemia secondary to PJP in LCH presents unique challenges, including the prevention of catheter-related bloodstream infections associated with arterial and venous access. This study explores a case wherein ECMO was crucial in treating severe PJP-induced respiratory failure in a pediatric patient with LCH.<br><br>CASE PRESENTATION: A 3-year-old female with a history of LCH, undergoing long-term chemotherapy and corticosteroid treatment, was admitted with fever, dyspnea, and lethargy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid confirmed Pneumocystis jirovecii (PJ). Despite aggressive management with invasive high-frequency ventilation, inhaled nitric oxide, and prone positioning, the patient's oxygenation remained critically low, with severe hypercapnia and resultant severe respiratory acidosis, necessitating vasopressor support for hemodynamic stability and venoarterial (VA) ECMO intervention. Early initiation of VA ECMO facilitated ultraprotective lung ventilation and circulatory support, effectively preventing hemodynamic collapse. The patient was successfully decannulated after 13 days of ECMO support.<br><br>CONCLUSION: While PJP is a rare and extremely serious opportunistic infection, the VA ECMO support in this pediatric case effectively managed severe PJP without ECMO-related complications. This highlights ECMO as a potentially viable, relatively effective, and safe adjunctive therapy in the management of severe PJP infections in children.},
}
@article {pmid40205497,
year = {2025},
author = {Grønbæk, IMB and Halkjær, SI and Mollerup, S and Hansen, EH and Paulsen, SJ and Engel, S and Theede, K and Wilkens, R and Boysen, T and Petersen, AM},
title = {The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: results from a randomised, double-blind, placebo-controlled trial.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {19},
pmid = {40205497},
issn = {1757-4749},
support = {A6876//The Capital Region's Research Foundation for Health Research/ ; },
abstract = {BACKGROUND: The aetiology of Crohn's disease, a chronic inflammatory bowel disease, is multifactorial and not completely understood. However, the association with gut dysbiosis is well-established, and manipulation of the gut microbiota has gained interest as a treatment strategy. This study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (Bif195) on intestinal inflammation, symptoms, and the gut microbiome composition in patients with small intestinal Crohn's disease.<br><br>METHODS: This was a randomised, double-blind, placebo-controlled trial. Thirty-three patients with small intestinal Crohn's disease were assigned to eight weeks of treatment with Bif195 or placebo (1:1). The primary outcome was changes in bowel wall thickness measured by intestinal ultrasonography. Other outcomes were changes in symptom severity, quality of life, faecal calprotectin, fatigue, and specific inflammatory parameters on ultrasonography. Changes in the microbiome composition were also examined.<br><br>RESULTS: Bif195 did not affect the bowel wall thickness in the small intestine compared to placebo. Nor did we observe effects on secondary or clinical explorative outcomes. Analysis of the gut microbiome showed that the relative abundance of B. breve rose during the intervention in the Bif195 group, but the result was statistically non-significant. Surprisingly, we observed a clustering of baseline microbiome data into two groups that differed in several aspects including a statistically significant difference in the incidence of previous bowel resections among the participants. Furthermore, changes in symptom scores after eight weeks of intervention were significantly different across the two microbiome groups, with an interaction effect of p&#x2009;=&#x2009;0.04.<br><br>CONCLUSIONS: Eight weeks of treatment with Bif195 did not affect clinical outcomes for Crohn's disease. However, variations in baseline microbiome data influenced the results. This underscores the importance of assessing baseline microbiome data in intervention studies in Crohn's disease.<br><br>CLINICALTRIALS: gov NCT04842149.},
}
@article {pmid40205473,
year = {2025},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V},
title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf033},
pmid = {40205473},
issn = {1574-6941},
abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.},
}
@article {pmid40205381,
year = {2025},
author = {Chen, G and Yin, L and Zhang, H},
title = {Isolation and characterization of goose astrovirus genotype 1 causing enteritis in goslings from Sichuan Province, China.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {259},
pmid = {40205381},
issn = {1746-6148},
support = {ZYN2024087//Central University Basic Scientific Research Business Expenses Special Funds/ ; },
abstract = {Since 2017, goose astrovirus (GoAstV) has been widely prevalent in various provinces of China, causing economic losses in the goose industry, with outbreak mortality rates ranging from 10 to 60%. Notably, a goose farm in Sichuan Province has faced an outbreak of infectious disease in 1-3 weeks old goslings, with a mortality rate of approximately 30%. Viral metagenomic analysis of fecal samples identified Goose astrovirus genotype 1 (GoAstV-1), and PCR analysis confirmed the presence of GoAstV-1. Furthermore, we successfully isolated a GoAstV-C1 strain using goose embryos named AAstV/Goose/CHN/2023/C1 (GenBank No. PP108251), and its viral titer was calculated as 10^4.834 ELD50/0.5 mL using the Reed-Muench method. The genome size of GoAstV-C1 was about 7,261 nucleotides through amplifying with Sanger sequencing and assembling with SeqMan software. Phylogenetic analysis revealed that GoAstV-1 strains are classified into three major subtypes: A, B, and C, with the GoAstV-C1 strain identified as a unique variant within subtype B, characterized by distinct genetic divergence features. Experimental inoculation of one-day-old goslings with the virus resulted in a mortality rate of 5 out of 15 (p-value = 0.0421) and a significant reduction in weight gain compared to controls (p-value = 0.005). Pathological examination revealed that GoAstV-C1 infection caused severe damage to the liver, spleen, and kidneys. Interestingly, unlike most GoAstV, which leads to characteristic gout symptoms, our isolates GoAstV-C1 caused obvious intestinal damage characterized by necrosis, inflammatory infiltration, and crypt architectural disruption. We indicated that GoAstV-C1 displays a unique intestinal tropism rather than characteristic gout symptoms and elucidated genomic features and evolutionary relationships of GoAstV strains. These findings help advance our knowledge of the epidemiology and pathogenicity of GoAstV-1, and the predicted structure of capsid protein could serve as a potential target for designing novel antiviral drugs or vaccines against GoAstV-1.},
}
@article {pmid40204977,
year = {2025},
author = {Deng, Z and Poulsen, JS and Nielsen, JL and Weissbrodt, DG and Spanjers, H and van Lier, JB},
title = {Identification of protein-degraders in an anaerobic digester by protein stable isotope probing and metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {87},
pmid = {40204977},
issn = {1432-0614},
support = {201708450043//China Scholarship Council/ ; },
mesh = {Anaerobiosis ; *Metagenomics ; *Acinetobacter/metabolism/genetics ; Carbon Isotopes/metabolism ; Bacterial Proteins/metabolism/genetics ; Isotope Labeling ; Metabolic Networks and Pathways ; Proteomics ; *Bioreactors/microbiology ; Proteolysis ; Glucose/metabolism ; *Proteins/metabolism ; },
abstract = {Presence of carbohydrates hampers protein degradation in anaerobic digesters. To understand this phenomenon, we used proteogenomics to identify the active protein-degraders in the presence of low and high carbohydrates concentrations. Active metabolic pathways of the identified protein-degraders were investigated using proteomics with [13]C-protein substrates (protein stable isotope probing). Results showed that 1) Acinetobacter was the active protein-degraders under both protein-fed and protein-glucose mixture-fed conditions, 2) the relative abundance of Acinetobacter was not affected by the presence of carbohydrates, 3) the incorporation of the [13]C-labelled protein substrate was predominantly observed in outer membrane-bound proteins and porin proteins, which are associated with proteinases or the transportation of amino acids across the cell wall. The Acinetobacter metabolic model and the incubation conditions suggested that glucose and proteins were degraded through anaerobic respiration. The negative impact of carbohydrates on protein biodegradation was attributed to Acinetobacter's preference for carbohydrates. This work highlights that efficient degradation of protein and carbohydrate mixtures in anaerobic digesters requires a staged or time-phased approach and enrichment of active protein-degraders, offering a new direction for process optimization in anaerobic digestion systems. KEY POINTS: • Acinetobacter identified for the first time as main anaerobic protein-degrader • Metabolic model revealed protein degradation via anaerobic respiration • Metabolic pathway analysis indicated SO4[2-] or Fe[3+] as terminal electron acceptors.},
}
@article {pmid40204761,
year = {2025},
author = {Li, F and Hooi, SL and Choo, YM and Teh, CSJ and Toh, KY and Lim, LWZ and Lee, YQ and Chong, CW and Ahmad Kamar, A},
title = {Progression of gut microbiome in preterm infants during the first three months.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12104},
pmid = {40204761},
issn = {2045-2322},
support = {IF047-2021//International Funding/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; Prospective Studies ; *Bacteria/genetics/classification ; Infant ; Gestational Age ; Bifidobacterium/genetics/isolation &amp; purification ; Meconium/microbiology ; Metagenomics ; },
abstract = {The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.},
}
@article {pmid40204742,
year = {2025},
author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB},
title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12156},
pmid = {40204742},
issn = {2045-2322},
mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.},
}
@article {pmid40204671,
year = {2025},
author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH},
title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00246},
pmid = {40204671},
issn = {1520-5851},
abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.},
}
@article {pmid40204030,
year = {2025},
author = {Bao, Y and Feng, S and Yu, F and Ye, W and Xing, H and Zhu, X and Bao, W and Huang, M},
title = {Self-Regulating pH Pyrite-Construction waste Biofilter: Denitrification Performance, metabolic Pathways, and clogging Alleviation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132500},
doi = {10.1016/j.biortech.2025.132500},
pmid = {40204030},
issn = {1873-2976},
abstract = {Waste-based denitrification filters face challenges like alkalinity accumulation, low efficiency, and clogging. This study proposes a novel denitrification filter using construction waste and pyrite (WPDF) to address these issues. WPDF's performance, safety, and mechanisms were evaluated by measuring effluent, filler characteristics and metagenomics. Results demonstrated a high total nitrogen removal load (88.65 g N m[-3]d[-1]) with minimal biofilm (13 %) and filler accumulation (39 %), effectively mitigating clogging. Phosphorus removal relied on chemical precipitation in construction waste. WPDF was pH self-regulating and promoted the formation and release of fulvic acid. Pyrite promotes bio-metabolism, making WPDF enriched in energy metabolism (6 %) and transporter capacity (6 %). Functional prediction indicated that WPDF was more abundant in genes related to denitrification, glycolysis, and electron transport, which promoted the heterotrophic denitrification process. This study provides a novel, efficient, and eco-friendly possible solution for wastewater and offers new insights into the molecular mechanisms of carbon and nitrogen metabolism.},
}
@article {pmid40203979,
year = {2025},
author = {Genitsaris, S and Stefanidou, N and Kourkoutmani, P and Michaloudi, E and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M},
title = {Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121563},
doi = {10.1016/j.envres.2025.121563},
pmid = {40203979},
issn = {1096-0953},
abstract = {Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.},
}
@article {pmid40203710,
year = {2025},
author = {Qv, M and Wu, Q and Wang, W and Wang, H and Zhu, L},
title = {Metagenomic insights into the response of microbial metabolic function and extracellular polymeric substances from microalgae-bacteria consortia to fluoroquinolone antibiotics.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125283},
doi = {10.1016/j.jenvman.2025.125283},
pmid = {40203710},
issn = {1095-8630},
abstract = {Microalgae-bacteria consortia (MBC) are considered a promising bioremediation technology for removing pollutants from swine wastewater. However, the overuse of antibiotics poses challenges to the effective functioning of MBC. In this study, the removal efficiency of nutrients in wastewater by MBC under different antibiotic concentrations (0, 1, 5, 10 and 50 mg/L) was evaluated. The changes of functional microbial abundance were elucidated and the response mechanism of MBC against antibiotics was investigated. Antibiotics inhibited the accumulation of MBC biomass and reduced the removal efficiency of ammonia nitrogen and total phosphorus in wastewater by 8.39 % and 8.74 % respectively. In addition, antibiotics affected the relative abundance of microorganisms (Raineyella, from 30.72 % to 15.96 %) and functional genes (glnA, gudB, NirK, NirBD, NarB, NapAB, NorBC and NosZEPS) involved in N metabolism. MBC could defend against the adverse effects of antibiotics by regulating the content of proteins in the extracellular polymeric substances.},
}
@article {pmid40203094,
year = {2025},
author = {Isobe, N and Tanaka, K and Ishii, S and Shimane, Y and Okada, S and Daicho, K and Sakuma, W and Uetani, K and Yoshimura, T and Kimoto, K and Kimura, S and Saito, T and Nakajima, R and Tsuchiya, M and Ikuta, T and Kawagucci, S and Iwata, T and Nomaki, H},
title = {Fully circular shapable transparent paperboard with closed-loop recyclability and marine biodegradability across shallow to deep sea.},
journal = {Science advances},
volume = {11},
number = {15},
pages = {eads2426},
doi = {10.1126/sciadv.ads2426},
pmid = {40203094},
issn = {2375-2548},
abstract = {To mitigate marine pollution from single-use plastics, it is crucial to transition to next-generation commodity materials that are derived from biomass and are recyclable and marine biodegradable even at abyssal depths in case of the accidental release to the ocean. Here, we develop an optically transparent millimeter-thick paperboard called transparent paperboard (tPB) through dissolution and coagulation of cellulose. The tPB is made entirely of pristine cellulose and compositionally identical to paper. A cup-shaped tPB can hold just-boiled water without an internal film coating because of its high wet tensile properties and anisotropic thermal properties. In addition, the spent tPB is material recyclable in a closed system, where all chemicals and water are also recyclable. Furthermore, the marine biodegradability of tPB across shallow to abyssal depths is confirmed by on-site degradation tests and metagenomic analyses. Hence, tPB is expected to serve as a key fully circular commodity material in sustainable societies of the future.},
}
@article {pmid40202861,
year = {2025},
author = {Singh, AK and Sathaye, SB and Rai, AK and Singh, SP},
title = {Novel Cellobiose 2-Epimerase from Thermal Aquatic Metagenome for the Production of Epilactose.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c09753},
pmid = {40202861},
issn = {1520-5118},
abstract = {Epilactose is a prebiotic molecule that exerts a bifidogenic effect and increases calcium and iron absorption in the small intestine. This study identifies a novel cellobiose 2-epimerase gene (ceM) by investigating metagenomic data generated from a thermal aquatic habitat. The computation of secondary and tertiary structure analysis, molecular docking, and MD simulation analysis indicated the protein CEM to be a novel cellobiose 2-epimerase. The gene was expressed in Escherichia coli, followed by biochemical characterization of the purified protein. CEM is capable of transforming lactose into the high-value rare sugar, epilactose, in a wide range of temperatures (4-70 °C) and pH (6.0-10.0). The enzyme was exposed to 50 °C, and hardly a 10% loss in activity was recorded after 32 h of heat treatment, suggesting that CEM is a thermostable protein. CEM is a kinetically highly efficient enzyme, with a turnover number of 9832 ± 490 s[-1] for lactose to epilactose epimerization. The maximum conversion yield of 26% epilactose was obtained in 15 min of catalytic reaction. Further, the enzyme was successfully tested to transform lactose in milk and whey samples.},
}
@article {pmid40202719,
year = {2025},
author = {Huang, Z and Liu, C and Zhao, X and Guo, Y},
title = {The effect of elevated levels of the gut metabolite TMAO on glucose metabolism after sleeve gastrectomy.},
journal = {Archives of physiology and biochemistry},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/13813455.2025.2489721},
pmid = {40202719},
issn = {1744-4160},
abstract = {Purpose：Bariatric surgery can effectively alleviate obesity and diabetes by regulation of the gut microbiota. This study aimed to investigate the change in the gut microbiota metabolite TMAO and to explore its effect on glucose metabolism after sleeve gastrectomy (SG). Materials and methods：Diet-induced obesity mouse models were established, and the mice were randomly divided into four groups: an SG group, a sham-operated group pair-fed with the SG group (PF), a sham-operated group fed ad libitum (AL), and a lean control group (C). At 10 weeks post-surgery, the changes in glycogen content of liver, gut microbiota and the level of FMO3 in the liver were evaluated, and their correlation with TMAO production was analysed. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Results：At 10 weeks post-surgery, hepatocyte glycogen levels were restored, and serum TMA and TMAO levels were significantly increased. Faecal metagenomic sequencing results showed that the abundances of Ruminococcaceae and Lachnospiraceae, which were positively correlated with TMAO production, were significantly increased after surgery. While the changes in FMO3, the key enzyme producing TMAO in the liver was found decreased significantly after SG. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Inconsistent with the changing trend of TMAO, the expression of PERK, FOXO1, PCK, and G6PC significantly decreased after SG. Conclusions：SG can significantly reduce obesity and restore glucose metabolism. After surgery, TMAO metabolites increased in a microbiota-dependent manner.},
}
@article {pmid40202375,
year = {2025},
author = {Pan, C and Xu, P and Yuan, M and Wei, S and Lu, Y and Lu, H and Zhang, W},
title = {Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70344},
doi = {10.1002/jmv.70344},
pmid = {40202375},
issn = {1096-9071},
support = {//This study was supported by the Zhenjiang Science and Technology Innovation Funds-Clinical Medicine Key Laboratory and Scientific Research Project of Health Commission of Jiangsu Province./ ; },
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Virome ; Feces/virology ; *Breast Feeding ; Female ; Male ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; *Feeding Behavior ; Bacteriophages/genetics/classification/isolation &amp; purification ; Milk, Human/virology ; *Gastrointestinal Tract/virology ; },
abstract = {The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.},
}
@article {pmid40202358,
year = {2025},
author = {Alexandre, A and Gerard, &#xc0; and Sergio, I and Whim, T and Isabelle, L and Maria José, C and Lorena, I and Enrique, H and Gerardo, MA and Carolina, M and José, N and Vanessa, B and Rubén, L},
title = {Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13406},
pmid = {40202358},
issn = {1600-0765},
abstract = {AIMS: To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.<br><br>METHODS: In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.<br><br>RESULTS: The results indicated significant variation in &#x3b1;-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, &#x3b2;-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.<br><br>CONCLUSION: These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.},
}
@article {pmid40202322,
year = {2025},
author = {Scheffer, G and Chakraborty, A and Amundson, KK and Khan, R and Wilkins, MJ and Evans, P and Hubert, CRJ},
title = {Polymer biodegradation by Halanaerobium promotes reservoir souring during hydraulic fracturing.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0225324},
doi = {10.1128/aem.02253-24},
pmid = {40202322},
issn = {1098-5336},
abstract = {UNLABELLED: Hydraulically fractured shale reservoirs have facilitated studies of unexplored niches in the continental deep biosphere. In high-salinity North American shale systems, members of the genus Halanaerobium seem to be ubiquitous. Polymers like guar gum used as gelling agents in hydraulic fracturing fluids are known to be fermentable substrates, but metabolic pathways encoding these processes have not been characterized. To explore this, produced water samples from the Permian Basin were incubated both at 30°C to simulate above-ground storage conditions and at 60°C to simulate subsurface reservoir conditions. Guar metabolism coincided with Halanaerobium growing only at 30°C, revealing genes for polymer biodegradation through the mixed-acid fermentation pathway in different metagenome-assembled genomes (MAGs). Whereas thiosulfate reduction to sulfide is often invoked to explain the dominance of Halanaerobium in these settings, genes for thiosulfate metabolism were lacking in Halanaerobium genomes with high estimated completeness. Sulfide production was observed in 60°C incubations, with corresponding enrichment of Desulfohalobium and Desulfovibrionaceae that possess complete pathways for coupling mannose and acetate oxidation to sulfate reduction. These findings outline how production of fermentation intermediates (mannose and acetate) by Halanaerobium in topside settings can result in reservoir souring when these metabolites are introduced into the subsurface through produced water reuse.<br><br>IMPORTANCE: Hydraulically fractured shale oil reservoirs are ideal for studying extremophiles such as thermohalophiles. During hydraulic fracturing, reservoir production water is stored in surface ponds prior to reuse. Microorganisms in these systems therefore need to withstand various environmental changes such as the swing between warm downhole oil reservoir temperatures and cooler surface conditions. While most studies on hydraulically fractured oil reservoirs mimic the environmental conditions found in oil wells, this study follows this water cycle during fracking and the associated microbial metabolic potential during topside-produced water storage and subsurface oil reservoir conditions. Of particular interest are members of the genus Halanaerobium that have been reported to reduce thiosulfate contributing to souring of oil reservoirs. Here, we show that some Halanaerobium strains were unable to grow at hotter temperatures reflective of oil reservoir conditions and lack genes for thiosulfate reduction, despite the proposed importance of this metabolism in other studies. Rather, it is likely that these organisms metabolize complex organics in fracking fluids at lower temperatures, thereby generating substrates that support reservoir souring by thermophilic sulfate-reducing bacteria at higher temperatures. In this way, Halanaerobium promotes souring indirectly by feeding sulfate-reducing microorganisms fermentation products (e.g., acetate and hydrogen) rather than via direct sulfidogenesis via thiosulfate reduction. Therefore, the novelty of this research is not within the detection of known oil reservoir colonizing bacteria but rather in the relationship between bacteria and the indirect involvement of Halanaerobium, promoting souring throughout the produced water reuse cycle.},
}
@article {pmid40202301,
year = {2025},
author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J},
title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149624},
doi = {10.1128/msystems.01496-24},
pmid = {40202301},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.<br><br>IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.},
}
@article {pmid40201781,
year = {2025},
author = {Belkina, D and Stepanov, I and Makarkina, M and Porotikova, E and Lifanov, I and Kozhevnikov, E and Gorislavets, S and Vinogradova, S},
title = {In-depth population genetic study of Vitis vinifera ssp. sylvestris from the Black Sea region and its virome.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1536862},
pmid = {40201781},
issn = {1664-462X},
abstract = {The spread of cultivated grapevine from primary centers of origin is inevitably accompanied by the range expansion of its pathogens, including viruses. A limited number of wild Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi populations have survived in the centers of grapevine domestication and can be used for comprehensive studies. We analyzed 50 grapevines collected in protected areas of the Black Sea region, which belong to the Caucasian domestication center. Based on genotyping of grapevines using simple sequence repeats as DNA markers, we determined the phylogenetic placement of V. vinifera ssp. sylvestris from the Black Sea region compared to cultivated and wild grapevines of the world. Using high-throughput sequencing of total RNA, we obtained the viromes of these grapevines. Ten viruses and one viroid were identified. The most common viruses detected were Vitis cryptic virus, grapevine rupestris stem pitting-associated virus, grapevine Pinot gris virus, and grapevine virus T. Among the economically significant viruses, we identified grapevine leafroll-associated virus 1 and grapevine virus A. A total of 91 complete or nearly complete virus genomes and one viroid genome were assembled, and phylogenetic analysis was performed. Two novel (+) ssRNA viruses were discovered, tentatively named Abrau grapevine-associated virus in the order Hepelivirales and Taurida grapevine-associated virus in the order Picornavirales. It is important to comprehensively consider the phylogeography of both viruses and their plant hosts. This is the first study that simultaneously addresses the population genetics of V. vinifera ssp. sylvestris from the Caucasian domestication center and its viruses.},
}
@article {pmid40201723,
year = {2025},
author = {Luo, H and Jiang, Y and He, Y and Zhou, H},
title = {Clinical Value of Metagenomic Next-Generation Sequencing From Blood Samples to Identify Pneumocystis jirovecii Pneumonia in Patients With Human Immunodeficiency Virus.},
journal = {Open forum infectious diseases},
volume = {12},
number = {4},
pages = {ofaf170},
pmid = {40201723},
issn = {2328-8957},
abstract = {BACKGROUND: The aim of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for identifying Pneumocystis jirovecii pneumonia (PJP) in patients with human immunodeficiency virus (HIV).<br><br>METHODS: A total of 76 people with HIV (PWH) with suspected lung infections were enrolled in the study. The patients were divided into two groups: the PJP group and the non-PJP group.All patients underwent pulmonary computed tomography scans, and blood or respiratory tract specimens were subjected to mNGS and conventional microbiological tests. Patient characteristics were collected from their medical records.<br><br>RESULTS: Thirty patients were diagnosed with PJP and 46 were confirmed to have non-P jirovecii (Pj) infectious pneumonia. mNGS was conducted on bronchoalveolar lavage fluid samples from 25 patients and on blood samples from 59 patients. Twenty-one of 22 (95.5%) blood samples from the PIP group contained sequences of Pi, with the number of specific reads for circulating Pj sequences ranging from 2 to 2035. In the non-PJP group, 4 blood samples exhibited low Pj sequences, ranging from 1 to 2 reads. The sensitivity and specificity for blood samples were 95.5% (95% confidence interval [CI], 91.2%-98.4%) and 90.0% (95% Cl, 89.5%-100%), respectively.<br><br>CONCLUSIONS: Our study indicates that mNGS of blood samples exhibits high sensitivity and specificity for diagnosing PJP in PWH. Caution should be exercised when interpreting low Pj mNGS read counts in blood samples; the definitive diagnosis of PJP relies on the synthesis of clinical data with Pj mNGS results. Further studies are necessary to validate this finding.},
}
@article {pmid40201438,
year = {2025},
author = {Lu, W and Yi, X and Ge, Y and Zhang, X and Shen, K and Zhuang, H and Deng, Z and Liu, D and Cao, J and Ma, C},
title = {Effects of dietary fiber on the composition, function, and symbiotic interactions of intestinal microbiota in pre-weaned calves.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1554484},
pmid = {40201438},
issn = {1664-302X},
abstract = {INTRODUCTION: Dietary fiber plays a crucial role in maintaining gastrointestinal health. However, its protective effects on the intestinal health of calves remain to be fully elucidated. This study aimed to investigate the impact of dietary fiber supplementation on the intestinal microbiota of pre-weaned calves and its potential role in modulating microbial metabolic pathways.<br><br>METHODS: A randomized controlled trial was conducted, enrolling 135 calves that were randomly assigned into three groups: (1) inulin supplementation, (2) psyllium husk powder (PHP) supplementation, and (3) a control group receiving no dietary fiber. Fecal microbiota samples were collected from calves without diarrhea at five time points (0, 7, 14, 28, and 56 days of age). Metagenomic sequencing was performed to analyze microbial composition and functional pathways. Additionally, a differential analysis of carbohydrate-active enzymes (CAZymes) was performed to evaluate the effect of dietary fiber on carbohydrate metabolism enzyme activity within the intestinal microbiota.<br><br>RESULTS: Calves supplemented with dietary fiber exhibited a significant increase in the abundance of Bifidobacterium and Prevotella compared to the control group. These bacterial genera contributed to intestinal protection by modulating secondary bile acid metabolism and flavonoid metabolism pathways. CAZymes differential analysis revealed an increased abundance of carbohydrate metabolism enzymes in response to dietary fiber supplementation, with distinct microbial community compositions observed among different fiber treatments. Notably, at 56 days of age, calves fed PHP harbored intergeneric symbiotic clusters comprising Clostridium, Prevotella, and Bacteroides, suggesting a cooperative microbial network that may contribute to intestinal homeostasis.<br><br>DISCUSSION: The findings of this study highlight the beneficial effects of dietary fiber on calf intestinal microbiota, particularly in enhancing microbial diversity and enzymatic activity related to carbohydrate metabolism. The observed microbial symbiosis in PHP-fed calves suggests a potential role in maintaining intestinal homeostasis. These insights provide a theoretical foundation for optimizing dietary interventions to promote gut health in calves during the transition period. Further research is warranted to explore the mechanistic interactions between dietary fiber, gut microbiota, and host health outcomes.},
}
@article {pmid40201435,
year = {2025},
author = {Tang, J and Li, P and Xu, H and Han, J},
title = {Clinical application of metagenomic next-generation sequencing in rapid diagnosis and prognostic assessment of herpes simplex encephalitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1534513},
pmid = {40201435},
issn = {1664-302X},
abstract = {PURPOSE: Herpes simplex encephalitis (HSE) ranks among the most common causes of severe viral encephalitis. It leads to meningitis or encephalitis, with patients frequently encountering adverse outcomes. In this study, we utilized metagenomic next-generation sequencing (mNGS) to rapidly and accurately detect and identify the HSV pathogen directly from cerebrospinal fluid (CSF) samples, aiming to achieve a definitive diagnosis for encephalitis patients.<br><br>METHODS: From 2018 to 2023, we prospectively identified and enrolled 28 patients diagnosed with HSE at Hengshui People's Hospital. CSF samples were subjected to mNGS to facilitate the diagnosis and characterization of HSE in this cohort. We compiled the clinical characteristics, supplementary examinations, and outcomes of HSE patients, with prognosis assessed using the Glasgow Outcome Scale (GOS) scores at discharge, 1&#x202f;month post-discharge, and 3&#x202f;months thereafter.<br><br>RESULTS: In this cohort of 28 patients, 12 were females and 16 males, with a mean age of 41.82&#x202f;&#xb1;&#x202f;18.23. HSE manifested with a variety of clinical symptoms, the most prevalent being headaches (67.9%), fever exceeding 38&#xb0;C (60.7%), and altered consciousness (60.7%). Seizures (42.9%), vomiting (35.7%), and speech deficits (35.7%) were frequently observed, with a minority of patients displaying personality changes (28.6%). CSF analysis revealed pleocytosis and a mild increase in protein levels. Magnetic resonance imaging (MRI) abnormalities (28.6%) were primarily confined to the frontal and temporal lobes as well as limbic regions, with no indications of cerebral hemorrhage. Half of the patients exhibited Electroencephalogram (EEG) changes suggestive of encephalitis. HSE was confirmed through mNGS analysis of CSF within 3&#x202f;days of admission. All patients received empirical treatment with ganciclovir, with 46.4% undergoing hormonotherapy and 32.1% receiving immunoglobulin therapy. At the three-month follow-up, 32.1% had GOS scores <5.<br><br>CONCLUSION: HSE often presents with nonspecific signs of encephalitis, and it's not easy for traditional CNS examinations to confirm the diagnosis. mNGS serves as a cutting-edge diagnostic tool for the rapid and precise identification of HSE, facilitating timely clinical diagnosis and intervention to prevent the progression of the disease.},
}
@article {pmid40201423,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J},
title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf049},
pmid = {40201423},
issn = {2730-6151},
abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.},
}
@article {pmid40201367,
year = {2025},
author = {Wen, Y and Zhang, W and Li, Y and Liao, X and Xu, J and Zhen, R and Qin, P},
title = {Epidemiological characteristics of human psittacosis in Guangzhou, China, January 2021 to June 2024.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1526990},
pmid = {40201367},
issn = {2296-2565},
mesh = {Humans ; China/epidemiology ; Male ; Middle Aged ; Adult ; *Psittacosis/epidemiology ; Female ; Aged ; Animals ; Seasons ; Zoonoses/epidemiology ; Adolescent ; Young Adult ; Prevalence ; Child ; },
abstract = {BACKGROUND: Psittacosis is a global and underappreciated zoonosis, with increasing reported cases in many countries. There have been several outbreaks and even deaths of psittacosis reported in China. Understanding its epidemiological characteristics and dimensions is crucial for formulating precise prevention and control strategies. This study aimed to analyze the epidemiological characteristics of human psittacosis in Guangzhou, China.<br><br>METHODS: The demographic characteristics, clinical manifestations, temporal patterns, geographic distribution and potential exposures of psittacosis in Guangzhou were analyzed based on the surveillance data and epidemiological investigation conducted between January 2021 and June 2024. Seasonal and trend decomposition using LOESS was applied to decompose the number of psittacosis cases into trend, seasonal and remainder component.<br><br>RESULTS: A total of 148 cases were reported, with a significant increase in the number of psittacosis cases over the study period. Most of cases were sporadic and detected by metagenomic next-generation sequencing (mNGS). Psittacosis was predominant males aged 40-79&#x202f;years. Fever and pneumonia were the most commonly observed clinical manifestations. A seasonal trend was observed in the number of psittacosis cases with a high prevalence of cases in December and March. A total of 108 local cases (87%) occurred in rural regions. Among local cases, 67.7% reported a history of contact with birds or poultry, and 17.7% had been exposed to a related environment. The suspected source of infection differed between urban and rural areas, with parrots being the primary source in urban areas and poultry in rural areas.<br><br>CONCLUSION: Increasing clinicians' awareness, enhancing epidemiological surveillance, paying close attention to the epidemic in rural areas, and implementing measures against avian influenza, will be conducive to preventing and controlling psittacosis.},
}
@article {pmid40200351,
year = {2025},
author = {Zhang, Z and Huang, Z and Fang, X and Bai, G and Li, W and Zhang, W and Zhang, C},
title = {Diagnosis and surgical treatment of chronic destructive septic hip arthritis.},
journal = {Arthroplasty (London, England)},
volume = {7},
number = {1},
pages = {19},
pmid = {40200351},
issn = {2524-7948},
support = {2023Y9092//Joint Funds for the Innovation of Science and Technology, Fujian province/ ; 2022Y4003//University-Industry Research Cooperation Project of Science and Technology, Fujian province/ ; YXRQN-ZCF2023//The First Affiliated Hospital of Fujian Medical University Excellent Talent Program/ ; YJCRC-B-ZWM2024//The First Affiliated Hospital of Fujian Medical University Excellent Talent Program/ ; },
abstract = {Septic hip arthritis (SHA) is a relatively rare but hazardous disease. Much controversy exists regarding the definition, diagnosis and treatment of chronic destructive SHAs. This review aims to provide an overview of the diagnostic and therapeutic approaches for chronic, destructive SHA and suggest possible research directions for this disease's future diagnosis and treatment. There is no unified naming or classification standard for SHAs. Chronic destructive SHA still requires a comprehensive diagnosis combining history, signs, bacterial culture, histopathological examination, inflammation and other indicators, of which metagenomic next-generation sequencing is a promising diagnostic tool. Previous treatment options for this disease include debridement, debridement + Girdlestone femoral head and neck resection, and debridement + Girdlestone femoral head and neck resection + two-stage arthroplasty. Among them, one-stage spacer implantation + two-stage arthroplasty is the current standard surgical option with a high success rate and low reinfection rate, while one-stage arthroplasty is a new treatment option proposed in recent years with unique advantages but limitations in terms of surgical indications. In the future, more high-quality studies are needed to provide the latest evidence to support clinical decision-making.},
}
@article {pmid40200155,
year = {2025},
author = {Zhou, Z and Hu, X and Wang, J and Wang, N},
title = {Invasive cerebral aspergillosis in a pregnant woman: a rare case of intracranial giant granuloma.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {478},
pmid = {40200155},
issn = {1471-2334},
mesh = {Humans ; Female ; Pregnancy ; Adult ; Antifungal Agents/therapeutic use ; *Neuroaspergillosis/diagnosis/drug therapy/pathology/surgery/microbiology ; *Granuloma/microbiology/pathology/diagnosis/surgery ; *Pregnancy Complications, Infectious/diagnosis/microbiology/drug therapy/pathology ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Brain/pathology/diagnostic imaging/microbiology ; },
abstract = {BACKGROUND: Invasive Cerebral Aspergillosis (ICA) is a rare fungal infection affecting the brain, primarily seen in individuals with compromised immune systems. Despite various treatment options, substantial cerebral granulomas caused by ICA still result in high mortality and recurrence rates.<br><br>CASE PRESENTATION: We report a rare instance of ICA in a 30-year-old pregnant woman. The infection initiated in the nasal cavity and progressed to form a large intracranial granuloma, leading to brain herniation. Diagnosis was confirmed through histopathology, Polymerase Chain Reaction (PCR), and metagenomic next-generation sequencing (mNGS) following decompressive craniotomy and sinus window drainage surgery. Prompt administration of antifungal medication resulted in a favorable prognosis.<br><br>CONCLUSION: This case highlights the critical roles of mNGS and PCR in the early diagnosis of ICA, as well as the pivotal importance of surgical interventions and prompt initiation of antifungal therapy in enhancing patient outcomes.},
}
@article {pmid40199830,
year = {2025},
author = {Singh, P and Haldhar, P and Das, T and Chaubey, G and Gupta, MK and Kumar, B},
title = {Thermal Stress and Its Effects on the Gut Microbiome of Parthenium Beetles.},
journal = {Archives of insect biochemistry and physiology},
volume = {118},
number = {4},
pages = {e70058},
doi = {10.1002/arch.70058},
pmid = {40199830},
issn = {1520-6327},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Stress, Physiological ; Bacteria/classification/isolation &amp; purification/genetics ; Hot Temperature ; RNA, Ribosomal, 16S/analysis ; },
abstract = {The gut microbiota plays a vital role in nutrient and energy utilization, as well as in the host's ability to adapt its immune system to environmental changes. As a biological control agent for the invasive Parthenium weed, the Parthenium beetle Zygogramma bicolorata (Z. bicolorata) Pallister is often exposed to fluctuating temperatures, which may induce stress in its natural habitat. This study utilized 16S amplicon sequencing to explore the impact of temperature stress on the gut microbiome of Z. bicolorata under cold (15°C), control (27°C), and hot (35°C) conditions. A total of 11 bacterial phyla and 149 genera were identified, with Firmicutes, Proteobacteria, and Cyanobacteria being the most abundant. Temperature treatments significantly influenced the diversity of the gut microbiota, as evidenced by alpha diversity measures. Principal coordinate analysis further revealed substantial variations in microbiome composition across the different temperature conditions. Additionally, PICRUSt2 analysis suggested that the gut microbiota is linked to metagenomic functions related to amino acid and carbohydrate transport, inorganic ion metabolism, and cellular processes. Our findings suggest that thermal stress alters the gut microbiome of Parthenium beetles, offering new insights into how these beetles may have ecologically adapted to temperature fluctuations, while also highlighting the potential role of gut microbes in maintaining beetle health under environmental stress.},
}
@article {pmid40199391,
year = {2025},
author = {Tan, Y and Li, L and Zhao, Z and Li, Y and Li, T and Li, Y and Sheng, X and Shen, L and Xu, Z and Song, S and Zhang, P},
title = {Simultaneous pollutant removal and organic matter sequestration by coral sand-pyrite-based electroactive constructed wetlands.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132498},
doi = {10.1016/j.biortech.2025.132498},
pmid = {40199391},
issn = {1873-2976},
abstract = {The development of integrated solutions for sewage treatment and soil restoration in remote regions remains a challenge. This study innovatively designed coral sand-pyrite-based electroactive constructed wetlands (E-CWs) to synchronize wastewater purification and organic matter (OM) enrichment. Metagenomic analyses revealed that the addition of pyrite increased the abundance of iron redox-related genes, whereas coral sand salinity promoted the enrichment of functional bacteria for OM decomposition. Furthermore, the combined substrate comprising coral sand and pyrite facilitated the adsorption and sequestration of OM, while providing a stable environment for microorganisms. This achieved dual objectives: efficient chemical oxygen demand removal (90.6 ± 2.4 %) from sewage and substantial OM sequestration in substrates (total organic carbon: 2.9-4.8 %). This study achieved sewage treatment through the combination of coral sand and pyrite as substrates of E-CWs and enhanced the OM content of the substrates, contributing to the improvement of local soil infertility.},
}
@article {pmid40198556,
year = {2025},
author = {Holden, S and Kim, SH and Chen, W and Li, X and Bakkeren, G and Brar, GS},
title = {Identification of Rust Fungi Using High-Throughput Sequencing Data from Environmental Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2898},
number = {},
pages = {151-188},
pmid = {40198556},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Basidiomycota/genetics/isolation &amp; purification/classification ; *Plant Diseases/microbiology ; *Fungi/genetics ; DNA, Fungal/genetics ; },
abstract = {Working with any plant-associated microbe comes with the inherent challenge that no environment is sterile, and a plant's metabiome is teeming with life. When collecting field samples outside of the laboratory, this issue is compounded further. Rust fungi, being obligate plant pathogens, are challenging to maintain, and strict protocols must be adhered to in the laboratory to prevent cross-contamination. In this era of big data and easy access to next generation sequencing (NGS), it is increasingly common for scientists to work with large sequencing datasets, which must first be evaluated for quality and filtered for potentially nontarget reads. Sequencing data files from environmental samples often contain genetic material from organisms not targeted by the experimental design. This situation can lead to issues if researchers assume the presence of only their intended subjects. Additionally, the origin of some samples may be inherently unknown, making the main objective of certain sequencing experiments to identify all organisms present, not just the expected ones.This chapter details common in silico approaches for identifying and classifying samples from sequencing data, drawing on experiences with cereal rust samples collected in the field. While the concepts are broadly applicable, they may require some tailoring for your species of interest. The chapter does not cover population-genomics level approaches to sample classification; instead, it describes essential quality control steps that researchers should implement before conducting downstream analyses to ensure that their data is appropriate for the intended tests.},
}
@article {pmid40198136,
year = {2025},
author = {Fishman, JA and Denner, J and Scobie, L},
title = {International Xenotransplantation Association (IXA) Position Paper on Infectious Disease Considerations in Xenotransplantation.},
journal = {Transplantation},
volume = {},
number = {},
pages = {},
pmid = {40198136},
issn = {1534-6080},
abstract = {Clinical xenotransplantation has the potential to address shortages of human organs for patients with end-stage organ failure. Advances in genetic engineering, immunosuppressive regimens, and infectious disease diagnostics have improved prospects for clinical xenotransplantation. Management of the infectious risks posed by clinical xenotransplantation requires biosecure breeding and validated methods for microbiological surveillance of source animals and recipients. Novel infection control protocols may complement biosafety requirements. Infectious risks in xenotransplantation include both known human pathogens common to immunosuppressed organ recipients and from porcine organisms or xenozoonoses for which the clinical manifestations are less well defined and for which microbial assays and therapies are more limited. Some pig-specific organisms do not infect human cells but have systemic manifestations when active within the xenograft. The human risk posed by porcine endogenous retroviruses (PERV) is uncertain. There are no documented transmissions of PERV in humans and swine are available with inactivated genomic PERV loci. Metagenomic sequencing will complement more traditional diagnostic tools in the detection of any unknown pathogens in xenotransplantation recipients. Such data are required for the development of protocols for donor and recipient microbiological surveillance, infection control, and antimicrobial therapies that will enhance the safety of clinical xenotransplantation.},
}
@article {pmid40197807,
year = {2025},
author = {Fishman, JA and Denner, J and Scobie, L},
title = {International Xenotransplantation Association (IXA) Position Paper on Infectious Disease Considerations in Xenotransplantation.},
journal = {Xenotransplantation},
volume = {32},
number = {2},
pages = {e70001},
doi = {10.1111/xen.70001},
pmid = {40197807},
issn = {1399-3089},
mesh = {*Transplantation, Heterologous/adverse effects/methods ; Animals ; Humans ; Swine ; *Heterografts/microbiology/virology ; Endogenous Retroviruses ; *Communicable Diseases/transmission ; },
abstract = {Clinical xenotransplantation has the potential to address shortages of human organs for patients with end-stage organ failure. Advances in genetic engineering, immunosuppressive regimens, and infectious disease diagnostics have improved prospects for clinical xenotransplantation. Management of the infectious risks posed by clinical xenotransplantation requires biosecure breeding and validated methods for microbiological surveillance of source animals and recipients. Novel infection control protocols may complement biosafety requirements. Infectious risks in xenotransplantation include both known human pathogens common to immunosuppressed organ recipients and from porcine organisms or xenozoonoses for which the clinical manifestations are less well defined and for which microbial assays and therapies are more limited. Some pig-specific organisms do not infect human cells but have systemic manifestations when active within the xenograft. The human risk posed by porcine endogenous retroviruses (PERV) is uncertain. There are no documented transmissions of PERV in humans and swine are available with inactivated genomic PERV loci. Metagenomic sequencing will complement more traditional diagnostic tools in the detection of any unknown pathogens in xenotransplantation recipients. Such data are required for the development of protocols for donor and recipient microbiological surveillance, infection control, and antimicrobial therapies that will enhance the safety of clinical xenotransplantation.},
}
@article {pmid40197788,
year = {2025},
author = {Arenas-Montes, J and Alcala-Diaz, JF and Garcia-Fernandez, H and Gutierrez-Mariscal, FM and Lopez-Moreno, A and Luque-Cordoba, D and Arenas-de Larriva, AP and Torres-Peña, JD and Luque, RM and Prodam, F and Priego-Capote, F and Delgado-Lista, J and Lopez-Miranda, J and Camargo, A},
title = {A microbiota pattern associated with cardiovascular events in secondary prevention: the CORDIOPREV study.},
journal = {European heart journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/eurheartj/ehaf181},
pmid = {40197788},
issn = {1522-9645},
support = {//Fundacion Patrimonio Comunal Olivarero/ ; //CEAS/ ; //Centro de Excelencia en Investigacion sobre Aceite de Oliva/ ; CVI-7450//Junta de Andalucia/ ; //Diputaciones de Jaen y C&#xf3;rdoba/ ; //Ministerio de Medio Ambiente, Medio Rural y Marino/ ; //Spanish Government/ ; AGL2012/39615//Ministerio de Ciencia e Innovaci&#xf3;n, Spain/ ; //MCIN/AEI/10.13039/501100011033/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI-0055-2021//Consejer&#xed;a de Salud y Familias, Junta de Andaluc&#xed;a/ ; //Consejeria de Innovaci&#xf3;n, Ciencia y Empresa, Proyectos de Investigaci&#xf3;n de Excelencia/ ; //European Union/ ; CP14/00114//Programa Miguel-Servet/ ; //Servicio Andaluz de Salud-Junta de Andalucia/ ; C1-0001-2022//Nicolas Monardes Programme Contract/ ; },
abstract = {BACKGROUND AND AIMS: Preventing new cardiovascular events in patients with established cardiovascular disease (CVD) is a daunting task for clinicians. Intestinal microbiota may help identify patients at risk, thus improving the strategies of secondary prevention. The aim of this study was to evaluate the baseline differences between the gut microbiota from coronary heart disease (CHD) patients suffering new major adverse cardiovascular events (MACEs) in the following 7 years, compared with CHD patients who did not undergo new MACE in this period, and to build a score associated with the risk of suffering new MACE.<br><br>METHODS: Within the framework of the CORDIOPREV study, a clinical trial that involved 1002 patients with CHD, intestinal microbiota was examined in patients with available faecal samples (n = 679, 132 MACE), through 16S metagenomics on the Illumina MiSeq and Quiime2 software. Lipopolysaccharide (LPS) was measured using limulus amoebocyte lysate test.<br><br>RESULTS: Random survival forest identified 10 bacterial taxa with a higher predictive power for MACE incidence. Receiver operating characteristic curves yielded an area under the curve of 65.2% (59.1%-71.3%) in the training set and 68.6% (59.3%-77.9%) in the validation set. The intestinal microbiota risk score was associated with a MACE incidence hazard ratio of 2.01 (95% confidence interval 1.37-3.22). Lipopolysaccharide analysis showed a greater LPS post-prandial fold change in the MACE group (P = .005).<br><br>CONCLUSIONS: These results reinforce the relationship between intestinal microbiota and CVD and suggest that a microbiota profile is associated with MACE in CHD patients, in addition to higher endotoxaemia.},
}
@article {pmid40197742,
year = {2025},
author = {He, C and Gonsior, M and Liu, J and Jiao, N and Chen, F},
title = {Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf049},
pmid = {40197742},
issn = {1751-7370},
abstract = {SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (< 2 Mbp), low GC content (< 40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 are distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.},
}
@article {pmid40197145,
year = {2025},
author = {Feng, KH and Qi, YH and Ye, ZX and Li, T and Jiao, GY and Zhang, CX and Chen, JP and Lu, G and Li, JM},
title = {Diversity and evolution analysis of RNA viruses in three wheat aphid species.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {353},
doi = {10.1186/s12864-025-11512-1},
pmid = {40197145},
issn = {1471-2164},
support = {2024YFD1400400//National Key Research and Development Program of China/ ; LY24C140001//Natural Science Foundation of Zhejiang Province/ ; 2024J016//Ningbo Natural Science Foundation/ ; 2023S029//Ningbo Commonweal Project/ ; },
mesh = {*Aphids/virology/genetics ; Animals ; },
abstract = {BACKGROUND: Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-generated transcriptome, the RNA virome and EVEs in the genomes of Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi were systematically investigated.<br><br>RESULTS: We identified 43 RNA viruses, including 12 novel and 31 known RNA viruses. These viruses were widely distributed and abundant in different geographic populations of three wheat aphid species. +ssRNA viruses were the dominant type of aphid viruses. Besides, 90 EVEs were discovered in the genomes of three aphid species. In addition, the EVEs exhibit potential domestication and novel functional roles within aphid genomes.<br><br>CONCLUSIONS: This study expands the understanding of RNA virus diversity in aphids and provides valuable insights into the potential functions of EVEs in virus-host coevolution.},
}
@article {pmid40197113,
year = {2025},
author = {Karabekmez, ME},
title = {Harnessing Human Holobiome and Meta-Multi-Omics Analyses for Medical Applications.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2025.0024},
pmid = {40197113},
issn = {1557-8100},
abstract = {Next-generation sequencing technology has revolutionized all fields of living systems, and its applications almost reinvented some research areas including metagenomics. The microbiotas in our body, including those of the oral, nasal, ocular, alveolar, skin regions, and particularly gut microbiota, have close linkages with our health status. Maturation of experimental techniques for metagenomics has been followed by other related omics platforms, for example, metatranscriptomics, metaproteomics, and all possible metacounterparts of multiomics studies. Now, we are on the eve of a meta-multi-omics era for the analysis of human holobiome in medical research. This era will help buttress the current efforts for systems medicine by illuminating the relationships between human holobiome and health or all human diseases including not only cancers but also infectious diseases, autoimmune diseases, obesity, aging, genetic disorders, and psychiatric conditions. Equally important, meta-multi-omics era is also poised to inform the determinants of human health and, by extension, help build individually tailored precision medicine interventions.},
}
@article {pmid40197060,
year = {2025},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0327524},
doi = {10.1128/spectrum.03275-24},
pmid = {40197060},
issn = {2165-0497},
abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.},
}
@article {pmid40197053,
year = {2025},
author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A},
title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116624},
doi = {10.1128/msystems.01166-24},
pmid = {40197053},
issn = {2379-5077},
abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.<br><br>IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.},
}
@article {pmid40197051,
year = {2025},
author = {Shamash, M and Sinha, A and Maurice, CF},
title = {Improving gut virome comparisons using predicted phage host information.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0136424},
doi = {10.1128/msystems.01364-24},
pmid = {40197051},
issn = {2379-5077},
abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.<br><br>IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.},
}
@article {pmid40196042,
year = {2025},
author = {Wang, H and Zhu, W and Lei, J and Liu, Z and Cai, Y and Wang, S and Li, A},
title = {Gut microbiome differences and disease risk in colorectal cancer relatives and healthy individuals.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1573216},
pmid = {40196042},
issn = {2235-2988},
mesh = {Humans ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Family ; },
abstract = {Given the heightened focus on high-risk populations, this study aimed to provide insights into early susceptibility and preventive strategies for colorectal cancer (CRC) by focusing on high-risk populations. In this research, fecal samples from 1,647 individuals across three discovery cohorts and nine external validation cohorts were sequenced using whole-genome metagenomic sequencing. A prediction model based on random forest was constructed using the nine external cohorts and independently validated with the three discovery cohorts. A disease probability (POD) model based on microbial biomarkers was developed to assess CRC risk. We found that the gut microbiome composition of CRC relatives differed from that of controls, with enrichment of species such as Fusobacterium and Bacteroides and a reduction in beneficial genera like Coprococcus and Roseburia. Additionally, dietary red meat intake emerged as a risk factor. The POD model indicated an elevated risk of CRC in unaffected relatives. The findings suggest that the POD for CRC may be increased in unaffected relatives or individuals living in shared environments, although this difference did not reach statistical significance. Our study introduces a novel framework for assessing the risk of colorectal cancer in ostensibly healthy individuals.},
}
@article {pmid40196035,
year = {2025},
author = {Decadt, H and Díaz-Muñoz, C and Vermote, L and Pradal, I and De Vuyst, L and Weckx, S},
title = {Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1543079},
pmid = {40196035},
issn = {1664-302X},
abstract = {Metagenomic studies of the Gouda cheese microbiota and starter cultures are scarce. During the present study, short-read metagenomic sequencing (Illumina) was applied on 89 Gouda cheese and processed milk samples, which have been investigated before concerning their metabolite and taxonomic composition, the latter applying amplicon-based, high-throughput sequencing (HTS) of the full-length 16S rRNA gene. Selected samples were additionally investigated using long-read metagenomic sequencing (Oxford Nanopore Technologies, ONT). Whereas the species identified by amplicon-based HTS and metagenomic sequencing were identical, the relative abundances of the major species differed significantly. Lactococcus cremoris was more abundant in the metagenomics-based taxonomic analysis compared to the amplicon-based one, whereas the opposite was true for the non-starter lactic acid bacteria (NSLAB). This discrepancy was related to a higher fragmentation of the lactococcal DNA compared with the DNA of other species when applying ONT. Possibly, a higher fragmentation was linked with a higher percentage of dead or metabolically inactive cells, suggesting that full-length 16S rRNA gene amplicon-based HTS might give a more accurate view on active cells. Further, fungi were not abundantly present in the Gouda cheeses examined, whereas about 2% of the metagenomic sequence reads was related to phages, with higher relative abundances in the cheese rinds and long-ripened cheeses. Intraspecies differences found by short-read metagenomic sequencing were in agreement with the amplicon sequence variants obtained previously, confirming the ability of full-length 16S rRNA gene amplicon-based HTS to reach a taxonomic assignment below species level. Metagenome-assembled genomes (MAGs) were retrieved for 15 species, among which the starter cultures Lc. cremoris and Lactococcus lactis and the NSLAB Lacticaseibacillus paracasei, Loigolactobacillus rennini, and Tetragenococcus halophilus, although obtaining MAGs from Lc. cremoris and Lc. lactis was more challenging because of a high intraspecies diversity and high similarity between these species. Long-read metagenomic sequencing could not improve the retrieval of lactococcal MAGs, but, overall, MAGs obtained by long-read metagenomic sequencing solely were superior compared with those obtained by short-read metagenomic sequencing solely, reaching a high-quality draft status of the genomes.},
}
@article {pmid40195635,
year = {2025},
author = {Lv, H and Zhou, J and Guo, Y and Liao, S and Chen, H and Luo, F and Xu, J and Zhang, Z and Zhang, Z},
title = {Uniportal endoscopic decompression and debridement for infectious diseases of spine with neurological deficits: a retrospective study in China.},
journal = {Asian spine journal},
volume = {},
number = {},
pages = {},
doi = {10.31616/asj.2025.0020},
pmid = {40195635},
issn = {1976-1902},
abstract = {STUDY DESIGN: A retrospective study.<br><br>PURPOSE: To evaluate the clinical efficacy of uniportal endoscopic decompression and debridement (UEDD) in treating infectious diseases of the spine (IDS) with neurological deficits.<br><br>OVERVIEW OF LITERATURE: IDS patients with neurological deficits often require urgent surgical decompression. However, the efficacy of UEDD in this complex patient population is not well-characterized.<br><br>METHODS: This retrospective study analyzed 32 consecutive IDS patients who underwent UEDD surgery. Clinical features, laboratory data (erythrocyte sedimentation rate and C-reactive protein), and treatment outcomes were analyzed.<br><br>RESULTS: Definite microorganisms were identified in 27 patients (84.3%), with 24 (88.9%) meeting cure criteria. The cure rate was significantly higher in the detected pathogen group compared to the undetected pathogen group (88.9% vs. 80%; &#x3c7;&#xb2;=19.36, p<0.0001). Metagenomic next generation sequencing (mNGS) provided faster diagnosis (41.72&#xb1;6.81 hours) compared to tissue culture (95.74&#xb1;35.47 hours, p<0.05). The predominant causative pathogen was Mycobacterium tuberculosis, followed by Staphylococcus aureus. Significant improvements were observed in Visual Analog Scale pain scores, from a mean of 7.9 preoperatively to 1.06 at 1 year postoperatively. The Oswestry Disability Index revealed a similar trend, showing significant improvement (p<0.05).<br><br>CONCLUSIONS: UEDD is a viable alternative to traditional open surgery for managing IDS in high-risk patients. UEDD offers a dual therapeutic-diagnostic advantage during the initial admission phase, enabling simultaneous debridement, neurological decompression, and targeted biopsy in a single intervention. Compared with traditional tissue culture, mNGS enables rapid microbiological diagnosis and extensive pathogen coverage.},
}
@article {pmid40195460,
year = {2025},
author = {Bhagat, NR and Bharti, VK and Shukla, G and Rishi, P and Chaurasia, OP},
title = {Gut bacteriome dynamics in high altitude-adapted chicken lines: a key to future poultry therapeutics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11910},
pmid = {40195460},
issn = {2045-2322},
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Altitude ; Metagenomics/methods ; *Bacteria/genetics/classification ; *Adaptation, Physiological ; Metagenome ; },
abstract = {High-altitude-adapted chickens harbor a unique gut bacteriome essential for their survival under extremely cold and hypoxic environment, however, little is known about their population and functional dynamics, limiting their application in poultry production. Hence, this study employed amplicon-based metagenomics to examine the gut bacterial diversity and their functional profile in two high-altitude-adapted chicken lines, e.g. LEHBRO-1 and LEHBRO-3. The results revealed significant variations in taxonomic abundance at the phylum level, with Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria predominating in LEHBRO-1, whereas Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria predominated in LEHBRO-3. Genus-level diversity and Linear Discriminant Analysis Effect Size (LEfSe) biomarker analysis also substantiated the differences in the gut bacterial communities between the two chicken lines. Furthermore, functional profiling revealed enrichment of carbohydrate, nucleotide, lipid, amino acid, fatty acid, energy, and glycan metabolic pathways in the gut bacteriomes of these high-altitude chicken lines. The Statistical Analysis of Metagenomic Profiles (STAMP) for metabolic profiling identified a significant difference in purine and protein metabolism between these two chicken lines. These findings indicate the unique gut bacteriome and their functional diversity in high-altitude-adapted chickens, which would provide a foundation for future research on gut therapeutics to improve chicken health and productivity in high-altitude areas.},
}
@article {pmid40195156,
year = {2025},
author = {Sefrji, FO and Abulfaraj, AA and Alshehrei, FM and Al-Andal, A and Alnahari, AA and Tashkandi, M and Baz, L and Barqawi, AA and Almutrafy, AM and Alshareef, SA and Alkhatib, SN and Abuauf, HW and Jalal, RS and Aloufi, AS},
title = {Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.},
journal = {Functional &amp; integrative genomics},
volume = {25},
number = {1},
pages = {82},
pmid = {40195156},
issn = {1438-7948},
mesh = {*Moringa oleifera/microbiology/genetics/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Energy Metabolism/genetics ; Soil Microbiology ; Bacteria/genetics/classification ; Adenosine Triphosphate/metabolism ; Metagenome ; },
abstract = {Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant-microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.},
}
@article {pmid40194944,
year = {2025},
author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F},
title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf036},
pmid = {40194944},
issn = {1574-6941},
abstract = {Monotreme and marsupial development is characterised by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.},
}
@article {pmid40194477,
year = {2025},
author = {Zhang, H and Zhang, X and Sun, H and Ling, H and Xie, R and Fang, L and Guo, M and Wu, X},
title = {Polyvinyl chloride microplastic triggers bidirectional transmission of antibiotic resistance genes in soil-earthworm systems.},
journal = {Environment international},
volume = {198},
number = {},
pages = {109414},
doi = {10.1016/j.envint.2025.109414},
pmid = {40194477},
issn = {1873-6750},
abstract = {The diffusion and distribution of ubiquitous microplastics and antibiotic resistance genes (ARGs) in soil ecosystems are easily influenced by earthworm activity. However, minimal research exists on the bidirectional dissemination of ARGs in the soil-earthworm ecosystems under microplastic stress. Focusing on the typical microplastic polyvinyl chloride (PVC) microspheres in simulated soil-earthworm (Eisenia fetida) systems, we characterized the PVC-triggered interactive transmission of ARGs between earthworm guts and their dwelling soils using shotgun metagenomics and qPCR methodologies. PVC exposure did not alter the diversity and relative abundance of ARGs in earthworm-uninoculated soils but significantly increased those in earthworm-inoculated soils. Meanwhile, the abundance of ARGs increased in the earthworm gut under PVC stress. Source tracking analysis showed a higher source proportion of soil-borne ARGs into earthworm gut under PVC treatments. Mechanistically, PVC-triggered increasing prevalence of ARGs was significantly related to both the bacterial community and mobile genetic elements-mediated horizontal transfer in the soils, whereas the bacterial community predominated the process in the earthworm guts. Overall, our findings reveal a PVC-triggered bidirectional transmission pattern of ARGs between earthworm guts and their dwelling soils and highlight the overlooked ecotoxicological risk of microplastics in soil-earthworm systems.},
}
@article {pmid40193404,
year = {2025},
author = {Aroney, STN and Newell, RJP and Nissen, JN and Camargo, AP and Tyson, GW and Woodcroft, BJ},
title = {CoverM: Read alignment statistics for metagenomics.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf147},
pmid = {40193404},
issn = {1367-4811},
abstract = {SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses 'Mosdepth arrays' for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.<br><br>CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.},
}
@article {pmid40193328,
year = {2025},
author = {Jagadesan, S and Guda, C},
title = {MetaDAVis: An R shiny application for metagenomic data analysis and visualization.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0319949},
doi = {10.1371/journal.pone.0319949},
pmid = {40193328},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; *Software ; *Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.},
}
@article {pmid40193099,
year = {2025},
author = {Chiu, CY and López-Labrador, FX and Wilson, MR and de Vries, JJC},
title = {The Regulatory Landscape for Clinical Metagenomic Testing.},
journal = {JAMA neurology},
volume = {},
number = {},
pages = {},
doi = {10.1001/jamaneurol.2025.0461},
pmid = {40193099},
issn = {2168-6157},
}
@article {pmid40193036,
year = {2025},
author = {Kim, SY and Seol, D and Jung, M and Kwak, W and Kim, H and Cho, S and Kim, TH},
title = {Assessing the Efficacy of Ligilactobacillus salivarius CLS0420 and Lacticaseibacillus paracasei CLPC0603 on Vaginal Well-Being in Healthy Women: A Pilot, Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40193036},
issn = {1867-1314},
abstract = {Despite the growing development of probiotics for preventing bacterial vaginosis (BV), their effectiveness in women without BV has not been thoroughly investigated. This pilot, randomized, double-blind, placebo-controlled study aims to assess the impact of orally administered probiotic strains, exhibiting in vitro antimicrobial activity against Gardnerella vaginalis and Candida albicans, on vaginal well-being in women without preexisting health conditions. Healthy women (n = 30, aged 19-50) were enrolled and randomly assigned using simple randomization to receive either probiotic or placebo capsules. After excluding dropouts, 26 participants (15 in the probiotic group, 11 in the placebo group) completed the study, undergoing a 3-week intervention. Vaginal well-being was assessed before and after the intervention using self-assessed health on a 5-point Likert scale, along with analysis of the vaginal microbiome by targeting the 16S-ITS-23S rRNA operon region with the Nanopore sequencing platform and MIrROR database. Notably, only the probiotic group exhibited a significant improvement in self-assessed overall gut and vaginal health following the intervention (p = 0.009 and p = 0.003, respectively). Nevertheless, no significant changes were observed in the vaginal bacterial community following the intervention and confirming the vaginal colonization of orally ingested probiotic strains through metagenome sequencing proved challenging. In summary, these findings suggest that while oral probiotics may improve perceived vaginal well-being, their role in modulating the vaginal microbiome in healthy women remains inconclusive. Additional research with a larger sample size is necessary to substantiate the endorsement of oral probiotic consumption for preventing BV or maintaining vaginal health in healthy women. This study was retrospectively registered at Clinical Research Information Service (CRIS) (KCT0008957, November 15, 2023).},
}
@article {pmid40192235,
year = {2025},
author = {Jiao, Y and Ren, J and Xie, S and Yuan, N and Shen, J and Yin, H and Wang, J and Guo, H and Cao, J and Wang, X and Wu, D and Zhou, Z and Qi, X},
title = {Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2488105},
doi = {10.1080/19490976.2025.2488105},
pmid = {40192235},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; *Bile Acids and Salts/metabolism ; Mice ; *NF-kappa B/metabolism/genetics ; Signal Transduction/radiation effects ; *Raffinose/metabolism ; Mice, Inbred C57BL ; Whole-Body Irradiation/adverse effects ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fecal Microbiota Transplantation ; Male ; *Acute Radiation Syndrome/microbiology/metabolism ; *Hematopoiesis/radiation effects ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Dysbiosis/microbiology ; },
abstract = {Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.},
}
@article {pmid40191975,
year = {2025},
author = {Okechukwu Paul-Chima, U and Chinyere Nkemjika, A and Melvin Nnaemeka, U and Onohuean, H},
title = {Harnessing plant metabolic pathways for innovative diabetes management: unlocking the therapeutic potential of medicinal plants.},
journal = {Plant signaling &amp; behavior},
volume = {20},
number = {1},
pages = {2486076},
doi = {10.1080/15592324.2025.2486076},
pmid = {40191975},
issn = {1559-2324},
mesh = {*Plants, Medicinal/metabolism ; Humans ; *Diabetes Mellitus/drug therapy/metabolism ; *Metabolic Networks and Pathways ; },
abstract = {The exploration of plant signaling pathways is transforming the way diabetes is managed, providing new, multi-target strategies for controlling this complex metabolic disorder. Medicinal plants are rich in bioactive compounds like phytohormones, flavonoids and polyphenols, which regulate key pathways including oxidative stress, inflammation, insulin resistance, and gut microbiota modulation. Research is emerging on the therapeutic potential of Momordica charantia, Cinnamomum verum and Trigonella foenum-graecum, which enhance insulin secretion, sensitivity and glucose homeostasis. These plant derived compounds, resveratrol and plant based insulin mimetics, not only address metabolic dysfunction but also offer holistic treatment for long term complications such as neuropathy and retinopathy. The development of precision medicine advances the tailoring of plant based therapies to individual metabolic responses, increasing efficacy and decreasing reliance on synthetic drugs with adverse side effects. Despite challenges of standardization, regulatory barriers, and limited clinical trials, incorporating medicinal plants into national diabetes management guidelines represents a cost effective and accessible option, particularly in resource limited settings. In this review, we highlight the importance of collaborative work across disciplines and the use of technologies such as artificial intelligence to speed research and optimize patient specific applications. The therapeutic power of plant signaling pathways is harnessed to develop sustainable, inclusive, and effective diabetes management strategies.},
}
@article {pmid40191290,
year = {2025},
author = {Kurt, H and Sever Kaya, D and Akçok, &#x130; and Sarı, C and Albayrak, E and Velioğlu, HM and Şamlı, HE and Özdüven, ML and Sürmeli, Y},
title = {Discovery and In Silico Characterization of Anatolian Water Buffalo Rumen-Derived Bacterial Thermostable Xylanases: A Sequence-Based Metagenomic Approach.},
journal = {ACS omega},
volume = {10},
number = {12},
pages = {12679-12698},
pmid = {40191290},
issn = {2470-1343},
abstract = {This study involved shotgun sequencing of rumen metagenomes from three Anatolian water buffalos, an exploration of the relationship between microbial flora and xylanases, and in silico analyses of thermostable xylanases, focusing on their sequence, structure, and dynamic properties. For this purpose, the rumen metagenome of three Anatolian water buffalos was sequenced and bioinformatically analyzed to determine microbial diversity and full-length xylanases. Analyses of BLAST, biophysicochemical characteristics, phylogenetic tree, and multiple sequence alignment were performed with Blastp, ProtParam, MEGA11 software, and Clustal Omega, respectively. Three-dimensional homology models of three xylanases (AWBRMetXyn5, AWBRMetXyn10, and AWBRMetXyn19) were constructed by SWISS-MODEL and validated by ProSA, ProCheck, and Verify3D. Also, their 3D models were structurally analyzed by PyMOL, BANΔIT, thermostability predictor, What If, and Protein Interaction Calculator (PIC) software. Protein-ligand interactions were examined by docking and MD simulation. Shotgun sequence and Blastp analyses showed that Clostridium (Clostridiales bacterial order), Ruminococcus (Oscillospiraceae bacterial family), Prevotella (Bacteroidales bacterial order), and Butyrivibrio (Lachnospiraceae bacterial family) were found as dominant potential xylanase-producer genera in three rumen samples. Furthermore, the biophysicochemical analysis indicated that three xylanases exhibited an aliphatic index above 80, an instability index below 40, and melting temperatures (T m) surpassing 65 °C. Phylogenetic analysis placed three xylanases within the GH10 family, clustering them with thermophilic xylanases, while homology modeling identified the optimal template as a xylanase from a thermophilic bacterium. The structural analysis indicated that three xylanases possessed the number of salt bridges, hydrophobic interactions, and T m score higher than 50, 165, and 70 °C, respectively; however, the reference thermophilic XynAS9 had 43, 145, and 54.41 °C, respectively. BANΔIT analysis revealed that three xylanases exhibited lower B'-factor values in the β3-α1 loop/short-helix at the N-terminal site compared to the reference thermophilic XynAS9. In contrast, six residues (G79, M123, D150, T199, A329, and G377) possessed higher B'-factor values in AWBRMetXyn5 and their aligned positions in AWBRMetXyn10 and AWBRMetXyn19, relative to XynAS9 including Gln, Glu, Ile, Lys, Ser, and Val at these positions, respectively. MD simulation results showed that the β9-η5 loop including catalytic nucleophile glutamic acid in the RMSF plot of three xylanases had a higher fluctuation than the aligned region in XynAS9. The distance analysis from the MD simulation showed that the nucleophile residue in AWBRMetXyn5 and AWBRMetXyn10 remained closer to the ligand throughout the simulation compared with XynAS9 and AWBRMetXyn19. The most notable difference between AWBRMetXyn5 and AWBRMetXyn10 was the increased amino acid fluctuations in two specific regions, the η3 short-helix and the η3-α3 loop, despite a minimal sequence difference of only 1.24%, which included three key amino acid variations (N345, N396, and T397 in AWBRMetXyn5; D345, K396, and A397 in AWBRMetXyn10). Thus, this study provided computational insights into xylanase function and thermostability, which could inform future protein engineering efforts. Additionally, three xylanases, especially AWBRMetXyn5, are promising candidates for various high-temperature industrial applications. In a forthcoming study, three xylanases will be experimentally characterized and considered for potential industrial applications. In addition, the amino acid substitutions (G79Q, M123E, D150I, T199K, A329S, and G377V) and the residues in the β3-α1 loop will be targeted for thermostability improvement of AWBRMetXyn5. The amino acids (N345, N396, and T397) and the residues on the β9-η5 loop, η3 short-helix, and η3-α3 loop will also be focused on development of the catalytic efficiency.},
}
@article {pmid40190795,
year = {2025},
author = {Zhang, Y and Dai, Y and Li, J and Cong, W and Zhang, Y and Nie, X and Wu, Q and Xue, Y},
title = {Climate Change and Human Pressure: Assessing the Vulnerability of Snow Leopard (Panthera uncia) Habitat Integrated With Prey Distribution on the Qinghai-Tibet Plateau.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71232},
pmid = {40190795},
issn = {2045-7758},
abstract = {Climate change is significantly altering the distribution of large carnivores and their primary prey species, with particular emphasis on the changing prey distribution in high-altitude regions. The Qinghai-Tibet Plateau, known for its rich biodiversity, is highly sensitive to climate change, affecting the habitats of snow leopards (Panthera uncia) and blue sheep (Pseudois nayaur). Our study identified blue sheep as the primary prey of snow leopards through metagenomic analysis and used bioclimatic data and Land Use/Cover Change (LUCC) information to model habitat suitability under three climate scenarios (RCP 2.6, RCP 4.5, and RCP 8.5). Projections showed that under RCP 4.5 and RCP 8.5, snow leopard habitats will decrease by 13.0% and 23.4%, while blue sheep habitats will decrease by 38.3% and 49.7%, respectively. These habitats are expected to shift to higher altitudes, with snow leopards experiencing a more significant shift. Based on these findings, we recommend adjusting protected area boundaries for S1 (Ideal distribution range), establishing ecological corridors for S2 (stepping stone), and implementing targeted measures to mitigate human-wildlife conflicts in S3 (potential conflict area). To protect these species, international efforts to reduce carbon emissions, cross-administrative cooperation, and community-based conservation strategies are essential.},
}
@article {pmid40190731,
year = {2025},
author = {Atencio, B and Malavin, S and Rubin-Blum, M and Ram, R and Adar, E and Ronen, Z},
title = {Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533115},
pmid = {40190731},
issn = {1664-302X},
abstract = {Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the attached microbial communities is of paramount importance, especially in the context of biofouling. However, obtaining samples of attached microbes that thrive under natural (undisturbed) conditions is challenging. Our study addresses this by retrieving sessile microbes on-site. We installed columns filled with site-specific rock cuttings at the wellhead, allowing fresh groundwater to flow continuously for approximately 60 days. We hypothesized that the attached microbial communities would differ structurally from planktonic microbes due to the aquifer's lithological and mineralogical composition. This study involved an exploratory examination of the microbial communities in different aquifers with distinct mineralogies, including quartzitic sandstone, calcareous, chert, and highly heterogeneous (clastic) aquifers in Israel's Negev Desert. Metagenomic analysis revealed both shared and distinct microbial communities among attached and planktonic forms in the various environments, likely shaped by the aquifers' physical, lithological, and mineralogical properties. A wealth of carbon-fixation pathways and energy-conservation strategies in the attached microbiome provide evidence for the potential productivity of these biofilms. We identified widespread genetic potential for biofilm formation (e.g., via pili, flagella, and extracellular polymeric substance production) and the interactome (e.g., quorum-sensing genes). Our assessment of these functions provides a genomic framework for groundwater management and biofouling treatment.},
}
@article {pmid40190171,
year = {2025},
author = {Milev, M and Roglev, B and Kondeva Rogleva, M and Georgieva, M and Miloshev, G and Ruskovska, T},
title = {Impact of (poly)phenol-rich dietary sources on DNA damage: Insights from human intervention studies using the Comet assay - a review and perspective.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-40},
doi = {10.1017/S000711452500073X},
pmid = {40190171},
issn = {1475-2662},
abstract = {(Poly)phenols are plant-derived food bioactives abundantly present in human diet. They exert positive effects on various aspects of human health, and in particular in reducing the risk of chronic non-communicable diseases. Dietary (poly)phenols have been reported to improve vascular function, blood lipids, insulin sensitivity, and to decrease systemic inflammation. Evidence also suggests that (poly)phenols may exert protective effects on DNA, by reducing the extent of its damage. In recent years, advanced analytical methods, including transcriptomics, metabolomics, proteomics, and metagenomics, have been employed to unravel the complex impact of (poly)phenols in health and disease. Advances in bioinformatics enable an integrated multi-omics approach to data analysis, opening avenues for discovering new, previously unknown molecular mechanisms of action. Innovative solutions and automation of the Comet assay offer new opportunities for more in-depth analysis of the impact of (poly)phenols on DNA damage and its inclusion in integrative bioinformatic models. Such an approach has the potential to uncover new multi-level interactions and to reveal previously unknown factors underlying inter-individual variabilities in health-promoting effects of (poly)phenols. This review provides an insight into the application of the Comet assay in human intervention studies using (poly)phenol-rich dietary sources. Recent advancements in the Comet assay technology, and the prospects for more extensive use of this method in future human intervention studies with (poly)phenols could contribute to the development of personalized dietary recommendations for these plant-derived food bioactives.},
}
@article {pmid40190120,
year = {2025},
author = {Aboulalazm, FA and Kazen, AB and deLeon, O and Müller, S and Saravia, FL and Lozada-Fernandez, V and Hadiono, MA and Keyes, RF and Smith, BC and Kellogg, SL and Grobe, JL and Kindel, TL and Kirby, JR},
title = {Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2477819},
doi = {10.1080/19490976.2025.2477819},
pmid = {40190120},
issn = {1949-0984},
mesh = {Animals ; *Risperidone/adverse effects ; *Limosilactobacillus reuteri/metabolism ; *Weight Gain/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Antipsychotic Agents/adverse effects ; Probiotics/administration &amp; dosage ; Feces/microbiology ; Energy Metabolism/drug effects ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {The role of xenobiotic disruption of microbiota, corresponding dysbiosis, and potential links to host metabolic diseases are of critical importance. In this study, we used a widely prescribed antipsychotic drug, risperidone, known to influence weight gain in humans, to induce weight gain in C57BL/6J female mice. We hypothesized that microbes essential for maintaining gut homeostasis and energy balance would be depleted following treatment with risperidone, leading to enhanced weight gain relative to controls. Thus, we performed metagenomic analyses on stool samples to identify microbes that were excluded in risperidone-treated animals but remained present in controls. We identified multiple taxa including Limosilactobacillus reuteri as a candidate for further study. Oral supplementation with L. reuteri protected against risperidone-induced weight gain (RIWG) and was dependent on cellular production of a specialized metabolite, reutericyclin. Further, synthetic reutericyclin was sufficient to mitigate RIWG. Both synthetic reutericyclin and L. reuteri restored energy balance in the presence of risperidone to mitigate excess weight gain and induce shifts in the microbiome associated with leanness. In total, our results identify reutericyclin production by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.},
}
@article {pmid40189999,
year = {2025},
author = {Peng, K and Gao, Y and Li, C and Wang, Q and Yin, Y and Hameed, MF and Feil, E and Chen, S and Wang, Z and Liu, YX and Li, R},
title = {Benchmarking of analysis tools and pipeline development for nanopore long-read metagenomics.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2025.03.044},
pmid = {40189999},
issn = {2095-9281},
}
@article {pmid40189749,
year = {2025},
author = {Birebent, R and Drubay, D and Alves Costa Silva, C and Marmorino, F and Vitali, G and Piccinno, G and Hurtado, Y and Bonato, A and Belluomini, L and Messaoudene, M and Routy, B and Fidelle, M and Zalcman, G and Mazieres, J and Audigier-Valette, C and Moro-Sibilot, D and Goldwasser, F and Scherpereel, A and Pegliasco, H and Ghiringhelli, F and Reni, A and Barlesi, F and Albiges, L and Planchard, D and Martinez, S and Besse, B and Segata, N and Cremolini, C and Zitvogel, L and Iebba, V and Derosa, L},
title = {Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.},
journal = {Oncoimmunology},
volume = {14},
number = {1},
pages = {2484880},
doi = {10.1080/2162402X.2025.2484880},
pmid = {40189749},
issn = {2162-402X},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Dysbiosis/microbiology ; Middle Aged ; *Colorectal Neoplasms/mortality/microbiology/pathology ; Aged ; Prognosis ; *Carcinoma, Non-Small-Cell Lung/mortality/microbiology/pathology ; *Lung Neoplasms/mortality/microbiology/pathology ; Akkermansia/isolation &amp; purification ; *Urogenital Neoplasms/mortality/microbiology/pathology ; },
abstract = {Deviations in the diversity and composition of the gut microbiota are called "gut dysbiosis". They have been linked to various chronic diseases including cancers and resistance to immunotherapy. Stool shotgun based-metagenomics informs on the ecological composition of the gut microbiota and the prevalence of homeostatic bacteria such as Akkermansia muciniphila (Akk), while determination of the serum addressin MAdCAM-1 instructs on endothelial gut barrier dysfunction. Here we examined patient survival during chemo-immuno-therapy in 955 cancer patients across four independent cohorts of non-small cell lung (NSCLC), genitourinary (GU) and colorectal (CRC) cancers, according to hallmarks of gut dysbiosis. We show that Akk prevalence represents a stable and favorable phenotype in NSCLC and CRC cancer patients. Over-dominance of Akk above the healthy threshold was observed in dismal prognosis in NSCLC and GU and mirrored an immunosuppressive gut ecosystem and excessive intestinal epithelial exfoliation in NSCLC. In CRC, the combination of a lack of Akk and low sMAdCAM-1 levels identified a subset comprising 28% of patients with reduced survival, independent of the immunoscore. We conclude that gut dysbiosis hallmarks deserve integration within the diagnosis toolbox in oncological practice.},
}
@article {pmid40189708,
year = {2025},
author = {Gen-Jiménez, A and Flores-Félix, JD and Rincón-Molina, CI and Manzano-Gómez, LA and Villalobos-Maldonado, JJ and Ruiz-Lau, N and Roca-Couso, R and Ruíz-Valdiviezo, VM and Rincón-Rosales, R},
title = {Native Rhizobium biofertilization enhances yield and quality in Solanum lycopersicum under field conditions.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {4},
pages = {126},
pmid = {40189708},
issn = {1573-0972},
support = {19337.24-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; },
mesh = {*Solanum lycopersicum/growth &amp; development/microbiology ; *Rhizobium/physiology ; Soil Microbiology ; *Fertilizers ; Soil/chemistry ; Fruit/growth &amp; development ; Nitrogen/analysis/metabolism ; Microbiota ; Agriculture/methods ; },
abstract = {In response to growing concerns about the environmental and economic impacts of chemical fertilizers, this study explores the potential of biofertilization using native Rhizobium strains to enhance the growth, yield, and quality of Solanum lycopersicum (tomato) under field conditions. The experiment assessed the effects of Rhizobium biofertilization on plant performance and soil microbial communities by applying R. calliandrae, R. jaguaris, R. mayense, and a bacterial consortium, in comparison to conventional chemical fertilization. Key parameters such as plant height, fruit yield, macronutrient and micronutrient content, and fruit quality (lycopene and β-carotene levels) were measured. Results showed that R. calliandrae and R. jaguaris significantly enhanced fruit yield, nitrogen, potassium, manganese, and boron levels, while also improving fruit quality compared to the control. The impact of strain inoculation on the structure of the microbial community was also examined. Metataxonomic analysis of rhizospheric soils revealed no significant changes in microbial diversity, indicating that biofertilization with Rhizobium strains promotes plant growth without disrupting the composition of the soil microbiome. These findings suggest that Rhizobium biofertilization is a viable and sustainable alternative to chemical fertilizers, providing benefits to both crop productivity and soil health while minimizing the environmental footprint associated with conventional agricultural practices. The study underscores the importance of carefully selecting bacterial species with complementary functions to maximize the effectiveness of biofertilization strategies.},
}
@article {pmid40189564,
year = {2025},
author = {He, Y and Zhuo, S and Li, M and Pan, J and Jiang, Y and Hu, Y and Sanford, RA and Lin, Q and Sun, W and Wei, N and Peng, S and Jiang, Z and Li, S and Li, Y and Dong, Y and Shi, L},
title = {Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {94},
pmid = {40189564},
issn = {2049-2618},
support = {42472366, 92051111 and 42272353//National Natural Science Foundation of China/ ; 122-G1323522144//Fundamental Research Funds for the Chinese Central Government via China University of Geosciences (Wuhan)/ ; },
mesh = {*Symbiosis ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; Folic Acid/biosynthesis ; Ecosystem ; Phylogeny ; Genome, Bacterial ; *Microbiota ; },
abstract = {BACKGROUND: Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B9) were analyzed and assessed.<br><br>RESULTS: In the highly alkaline serpentinite-like ecosystem (pH&#x2009;=&#x2009;10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 &#x394;folA. Further assessment of the available CPR genomes (n&#x2009;=&#x2009;4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.<br><br>CONCLUSIONS: This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.},
}
@article {pmid40189545,
year = {2025},
author = {Serrana, JM and Nascimento, FJA and Dessirier, B and Broman, E and Posselt, M},
title = {Environmental drivers of the resistome across the Baltic Sea.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {92},
pmid = {40189545},
issn = {2049-2618},
mesh = {*Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; *Geologic Sediments/microbiology ; Metagenome ; Salinity ; Anti-Bacterial Agents/pharmacology ; Temperature ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.<br><br>RESULTS: We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150&#xa0;km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.<br><br>CONCLUSIONS: We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.},
}
@article {pmid40189243,
year = {2025},
author = {Chitcharoen, S and Sawaswong, V and Klomkliew, P and Chanchaem, P and Payungporn, S},
title = {Comparative analysis of human gut bacterial microbiota between shallow shotgun metagenomic sequencing and full-length 16S rDNA amplicon sequencing.},
journal = {Bioscience trends},
volume = {},
number = {},
pages = {},
doi = {10.5582/bst.2024.01393},
pmid = {40189243},
issn = {1881-7823},
abstract = {The human gut microbiome is increasingly recognized as important to health and disease, influencing immune function, metabolism, mental health, and chronic illnesses. Two widely used, cost-effective, and fast approaches for analyzing gut microbial communities are shallow shotgun metagenomic sequencing (SSMS) and full-length 16S rDNA sequencing. This study compares these methods across 43 stool samples, revealing notable differences in taxonomic and species-level detection. At the genus level, Bacteroides was most abundant in both methods, with Faecalibacterium showing similar trends but Prevotella was more abundant in full-length 16S rDNA. Genera such as Alistipes and Akkermansia were more frequently detected by full-length 16S rDNA, whereas Eubacterium and Roseburia were more prevalent in SSMS. At the species level, Faecalibacterium prausnitzii, a key indicator of gut health, was abundant across both datasets, while Bacteroides vulgatus was more frequently detected by SSMS. Species within Parabacteroides and Bacteroides were primarily detected by 16S rDNA, contrasting with higher SSMS detection of Prevotella copri and Oscillibacter valericigenes. LEfSe analysis identified 18 species (9 species in each method) with significantly different detection between methods, underscoring the impact of methodological choice on microbial diversity and abundance. Differences in classification databases, such as Ribosomal Database Project (RDP) for 16S rDNA and Kraken2 for SSMS, further highlight the influence of database selection on outcomes. These findings emphasize the importance of carefully selecting sequencing methods and bioinformatics tools in microbiome research, as each approach demonstrates unique strengths and limitations in capturing microbial diversity and relative abundances.},
}
@article {pmid40188788,
year = {2025},
author = {Lu, H and Miao, J and Zhang, N and Ji, J and Zhang, R and Zhu, S and Wei, X},
title = {Targeting regulation of nitrate removal and chlorophenol degradation through hydrogen/oxygen switching.},
journal = {Water research},
volume = {281},
number = {},
pages = {123581},
doi = {10.1016/j.watres.2025.123581},
pmid = {40188788},
issn = {1879-2448},
abstract = {Nitrate is a common co-contaminant with 2,4-dichlorophenol (2,4-DCP) in water, presenting a challenge for environmental remediation. Under anaerobic conditions, the ring cleavage of chlorophenol is inefficient, while under aerobic conditions, nitrate removal is hindered. In this study, a microbial consortium capable of hydrogenotrophic denitrification and 2,4-DCP degradation was cultured, aiming to achieve efficient nitrate removal and 2,4-DCP degradation by alternately switching between hydrogen (H2) and oxygen (O2). Under H2 conditions, nitrate removal exceeded 90 %, while under O2 conditions, 2,4-DCP degradation reached 100 %. Under H2 conditions, the abundance of the Nar gene which was involved in nitrate reduction was higher than that under O2 conditions, promoting hydrogenotrophic denitrification. In contrast, under O2 conditions, 2,4-DCP degradation occurred via hydroxylation, ring-cleavage, dechlorination, and mineralization through the TCA cycle. Metagenomic and metabolomic analysis was performed to explore microbial metabolic pathways and potential synergistic mechanisms involved in hydrogenotrophic denitrification and 2,4-DCP biodegradation. In the H2-atmosphere, microbes (Methylobacillus and Chromobacterium), genes (E3.1.1.45 and speG), and metabolites (Cytosine and Uridine) may play a crucial role in hydrogenotrophic denitrification. In the O2-atmosphere, the functional genus of Paracoccus and Aquamicrobium associated with genes (tfdB and tfdC) may contribute to 2,4-DCP and its metabolites 2-Chloromaleylacetate degradation. These findings confirmed the role of functional microbial communities through H2/O2 regulation. This work provides a promising technological reference for treating industrial wastewater containing phenols and nitrogen.},
}
@article {pmid40188743,
year = {2025},
author = {Deng, K and Wang, L and Nguyen, SM and Shrubsole, MJ and Cai, Q and Lipworth, L and Gupta, DK and Zheng, W and Shu, XO and Yu, D},
title = {A dietary pattern promoting gut sulfur metabolism is associated with increased mortality and altered circulating metabolites in low-income American adults.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105690},
doi = {10.1016/j.ebiom.2025.105690},
pmid = {40188743},
issn = {2352-3964},
abstract = {BACKGROUND: Excessive hydrogen sulfide in the gut, generated by sulfur-metabolising bacteria from foods, has been linked to intestinal inflammation and human diseases. We aim to investigate the interplay between diet and sulphur-metabolising bacteria in relation to mortality and circulating metabolites in understudied populations.<br><br>METHODS: In the Southern Community Cohort Study (SCCS), a prospective cohort of primarily low-income American adults, habitual diets were assessed using a food frequency questionnaire at baseline (2002-2009). A sulfur microbial diet score (SMDS) was developed among 514 Black/African American participants by linking habitual dietary intakes with the abundance of sulfur-metabolising bacteria profiled by faecal shotgun metagenomics. The SMDS was then constructed among all eligible SCCS participants (50,114 Black/African American and 23,923 non-Hispanic White adults), and its associations with mortality outcomes were examined by Cox proportional hazards model and Fine-Grey subdistribution hazard model. The association between SMDS and 1110 circulating metabolites was examined by linear regression among 1688 SCCS participants with untargeted metabolomic profiling of baseline plasma samples.<br><br>FINDINGS: Over an average 13.9-year follow-up, SMDS was associated with increased all-cause mortality (HR [95% CI] for the highest vs. lowest quartiles: 1.21 [1.15-1.27]) and cardiovascular disease (1.18 [1.08-1.29]), cancer (1.13&#xa0;[1.02-1.25]), and gastrointestinal cancer-specific (1.22 [1.00-1.49]) mortality among Black/African American participants (all P-trend<0.05). The associations were largely consistent across participant subgroups. Similar results were observed among non-Hispanic White participants. The SMDS was associated with 112 circulating metabolites, which mediated 36.15% of the SMDS-mortality association (P&#xa0;=&#xa0;0.002).<br><br>INTERPRETATION: A dietary pattern promoting sulfur-metabolising gut bacteria may contribute to increased total and disease mortality in low-income American adults.<br><br>FUNDING: This study was funded by the National Institutes of Health, United States, to Vanderbilt University Medical Center, United States, and Anne Potter Wilson Chair endowment to Vanderbilt University, United States.},
}
@article {pmid40188549,
year = {2025},
author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F},
title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138164},
doi = {10.1016/j.jhazmat.2025.138164},
pmid = {40188549},
issn = {1873-3336},
abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.},
}
@article {pmid40188455,
year = {2025},
author = {Li, Z and Xu, H and Zhang, L and Zhou, Y},
title = {Genome-Resolved Metagenomic and Metatranscriptomics Reveal Feammox Metabolism of Anaerobic Ammonia Oxidation Bacteria in Microaerobic Granular Sludge.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13580},
pmid = {40188455},
issn = {1520-5851},
abstract = {Anammox is an energy-efficient nitrogen removal process in which anammox bacteria (AnAOB) oxidize NH4[+]-N to N2 using NO2[-]-N as the electron acceptor. Recent evidence suggests that AnAOB can perform extracellular electron transfer (EET), potentially coupling Fe(III) reduction with NH4[+]-N oxidation (Feammox). However, whether AnAOB directly participate in Feammox within complex wastewater treatment systems remains unclear. Here, we investigated the iron-mediated nitrogen metabolism pathways in a microaerobic granular sludge (MGS) reactor by integrating enzyme inhibition assays with analyses of gene dynamics and co-occurrence patterns of nitrogen- and iron-cycling genes. Results demonstrate that AnAOB contributed to Feammox activity. The iron reduction gene CT573071, coding a porin-cytochrome c protein complex associated with EET, co-occurred with hao, hzsABC, and hdh genes in Candidatus Kuenenia, suggesting its role in Feammox. Furthermore, four high-quality metagenome-assembled genomes (MAGs) affiliated with Kuenenia stuttgartiensis_A harbored CT573071, hao-like, hzsABC, and hdh genes, along with the hao-cluster, which catalyzes the oxidation of NH4[+]-N to hydroxylamine. This genomic evidence further supports their dual metabolic capacity. Metatranscriptomic analysis confirmed CT573071 upregulation and its coexpression with the hao, hzsABC, and hdh genes. These findings establish the potential role of K. stuttgartiensis_A in Feammox, providing novel insights into nitrogen removal in low-strength wastewater treatment systems.},
}
@article {pmid40187695,
year = {2025},
author = {Palumbo, S and Lucarelli, G and Lasorsa, F and Damiano, R and Autorino, R and Aveta, A and Spena, G and Perdonà, S and Russo, P and Giulioni, C and Cafarelli, A and Finati, M and Siracusano, S and Pandolfo, SD},
title = {Urobiome and Inflammation: A Systematic Review on Microbial Imbalances and Diagnostic Tools for Urinary Disorders.},
journal = {Urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urology.2025.03.050},
pmid = {40187695},
issn = {1527-9995},
abstract = {OBJECTIVE: To synthesize current knowledge on urobiome alterations, innovative diagnostic advancements, and emerging therapeutic strategies targeting urobiome dysbiosis in inflammatory urinary tract disorders, including urinary tract infections (UTIs), non-gonococcal urethritis (NGU), and interstitial cystitis.<br><br>METHODS: A systematic review was conducted by screening the most important scientific databases. The search included the keywords: (microbiome) OR (microbial) OR (bacteria) OR (bacterial profile) AND (urine) OR (urinary) AND (first-morning sample) OR (first void). Only original studies in English involving human specimens were considered.<br><br>RESULTS: Of the 760 articles initially identified, a final sample of 20 original studies met the inclusion criteria. Disruptions in the urobiome composition were associated with increased colonization by pathogens such as Escherichia coli and Mycoplasma genitalium, resulting in inflammation and recurrent urinary conditions. Advanced diagnostic techniques, including metaproteomics, metagenomics, and point-of-care assays like NG-LFA, demonstrated enhanced capabilities for rapid pathogen detection and differentiation of inflammatory conditions. Therapeutic interventions targeting urobiome dysbiosis, particularly probiotics (Lactobacillus rhamnosus, L. reuteri, L. crispatus), showed promising efficacy in reducing recurrence and inflammation in clinical trials.<br><br>CONCLUSIONS: Urobiome dysbiosis plays a critical role in inflammatory urinary tract disorders. Innovative diagnostic methods and targeted therapeutic approaches, especially probiotics, offer substantial potential to improve patient outcomes. Further research is warranted to refine these strategies and validate their clinical applicability.},
}
@article {pmid40187301,
year = {2025},
author = {Peng, Q and Wu, Z and Qian, D and Ren, H and Xie, G},
title = {Comprehensive multi-omics analysis of secondary distillate from fermented Huangjiu residue: Insights into flavor formation and microbial dynamics.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144145},
doi = {10.1016/j.foodchem.2025.144145},
pmid = {40187301},
issn = {1873-7072},
abstract = {Huangjiu residue distillate, or Zaoshao, is a traditional Chinese liquor produced from the fermentation and distillation of Huangjiu lees. This study investigates the fermentation mechanisms and flavor formation of secondary Zaoshao, derived from the second round of Huangjiu lees fermentation, using flavoromics, amino acid and organic acid profiling, and metagenomics. Flavoromics identified ethyl octanoate, ethyl decanoate, ethyl dodecanoate, ethyl hexadecanoate, and ethyl (Z)-octadec-9-enoate as key flavor compounds. Amino acid and organic acid profiling showed continuous increases in amino acid content and significant changes in organic acids during fermentation. Metagenomics identified 9 dominant genera and 10 key species, with Saccharomyces, Saccharopolyspora, Aspergillus, Streptomyces, and Bacillus playing crucial roles in fermentation and flavor formation. These findings provide insights into microbial community functions and offer a foundation for regulating microbial consortia to enhance the flavor quality of secondary Zaoshao.},
}
@article {pmid40187295,
year = {2025},
author = {Coskuner-Weber, O and Alpsoy, S and Yolcu, O and Teber, E and de Marco, A and Shumka, S},
title = {Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.},
journal = {Computational biology and chemistry},
volume = {118},
number = {},
pages = {108444},
doi = {10.1016/j.compbiolchem.2025.108444},
pmid = {40187295},
issn = {1476-928X},
abstract = {The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.},
}
@article {pmid40187264,
year = {2025},
author = {Kwon, H and Li, B and Xu, M and Wang, Q and Maqbool, T and Lu, H and Winkler, M and Jiang, D},
title = {Minimizing byproduct formation in bioelectrochemical denitrification with anammox bacteria.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138110},
doi = {10.1016/j.jhazmat.2025.138110},
pmid = {40187264},
issn = {1873-3336},
abstract = {Autotrophic bioelectrochemical denitrification (BED) holds promise for nitrate remediation. However, the accumulation of byproducts such as NO2[-], N2O, and NH4[+], poses a significant challenge to effluent quality and climate adaptation. This study hypothesized that introducing anaerobic ammonium oxidation bacteria (anammox) to BED could alleviate this issue through synergy: a) anammox can utilize NH4[+] and NO2[-] from BED without producing N2O, as seen in canonical denitrification, and b) BED can recycle NO3[-] from the anammox anabolic pathway. Results showed that Anammox_BED reduced NO2[-] accumulation by two-thirds, lowered the relative abundance of N2O by 80 %, and eliminated NO. Metagenomic analysis revealed that the anammox species Ca. Brocadia sapporoensis tripled in abundance in the bulk sludge. Meanwhile, Pseudomonas stutzeri and Bosea robiniae, species capable of reducing nitrate via extracellular electron transfer (EET) and supplying NO2[-] to anammox, halved in relative abundance, while the abundance of Stenotrophomonas acidaminiphila, a non-EET, ammonia assimilation species, doubled following anammox introduction. Metatranscriptomic analysis found upregulation of denitrification-related functional genes in Anammox_BED biofilm and survival- and motility- related genes in bulk sludge, possibly due to insufficient substrate. Overall, BED-Anammox successfully diverted the rate-limiting EET nitrite reduction towards anammox-driven nitrite utilization thereby mitigating the generation of unwanted intermediates.},
}
@article {pmid40187012,
year = {2025},
author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A},
title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105089},
doi = {10.1016/j.psj.2025.105089},
pmid = {40187012},
issn = {1525-3171},
abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.},
}
@article {pmid40186063,
year = {2025},
author = {Saveetha, K and Somala, CS and Anand, T and Balamurugan, D and Vasudevan, V and Saravanan, KM and Senthil, R},
title = {Impact of Soil Microbiomes on Mung Bean Cultivation: Insights from 16S rRNA Metagenomics.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40186063},
issn = {1559-0305},
abstract = {Cyclic nutrient processes, soil health maintenance, and plant development are contingent upon soil microbiomes. The microbial makeup of the soil of Maruthupandiyar College, Thanjavur, is assessed using 16S rRNA gene sequencing. QIIME2, in conjunction with the SILVA database, analyzed the sequencing data to examine microbial diversity and composition. The experimental results revealed a diverse array of bacteria in soil physicochemical properties. The alpha and beta diversity assessment revealed significant microbial community complexity and distribution patterns disparities. The research revealed bacterial groups associated with biological nitrogen fixing, suggesting their potential to enhance mung bean growth. The current study illustrates the significance of microbial interactions in soil for sustaining soil fertility and enhancing crop output. Research findings provide essential insights into improving the sustainability of tropical agriculture through intentional microbial management to create sustainable soil health systems.},
}
@article {pmid40185904,
year = {2025},
author = {Wang, D and Gui, S and Pu, J and Zhong, X and Yan, L and Li, Z and Tao, X and Yang, D and Zhou, H and Qiao, R and Zhang, H and Cheng, X and Ren, Y and Chen, W and Chen, X and Tao, W and Chen, Y and Chen, X and Liu, Y and Xie, P},
title = {PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40185904},
issn = {1476-5578},
support = {CSTB2024NSCQ-MSX1027//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; CSTB2024NSCQ-QCXMX0033//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; 82371526//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info .},
}
@article {pmid40185827,
year = {2025},
author = {Chornchoem, P and Tandhavanant, S and Saiprom, N and Preechanukul, A and Thongchompoo, N and Sensorn, I and Chantratita, W and Chantratita, N},
title = {Metagenomic evaluation, antimicrobial activities, and immune stimulation of probiotics from dietary supplements and dairy products.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11537},
pmid = {40185827},
issn = {2045-2322},
support = {220211/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Probiotics/pharmacology ; *Dietary Supplements/microbiology ; *Dairy Products/microbiology ; *Metagenomics/methods ; Humans ; Lactobacillus/genetics ; Killer Cells, Natural/immunology/drug effects ; Bifidobacterium/genetics ; Animals ; Macrophages/immunology/drug effects ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Mice ; },
abstract = {Probiotics are widely marketed as dietary supplements and dairy products for their purported antimicrobial and immunomodulatory activities, often with limited supporting evidence. We identified and isolated probiotics from commercial dietary supplements and dairy products using metagenomics and cultured-based methods. We assessed their anti-bacterial activity against diverse pathogens and investigated their immunomodulatory effects on phagocytes and natural killer (NK) cells. Metagenomic analysis revealed that Lactobacillus and Bifidobacterium were the predominant genera in dietary supplements, while Streptococcus spp. was dominated in dairy products. However, only 37% of the predominant microorganisms identified by metagenomics were accurately listed on product labels. Among 70 representative probiotic strains, 4.3-17.1% probiotic strains demonstrated strong antibacterial-effects against pathogenic bacteria. Notably, specific strains of Bifidobacterium longum and Lactobacillus plantarum exhibited strong antagonistic activity against extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli. Some strains of Lactobacillus spp. significantly enhanced phagocytic activity in monocytes and increased IFN-γ production in NK cells, while members of Lactobacillus rhamnosus significantly suppressed TNF-α, IL-6, and IL-8 production in lipopolysaccharide-stimulated macrophages. In contrast, Bifidobacterium animalis stimulated the production of anti-inflammatory cytokines. This study highlights discrepancies in probiotic labeling and demonstrates the antimicrobial and immunomodulatory potential of specific probiotic strains, suggesting their utility in enhancing health and wellness.},
}
@article {pmid40185819,
year = {2025},
author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S},
title = {Oral microbiome dysbiosis in cryptogenic ischemic stroke patients with high-risk patent foramen ovale.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11535},
pmid = {40185819},
issn = {2045-2322},
support = {286246//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 355532//Research Council of Finland/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
mesh = {Humans ; *Foramen Ovale, Patent/complications/microbiology ; Female ; Male ; *Ischemic Stroke/microbiology/etiology/complications ; *Dysbiosis/microbiology/complications ; *Microbiota ; Adult ; Middle Aged ; Saliva/microbiology ; Case-Control Studies ; *Mouth/microbiology ; Risk Factors ; },
abstract = {Patent foramen ovale (PFO) is the most common congenital heart abnormality of foetal origin and has been associated with cryptogenic ischemic stroke (CIS) through several mechanisms, with most theories supporting paradoxical embolism. Other possible but unknown contributing factors, such as the role of the microbiome in PFO-associated strokes, remain unclear. We analysed saliva metagenomes to study the differences in the oral microbiome between young-onset CIS patients with clinically relevant high-risk PFO (n = 52) and those without PFO (n = 52). Age- and sex-matched stroke-free controls (n = 16) with high-risk PFO were included for the comparison. Beta diversity was significantly different between patients and controls with high-risk PFO, but not between patients with and without high-risk PFO. The phylum Ascomycota and class Saccharomycetes were significantly more abundant in patients with high-risk PFO than in those without high-risk PFO. Additionally, the abundance of Lactococcus, including Lactococcus raffinolactis and L. cremoris, was higher in controls with high-risk PFO than in patients with high-risk PFO. These findings highlight that oral dysbiosis and high-risk PFO may form a critical but under-recognized combination in the aetiology of CIS. Future research should focus on elucidating the precise mechanisms of these interactions and developing targeted interventions.},
}
@article {pmid40185271,
year = {2025},
author = {Guajardo-Leiva, S and Díez, B and Rojas-Fuentes, C and Chnaiderman, J and Castro-Nallar, E and Catril, V and Ampuero, M and Gaggero, A},
title = {From sewage to genomes: expanding our understanding of the urban and semi-urban wastewater RNA virome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121509},
doi = {10.1016/j.envres.2025.121509},
pmid = {40185271},
issn = {1096-0953},
abstract = {Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. In this study, we explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. We identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences from the Orthornavirae kingdom, clustering into 4,989 viral species. Using extensive databases of 14,150 family-level representative sequences, we classified 90% of our sequences at the family level. Our analysis revealed that treatment reduced viral richness and evenness (Shannon index), but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Species turnover, influenced by catchment area and treatment, accounted for 54% of sample dissimilarities (Weighted Unifrac). Biomarker analysis indicated that families like Astroviridae and Fiersviridae were more abundant in influents, while Reoviridae and Virgaviridae dominated effluents. This suggests that viral resistance to treatment varies and cannot be solely attributed to genome type, size, or morphology. We traced viral genomes through time and space, identifying sequences like the Pepper Mild Mottle Virus (PMMoV) from the Virgaviridae family over large distances and periods, highlighting its wastewater marker potential. High concentrations of human pathogens, such as Rotavirus (Reoviridae) and Human Astrovirus (Astroviridae), were found in both influents and effluents, stressing the need for continuous monitoring, especially for treated wastewater reuse.},
}
@article {pmid40185197,
year = {2025},
author = {Jiang, Y and Yang, J and Liu, Y and Liu, Y and Zhou, W and Yang, B and Hu, B and Wu, H},
title = {A Neonate with Meningitis Caused by probiotic-related Clostridium butyricum.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {107900},
doi = {10.1016/j.ijid.2025.107900},
pmid = {40185197},
issn = {1878-3511},
abstract = {Clostridium butyricum (C. butyricum), a normal gut bacterium in humans, is commonly used as a probiotic. We described a 26-day-old premature neonate who was diagnosed with probiotic-related C. butyricum meningitis. Upon the admission, suppurative meningitis was considered based on cerebrospinal fluid (CSF) biochemical test and neuroimaging examination, and C. butyricum was subsequently identified by CSF metagenomic next-generation sequencing. Given the history of administrating living C. butyricum products before admission, probiotics-associated suppurative meningitis was considered a high possibility, leading to the confirmation of anti-infection treatment including vancomycin and meropenem. Following this therapy, the infant's CSF profiles demonstrated improvement. Additionally, further phylogenetic analysis confirmed the high homologous of C. butyricum from CSF with probiotics. This is the first report of C. butyricum infection in neonates, highlighting the importance for prudence in administrating probiotics for neonates, particularly in high-risk groups such as preterm infants, those with central venous catheters and intestinal diseases.},
}
@article {pmid40185186,
year = {2025},
author = {Liu, Y and Pei, Y and Wang, H and Yang, Z},
title = {Lead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126187},
doi = {10.1016/j.envpol.2025.126187},
pmid = {40185186},
issn = {1873-6424},
abstract = {Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.},
}
@article {pmid40185016,
year = {2025},
author = {Yang, M and Yang, H and Wang, W and Fang, H and Huang, L and Li, D and Fu, L and Ding, S and Li, XD and Liu, CQ and Wei, G and Li, D and Cui, G and Fan, Z and Zeng, F},
title = {Impact of particle-attached microbial denitrification on N2O production in an agricultural-urban watershed.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125223},
doi = {10.1016/j.jenvman.2025.125223},
pmid = {40185016},
issn = {1095-8630},
abstract = {Anthropogenically influenced rivers are key hotspots for nitrous oxide (N2O) emissions. However, the seasonal and spatial heterogeneity of N2O emissions in subtropical riverine systems, particularly the role of particle-attached microbes (PAM) in regulating N2O production, remains poorly understood, contributing to uncertainties in global N2O estimates. This study investigates the potential impacts of PAM-driven nitrogen transformations on N2O production in the Dongjiang River under agricultural and urban influences. Water samples collected during the wet and dry seasons were analyzed for N2O concentrations, dual nitrogen-oxygen isotopes (δ[15]N-NO3[-], δ[18]O-NO3[-]), and metagenomic sequencing of PAM. All samples exhibited N2O supersaturation, with emissions significantly higher in the dry season than in the wet season. A linearly positive δ[15]N-δ[18]O correlation, accompanied by lower NO3[-] in the bottom layers than the surface layers in the dry season indicates active denitrification, leading to elevated N2O concentrations. PAM-driven denitrification was identified as the dominant nitrogen transformation process, supported by higher abundances of denitrification genes (nirKS, norBC, nosZ) relative to nitrification genes (amoABC). Despite aerobic water column conditions, low-oxygen microhabitats around suspended particles facilitated N2O production. A significantly positive correlation (p < 0.05, R[2] = 0.42) between N2O concentrations and the nirK/nosZ gene ratio suggests that gene expression imbalances contributed to net N2O accumulation. Additionally, the downstream urban area exhibited lower DO and higher DOC levels, enhancing denitrification and increasing N2O production by 4.7 % compared to the upstream agricultural region. Seasonal differences further influenced N2O dynamics: higher DOC/NO3[-] ratios in the dry season promoted heterotrophic denitrification, while elevated temperatures in the wet season favored complete denitrification, reducing N2O emissions. These findings provide critical insights into PAM-driven nitrogen cycling, informing strategies for mitigating N2O emissions and managing nitrogen pollution in subtropical riverine systems.},
}
@article {pmid40184966,
year = {2025},
author = {Tu, M and Lin, H and Zhang, X and Zhang, X and Yan, J},
title = {Elemental sulfur facilitates co-metabolism of Cr(VI) and nitrate by autotrophic denitrifiers in constructed wetlands.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138153},
doi = {10.1016/j.jhazmat.2025.138153},
pmid = {40184966},
issn = {1873-3336},
abstract = {The antagonistic microbial reduction of chromate and nitrate poses significant challenges for their simultaneous removal in autotrophic denitrifying systems. This study explored the treatment performance and mechanisms for the simultaneous removal of chromate (0, 2, and 10 mg·L[-1]) and nitrate (20 mg·L[-1]) in constructed wetland (CW) microcosms with elemental sulfur additions at 0-, 5-, and 25-times background levels. Results showed that sulfur-amended microcosms achieved chromate and nitrate removal up to 76.46 % and 28.12 % higher, respectively, than 0S groups. Notably, the nitrate removal rate constant was higher in the presence of chromate than its absence, exclusively in the 25S groups. In a sediment core assay, the 25S groups also exhibited substantially facilitating effect of chromate removal potential in the presence of nitrate. Metagenomic analyses revealed upregulations of denitrification and sulfur oxidation-related functional genes along with sulfur supplementation. Autotrophic denitrifiers including Dechloromonas, Thiobacillus, Sulfuricella, and Sulfuritalea made significant contributions to chromate and nitrate removal rates, as well as functional genes encoding sulfur, nitrogen, and chromium transformation, in response to sulfur addition. These findings shed first light on the co-metabolism of chromate and nitrate by sulfur-based autotrophic denitrifiers, emphasizing their pivotal role in denitrification systems, e.g., CWs, with chromate inputs.},
}
@article {pmid40184824,
year = {2025},
author = {Zhu, H and Mao, X and Sajnani, S and Yang, H and Li, T and Tan, S},
title = {Psychrophilic insights into petroleum degradation: Gene abundance dynamics.},
journal = {Enzyme and microbial technology},
volume = {188},
number = {},
pages = {110642},
doi = {10.1016/j.enzmictec.2025.110642},
pmid = {40184824},
issn = {1879-0909},
abstract = {Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.},
}
@article {pmid40184708,
year = {2025},
author = {He, D and Nong, Y and He, Y and Luo, Y and Li, C and Gao, J and Dang, C and Fu, J},
title = {Effect of pre-chlorination on bioelectricity production and stabilization of excess sludge by microbial fuel cell.},
journal = {Water research},
volume = {281},
number = {},
pages = {123564},
doi = {10.1016/j.watres.2025.123564},
pmid = {40184708},
issn = {1879-2448},
abstract = {Microbial fuel cell (MFC) is a technology that can generate electricity while degrading excess sludge. However, the complex components, intricate biological structures, and inhibitory compounds in sludge limit the application of MFC. Therefore, this study utilized chlorination as a sludge pretreatment method to improve the comprehensive performance of MFC in sludge treatment. Results showed that pre-chlorination at a dose of 0.2 mg/L increased output voltage of MFC by 500 % from approximately 100 mV to around 600 mV, and power density by 15.60 % from 3.15 W/m[3] to 3.64 W/m[3], and simultaneously increased the degradation of sludge MLSS (mixed liquor suspended solids), MLVSS (mixed liquor volatile suspended solids), EPS (extracellular polymeric substances) polysaccharide and protein by 9.64 %, 47.07 %, 18.63 % and 16.26 %, respectively. Molecular composition analysis of EPS in sludge by three-dimensional excitation emission matrix fluorescence spectroscopy (3D-EEM), Fourier transform infrared spectroscopy (FTIR) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated pre-chlorination significantly promoted the molecular transformation in MFC. The microbiome analysis of anode biofilm in MFC by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), metagenomics and metametabolomics revealed that pre-chlorination facilitated the development of biomass, enrichment of electricity-producing bacteria (EPB), enhancement of electricity-producing activity and metabolic activity. Moreover, the sludge EPS was the importance source for the microbial metabolites in MFC was validated by the joint analysis of FT-ICR-MS and metametabolomics.},
}
@article {pmid40184705,
year = {2025},
author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K},
title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.},
journal = {Water research},
volume = {281},
number = {},
pages = {123553},
doi = {10.1016/j.watres.2025.123553},
pmid = {40184705},
issn = {1879-2448},
abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.},
}
@article {pmid40184632,
year = {2025},
author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T},
title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf058},
pmid = {40184632},
issn = {1751-7370},
abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.},
}
@article {pmid40184383,
year = {2025},
author = {Shen, C and Wedell, E and Pop, M and Warnow, T},
title = {TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012593},
pmid = {40184383},
issn = {1553-7358},
mesh = {*Metagenomics/methods ; Algorithms ; *Software ; Computational Biology/methods ; Databases, Genetic ; Likelihood Functions ; Sequence Analysis, DNA/methods ; },
abstract = {We present TIPP3 and TIPP3-fast, new tools for abundance profiling in metagenomic datasets. Like its predecessor, TIPP2, the TIPP3 pipeline uses a maximum likelihood approach to place reads into labeled taxonomies using marker genes, but it achieves superior accuracy to TIPP2 by enabling the use of much larger taxonomies through improved algorithmic techniques. We show that TIPP3 is generally more accurate than leading methods for abundance profiling in two important contexts: when reads come from genomes not already in a public database (i.e., novel genomes) and when reads contain sequencing errors. We also show that TIPP3-fast has slightly lower accuracy than TIPP3, but is also generally more accurate than other leading methods and uses a small fraction of TIPP3's runtime. Additionally, we highlight the potential benefits of restricting abundance profiling methods to those reads that map to marker genes (i.e., using a filtered marker-gene based analysis), which we show typically improves accuracy. TIPP3 is freely available at https://github.com/c5shen/TIPP3.},
}
@article {pmid40183829,
year = {2025},
author = {Moscona, R and Wagner, T and Geva, M and Bucris, E and Erster, O and Zuckerman, NS and Mor, O},
title = {Newly designed amplicons-based method for near-full-length genome (NFLG) sequencing of HIV-1 group M recombinant forms.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {362},
pmid = {40183829},
issn = {1573-4978},
mesh = {*HIV-1/genetics ; Humans ; *Genome, Viral/genetics ; Phylogeny ; HIV Infections/virology/genetics ; Recombination, Genetic/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; Genotype ; },
abstract = {BACKGROUND: Over the years the spread of HIV-1 across the globe resulted in the creation of multiple subtypes and new recombinant forms (RFs). While the pol gene region of the HIV-1 genome is used for resistance mutations analysis and initial detection of RFs, whole genome sequencing analysis is required to determine recombination events across the viral genome. Here, we present a newly designed robust near-full length genome (NFLG) sequencing approach for the sequencing of HIV-1 genomes, out of clinical whole blood samples. This method has been successfully tested for various HIV-1 subtypes and RFs.<br><br>METHODS AND RESULTS: The method is based on an in-house developed set of 32 pan-genotypic primer pairs, divided into two pools, each containing 16 primer pairs covering the entire HIV-1 genome. Two parallel multiplex PCR reactions were used to generate 32 overlapping DNA fragments spanning the HIV-1 genome. Nextera XT protocol was used to obtain barcoded DNA libraries, which were sequenced with the Illumina Miseq platform using a V3 kit. A consensus sequence was determined for each sample and was used to define recombination events across the genome. For this aim, a combined analysis of several computational tools including HIV BLAST, phylogenetic analysis, RIP, SimPlot&#x2009;+&#x2009;&#x2009;+&#x2009;and jpHMM were employed. Overall, plasma samples from 33 patients suspected to carry RFs and 2 different, known pure subtypes controls, were included in this study. Genome coverage varied between RFs, while the gag and pol genes were nearly fully covered, the highly variable env gene region was not. Yet, these NFLG analyses enabled the identification of recombination events genome wide.<br><br>CONCLUSIONS: In summary, we describe a methodology for HIV-1 NFLG sequencing, which is based on partially overlapping, multiple PCR fragments, spanning the HIV-1 genome. Additionally, this newly refined method was compared to HIV-1 NFLG results of PCR-free metagenomic sequencing and proved to obtain greater coverage of the HXB2 reference genome. Yet, further testing and validation on a larger cohort is required. Still, this method enables sequencing of 20 different patient samples in a single MiSeq sequencing run and was used for the characterization of different HIV-1 RFs and pure subtypes circulating in Israel.},
}
@article {pmid40183042,
year = {2025},
author = {Li, T and Shafiul Alam, M and Yang, Y and Mohammad Al-Amin, H and Rahman, M and Islam, F and Conte, MA and Price, DC and Hang, J},
title = {Metagenome analysis of viruses associated with Anopheles mosquitoes from Ramu Upazila, Cox's Bazar District, Bangladesh.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19180},
pmid = {40183042},
issn = {2167-8359},
mesh = {*Anopheles/virology ; Animals ; Bangladesh ; Phylogeny ; *Mosquito Vectors/virology ; *Metagenome ; Male ; Female ; High-Throughput Nucleotide Sequencing ; },
abstract = {Bangladesh has a warm climate and landscapes favourable for the proliferation of mosquitoes. Mosquito-borne pathogens including malaria and arthropod-borne viruses (arboviruses) remain a serious threat to the public health requiring constant vector control and disease surveillance. From November 2018 to April 2019, Anopheles mosquitoes were collected in three unions in the Ramu Upazila (sub-district) of Cox's Bazar District, Bangladesh. The mosquito specimens were combined into pools based on date of collection, household ID, and sex. Metagenome next-generation sequencing was conducted to elucidate diversity of virus sequences in each pool. Homology-based taxonomic classification and phylogenetic analyses identified a broad diversity of putative viruses from 12 known families, with additional unclassified viruses also likely present. Analysis of male mosquitoes showed some of these viruses are likely capable of being vertically transmitted. Moreover, many of the assembled virus sequences share homology and phylogenetic affinity with segments in sequenced Anopheles genomes, and may represent endogenous viral elements derived from a past evolutionary relationship between these putative viruses and their mosquito hosts.},
}
@article {pmid40182804,
year = {2025},
author = {Sarwar, A and Aslam, B and Mahmood, S and Muzammil, S and Siddique, AB and Sarwar, F and Khurshid, M and Rasool, MH and Sasanya, J and Aljasir, SF},
title = {Distribution of multidrug-resistant Proteus mirabilis in poultry, livestock, fish, and the related environment: One Health heed.},
journal = {Veterinary world},
volume = {18},
number = {2},
pages = {446-454},
doi = {10.14202/vetworld.2025.446-454},
pmid = {40182804},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The emergence of multidrug-resistant (MDR) Proteus mirabilis in food-producing animals and their associated environments is a growing public health concern. The indiscriminate use of antimicrobials in animal husbandry exacerbates resistance development, posing significant threats to food safety and sustainability. This study investigates the distribution, antibiotic resistance patterns, and virulence-associated genes (VAGs) of P. mirabilis isolated from poultry, livestock, fish, and their environments in Pakistan under a One Health perspective.<br><br>MATERIALS AND METHODS: A total of 225 samples were collected from poultry (n = 100), livestock (n = 75), and aquatic sources (n = 50) from March 2023 to September 2024. Standard microbiological methods were employed for the isolation and identification of P. mirabilis. Polymerase chain reaction (PCR)-based detection of antibiotic resistance genes and VAGs was performed using specific primers. Antibiotic susceptibility was assessed through the disk diffusion method following Clinical and Laboratory Standards Institute 2022 guidelines. Statistical analyses, including analysis of variance and correlation models, were applied to assess the relationships between variables.<br><br>RESULTS: P. mirabilis was detected in 28.44% (64/225) of the total samples, with the highest occurrence observed in poultry (38%), followed by livestock (22.67%) and aquatic sources (18%). Resistance to ampicillin (100%), chloramphenicol (82%), cefepime (75%), and ciprofloxacin (75%) was widespread. PCR analysis revealed a high occurrence of extended-spectrum beta-lactamase-producing P. mirabilis carrying bla CTX-M (49%), bla OXA (54%), and bla TEM (25.67%) genes. In addition, VAGs such as zapA (39.53%), ucaA (34.88%), and hpmA (32.55%) were frequently identified. The presence of MDR P. mirabilis in fish and related environments (18%) is alarming, highlighting potential zoonotic and foodborne transmission risks.<br><br>CONCLUSION: The study underscores the widespread distribution of MDR P. mirabilis in animal-based food sources, raising significant concerns regarding food safety and antimicrobial resistance. The findings reinforce the need for stringent monitoring and regulatory policies to mitigate MDR bacterial dissemination across the food supply chain. Future research should employ metagenomic approaches for comprehensive surveillance and risk assessment.},
}
@article {pmid40182766,
year = {2025},
author = {Lazarevic, V and Gaïa, N and Pham, TT and de Lorenzi-Tognon, M and Girard, M and Mauffrey, F and Charretier, Y and Renzi, G and Huber, C and Schrenzel, J},
title = {Identification of causative agents of infective endocarditis by metagenomic next-generation sequencing of resected valves.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1532257},
doi = {10.3389/fcimb.2025.1532257},
pmid = {40182766},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Middle Aged ; Female ; *Heart Valves/microbiology/surgery ; Sensitivity and Specificity ; Aged ; *Endocarditis/microbiology/diagnosis/surgery ; Prospective Studies ; *Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Infective endocarditis (IE) is a rare and life-threatening condition with considerable mortality rates. Diagnosis is often complicated by negative blood culture results, limiting the accurate identification of causative pathogens. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) of cardiac valve specimens compared to conventional clinical laboratory methods for identifying pathogens in IE.<br><br>METHODS: Nineteen patients with suspected IE who were scheduled for surgical valve removal were prospectively enrolled. The metagenomic workflow included bacterial DNA enrichment from resected valves using the Molzym Ultra-Deep Microbiome Prep, sequencing of metagenomic libraries using the Illumina MiSeq platform, and Kraken 2 taxonomic assignments based on read data.<br><br>RESULTS: Valve mNGS achieved a sensitivity of 82.4% and a specificity of 100% relative to the final adjudicated pathogen diagnosis. Blood culture, considered the reference standard, exhibited slightly higher sensitivity (88.2%) with comparable specificity (100%). In comparison, valve culture (sensitivity: 29.4%, specificity: 50.0%) and microscopy (sensitivity: 35.3%, specificity: 100%) showed lower diagnostic performance. Delays between blood culture negativization and valve resection impacted mNGS sensitivity, likely due to pathogen clearance. Notably, valves resected within 12 days from blood culture negativization achieved 100% diagnostic accuracy, emphasizing the importance of timing for optimal mNGS results.<br><br>CONCLUSION: This study underscores mNGS as a valuable diagnostic tool for detecting IE pathogens, complementing traditional diagnostic methods. The detection of antibiotic resistance genes and multi-locus sequence typing profiles in some samples further demonstrated its utility.},
}
@article {pmid40182295,
year = {2025},
author = {Hou, J and Yin, H and Wang, D and Luo, J and Yang, W and Kang, T},
title = {The influence of rhizosphere soil microorganisms and environmental factors on gentiopicroside content in the roots and rhizomes of Gentiana scabra Bunge from Liaoning Province.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1554981},
doi = {10.3389/fmicb.2025.1554981},
pmid = {40182295},
issn = {1664-302X},
abstract = {BACKGROUND: Rhizosphere soil microorganisms, as the second genome of plants, play an important role in the formation of secondary metabolites of medicinal plants and are one of the key factors in the formation of the authenticity of medicinal materials.<br><br>METHODS: In this paper, the rhizosphere soils of Gentiana scabra Bunge from six producing areas in Liaoning Province were taken as the research objects. Through high-throughput sequencing technology, and with the help of PLS-DA and RDA, the impacts of rhizosphere soil microorganisms and environmental factors on the quality of G. scabra were explored in depth.<br><br>RESULTS: Alpha diversity shows that the diversity of bacterial communities varies significantly, while the regularity of fungi is weak; beta diversity shows that samples from different producing areas can be effectively grouped according to community structure. LDA effect shows that the differential species of bacteria and fungi vary among different producing areas. Indicator and random forest analysis show that Sphingomonas and Subgroup_2 are the main indicator species of the bacterial communities in the high-content group, which can increase the evenness of microbial communities and maintain or enhance species diversity. The regularity of fungal communities is relatively weak. Functional metagenomic analysis shows that the functions of soil microorganisms in the six producing areas are similar but the relative abundances are different. The main functions of bacteria are closely related to microbial metabolism in diverse environments, biosynthesis of secondary metabolites, metabolic pathways, etc.; fungi are mainly lichen parasite, plant saprotroph, and ericoid mycorrhizal. PLS-DA and RDA analysis show that properly adjusting the key environmental factors of Ca, pH, and rapidly available potassium, which have a great influence on G. scabra, can affect the abundances of microorganisms such as Subgroup_2, Burkholderia-Caballeronia-Paraburkholderia, Metarhizium, Bryobacter, Fusarium, Rhodanobacter, Cladophialophora, Sphingomonas and Trichoderma, and then regulate the content of gentiopicroside.<br><br>DISCUSSION: This study provides practical microbial approaches and strategies for improving gentiopicroside content in the roots and rhizomes of G. scabra, and lays a solid scientific foundation for ensuring the quality and safety of genuine medicinal materials and the stable and sustainable development of the G. scabra planting industry.},
}
@article {pmid40182288,
year = {2025},
author = {Lin, TS and Zhu, Z and Lin, X and Huang, HY and Li, LP and Li, J and Ni, J and Li, P and Chen, L and Tang, W and Liu, H and Se, X and Xie, M and Long, C and Chiu, CM and Fang, SH and Zhao, J and Lin, YC and Yu, X and Huang, HD},
title = {Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538265},
doi = {10.3389/fmicb.2025.1538265},
pmid = {40182288},
issn = {1664-302X},
abstract = {Bloodstream infections (BSIs) pose a significant diagnostic challenge, largely due to the limitations of traditional methods such as blood cultures. These methods often yield low positive rates, have lengthy processing times that delay treatment, and are limited in detecting only a narrow range of pathogens. Such delays and inaccuracies can critically impede timely clinical interventions, potentially compromising patient outcomes. Next-generation sequencing (NGS) is a powerful tool for rapid, precise pathogen identification. While metagenomic NGS (mNGS) offers broad pathogen coverage, it is often costly and complex. Targeted NGS (tNGS), however, focuses on key regions of clinically relevant pathogens, reducing costs and simplifying workflows while maintaining high sensitivity, making it more practical for routine diagnostics. In this study, we introduce a novel approach combining a human cell-specific filtration membrane with a multiplex tNGS panel to overcome these challenges. The filtration membrane, designed with surface charge properties to be electrostatically attractive to leukocytes for the selective capture of specific cells, demonstrated high efficiency in removing host cells and nucleic acids, achieving over a 98% reduction in host DNA and thereby minimizing background interference in pathogen detection. Additionally, we developed an effective multiplex tNGS panel targeting over 330 clinically relevant pathogens and verified its consistency with mNGS and blood culture results, demonstrating a significant improvement in detection sensitivity. By integrating these two methods, we achieved a synergistic enhancement in diagnostic capability, boosting pathogen reads by 6- to 8-fold, which enabled reliable identification even in cases of low-abundance pathogens. This approach provides faster, more accurate, and more sensitive detection of BSIs, enabling earlier identification of infections. This facilitates timely and targeted treatment, ultimately improving patient outcomes in critical care settings. Given the unique properties of the filtration membrane and the strengths of the tNGS panel, this approach shows promising applications in prenatal and genetic health support, as well as in advancing early cancer screening strategies.},
}
@article {pmid40182062,
year = {2025},
author = {Simon, SA and Soares, AR and Bornemann, TLV and Lange, A and Griesdorn, L and Fuentes, A and Dieckmann, M and Krok, BA and Ruff, SE and Hügler, M and Moraru, C and Probst, AJ},
title = {Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf041},
doi = {10.1093/ismeco/ycaf041},
pmid = {40182062},
issn = {2730-6151},
abstract = {Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2'-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.},
}
@article {pmid40182061,
year = {2025},
author = {Cheung, S and Morando, M and Magasin, J and Cornejo-Castillo, FM and Zehr, JP and Turk-Kubo, KA},
title = {NifH gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf038},
doi = {10.1093/ismeco/ycaf038},
pmid = {40182061},
issn = {2730-6151},
abstract = {Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase (nifH) gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived nifH sequences (e.g. Planctomycete- and Proteobacteria-affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that nifH amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the nifH genes. This is demonstrated by the presence of nifH genes that contain the nucleotide mismatches in a recent compilation of global ocean nifH amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived nifH genes accounted for 4.4% of the total amplicon sequence variants from the global ocean nifH amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that nifH amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups.},
}
@article {pmid40181528,
year = {2025},
author = {Sun, Q and Teng, R and Shi, Q and Liu, Y and Cai, X and Yang, B and Cao, Q and Shu, C and Mei, X and Zeng, W and Hu, B and Zhang, J and Qiu, H and Liu, L},
title = {Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.},
journal = {Clinical and translational medicine},
volume = {15},
number = {4},
pages = {e70297},
doi = {10.1002/ctm2.70297},
pmid = {40181528},
issn = {2001-1326},
support = {2022YFC2504405//National Key Research and Development Program of China/ ; 82341032//National Natural Science Foundation of China/ ; 81930058//National Natural Science Foundation of China/ ; 82270083//National Natural Science Foundation of China/ ; LGY2022025//Second Level Talents of the '333 High Level Talents Training Project' in the sixth phase in Jiangsu/ ; ZDXYS202205//Jiangsu Provincial Medical Key Laboratory/ ; HMJH-2020-0005//Hongmian Plan' Project of Guangzhou/ ; },
mesh = {Humans ; *Sepsis/diagnosis/microbiology/blood/drug therapy ; *Metagenomics/methods ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; Blood Culture/methods ; },
abstract = {BACKGROUND: Accurate pathogen identification is critical for managing sepsis. However, traditional microbiological methods are time-consuming and exhibit limited sensitivity, particularly with blood samples. Metagenomic sequencing of plasma or whole blood was highly affected by the proportion of host nucleic acid.<br><br>METHODS: We developed a Probe-Capture Metagenomic assay and established a multicentre prospective cohort to assess its clinical utility. In this study, 184 blood samples from patients suspected of sepsis were sent for blood culture and Probe-Capture Metagenomic sequencing before using antibiotics. The pathogen-positive rate and auxiliary abilities in diagnosis were compared among Probe-Capture Metagenomics, blood culture and real-time PCR (RT-PCR). Antibiotic therapy adjustments were based on the identification of pathogens, and changes in the Sequential Organ Failure Assessment (SOFA) score were monitored on days 0, 3 and 7 of admission.<br><br>RESULTS: A total of 184 sepsis patients were enrolled, with a mean age of 66 years (range 56-74). The Probe-Capture Metagenomics method, confirmed by RT-PCR, demonstrated a significantly higher pathogen detection rate than blood culture alone (51.6%&#xa0;vs. 17.4%, p&#xa0;<&#xa0;.001). When combining the results of blood culture and RT-PCR, Probe-Capture Metagenomics achieved a concordance rate of 91.8% (169/184), with a sensitivity of 100% and specificity of 87.1%. In terms of clinical impact, antibiotic therapy was adjusted for 64 patients (34.8%) based on the results from Probe-Capture Metagenomics, and 41 patients (22.3%) showed a&#xa0;>&#xa0;2-point decrease in SOFA score following antibiotic adjustments.<br><br>CONCLUSION: Probe-Capture Metagenomics significantly enhances the ability of pathogen detection compared with traditional metagenomics. Compared to blood culture and RT-PCR in sepsis patients, it leads to improved antibiotic treatment and better patient outcomes. This study, for the first time, evaluates the clinical impact of metagenomic sequencing by integrating antibiotic adjustments and SOFA score changes, indicating that approximately one-fifth of sepsis patients benefit from this advanced diagnostic approach.<br><br>TRIAL REGISTRATION: This study has been registered in clinical trials (clinicaltrials.gov) on 30 November 2018, and the registration number is NCT03760315.<br><br>KEY POINTS: Probe-Capture Metagenome had a significantly higher positive rate than blood culture (51.6%&#xa0;vs. 17.4%, p&#xa0;<&#xa0;.001). Combining blood culture and RT-PCR results, Probe-Capture Metagenome achieved a consistency rate of 91.8%. Antibiotics were adjusted in 34.8% of patients based on Probe-Capture Metagenome results, and 22.3% of patients experienced a more than 2-point decrease in SOFA score.},
}
@article {pmid40181443,
year = {2025},
author = {Xu, F and Chen, C and Lu, S and Xue, M and Ding, H and Song, Y and Zhang, Y and Sun, K and Tang, L and Wang, W and Wang, M and Tang, Y and Tan, D and Yao, C and Shi, D and Mao, E and Shao, M and Ying, Y and Zhou, C and Huang, L and Peng, H and Kuang, Z and Wang, S and Ma, Q and Sun, S and Guo, D and Gu, T and Yang, B and Ma, L and Gao, C and Lu, X and Zhang, H and Wang, R and Tong, C and Song, Z},
title = {Impact of metagenomics next-generation sequencing on etiological diagnosis and early outcomes in sepsis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {394},
pmid = {40181443},
issn = {1479-5876},
support = {2021YFC2501800//Key Technologies Research and Development Program/ ; 2023YFC0872500//Key Technologies Research and Development Program/ ; 2023YFC3043507//Key Technologies Research and Development Program/ ; 82072214//National Natural Science Foundation of China/ ; 23Y31900100//Science and Technology Commission of Shanghai Municipality/ ; 21MC1930400//Science and Technology Commission of Shanghai Municipality/ ; PWYts2021-17//Shanghai Pudong New Area Health Commission/ ; },
mesh = {Humans ; *Sepsis/diagnosis/microbiology/etiology/mortality ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Aged ; Treatment Outcome ; Prognosis ; Prospective Studies ; Adult ; },
abstract = {BACKGROUND: Clinical implications of metagenomics next-generation sequencing (mNGS) in sepsis have not been fully evaluated. This study aimed to determine the diagnostic, therapeutic, and prognostic impacts of mNGS in sepsis.<br><br>METHODS: This multicenter prospective study was conducted at 19 sites in China from 2020 to 2021, and 859 adult patients hospitalized with sepsis were enrolled. The advantages, challenges, knowledge gaps and privacy risks of mNGS were carefully introduced to all participants, and participants chose on their own to either receive conventional microbiological test (CMT) alone (conventional-test-only group, n&#x2009;=&#x2009;394) or receive mNGS test along with CMT (combined test group, n&#x2009;=&#x2009;465). For prognostic analysis, the primary endpoint was 28-day mortality. Secondary endpoints included 7-day mortality and average per-day hospital cost. Inverse probability of treatment weighting was used to balance covariates between groups. Concurrent CMT and mNGS results from patients in the combined test group were used for diagnostic analyses. Therapeutic impact of mNGS was evaluated based on subsequent antibiotic adjustment.<br><br>RESULTS: Compared with composite reference standard, the positive percent agreement of mNGS among infected site samples was significantly higher than that of CMT (92.0% [95% CI, 88.7 to 94.5] vs. 51.1% [95% CI, 45.9 to 56.2], p&#x2009;<&#x2009;0.001), while the negative percent agreement of mNGS was inferior to that of CMT (39.6% [95% CI, 29.5 to 50.4] vs. 69.2% [95% CI, 58.7 to 78.5], p&#x2009;<&#x2009;0.001). The mNGS test identified causal microbes in 344 (74.0%) patients, and concomitant antibiotic changes occurred in 136 patients (29.2%). Death by day 7 occurred in 24 of 465 (5.2%) patients in the combined test group and in 34 of 394 (8.6%) patients in the conventional-test-only group (hazard ratio, 0.44 [95% CI, 0.26 to 0.77], p&#x2009;=&#x2009;0.004). However, no significant difference in 28-day mortality was observed between two study groups (hazard ratio, 0.82 [0.56 to 1.20], p&#x2009;=&#x2009;0.300).<br><br>CONCLUSIONS: The mNGS test of infected site samples exhibited 40% higher pathogen detection rate than CMT in patients with sepsis, which led to improved etiological diagnosis and tailored antibiotic therapy. Additional use of mNGS halved the risk of early death in 7 days, but did not improve 28-day survival in patients with sepsis.<br><br>TRIAL REGISTRATION: chictr.org.cn Identifier: ChiCTR2000031113. Registered 22 March 2020.},
}
@article {pmid40181255,
year = {2025},
author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C},
title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {193},
pmid = {40181255},
issn = {1471-2180},
support = {P 32697//Austrian Science Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation &amp; purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.<br><br>METHODS: Shotgun metagenomic data from the stool samples of young adults (n&#x2009;=&#x2009;127, Age: 19-59 y), older adults (n&#x2009;=&#x2009;86, Age: 60-99 y), and centenarians (n&#x2009;=&#x2009;34, age: 100-109 years) were analyzed.<br><br>RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.<br><br>CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.},
}
@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}
@article {pmid40180909,
year = {2025},
author = {Bedarf, JR and Romano, S and Heinzmann, SS and Duncan, A and Traka, MH and Ng, D and Segovia-Lizano, D and Simon, MC and Narbad, A and Wüllner, U and Hildebrand, F},
title = {A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {66},
pmid = {40180909},
issn = {2373-8057},
support = {BB/CCG2260/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Current treatment of Parkinson's Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required. A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD. A prospective, controlled pilot study (DRKS00034528) was conducted on 11 couples (PD patient plus healthy spouse as control (CO)). Participants followed a 4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose. Gut metagenomes, faecal and urinary metabolites, and clinical characteristics were assessed. The dietary intervention significantly augmented faecal SCFA and increased Bifidobacteria spp., reducing PD-related gastrointestinal symptoms. The pre-existing bacterial dysbiosis in PD (depletion of Blautia, Dorea, Erysipelatoclostridium) persisted. Bacterial metabolite composition in faeces and urine positively changed with the intervention: Brain-relevant gut metabolic functions involved in neuroprotective and antioxidant pathways, including S-adenosyl methionine, glutathione, and inositol, improved in PD. These promising results warrant further investigation in larger cohorts.},
}
@article {pmid40180580,
year = {2025},
author = {Chiu, CY and Servellita, V and de Lorenzi-Tognon, M and Benoit, P and Sumimoto, N and Foresythe, A and Cerqueira, FM and Williams-Bouyer, N and Ren, P and Herrera, LNS and Gaston, DC and Sayyad, L and Whitmer, SL and Klena, J and Vikram, HR and Gold, JAW and Gade, L and Parnell, L and Misas, E and Chiller, TM and Griffin, IS and Basavaraju, SV and Smith, DJ and Litvintseva, AP and Chow, NA},
title = {Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023.},
journal = {Emerging infectious diseases},
volume = {31},
number = {5},
pages = {},
doi = {10.3201/eid3105.241657},
pmid = {40180580},
issn = {1080-6059},
abstract = {We used metagenomic next-generation sequencing (mNGS) to investigate an outbreak of Fusarium solani meningitis in US patients who had surgical procedures under spinal anesthesia in Matamoros, Mexico, during 2023. Using a novel method called metaMELT (metagenomic multiple extended locus typing), we performed phylogenetic analysis of concatenated mNGS reads from 4 patients (P1-P4) in parallel with reads from 28 fungal reference genomes. Fungal strains from the 4 patients were most closely related to each other and to 2 cultured isolates from P1 and an additional case (P5), suggesting that all cases arose from a point source exposure. Our findings support epidemiologic data implicating a contaminated drug or device used for epidural anesthesia as the likely cause of the outbreak. In addition, our findings show that the benefits of mNGS extend beyond diagnosis of infections to public health outbreak investigation.},
}
@article {pmid40180222,
year = {2025},
author = {Yang, Y and Wang, D and Li, L and Song, J and Yang, X and Li, J},
title = {Evolution of enteric viruses in the progression of colorectal cancer via the adenoma-carcinoma sequence pathway.},
journal = {Virus research},
volume = {},
number = {},
pages = {199569},
doi = {10.1016/j.virusres.2025.199569},
pmid = {40180222},
issn = {1872-7492},
abstract = {The global incidence of colorectal cancer (CRC) is increasing. In the majority of CRC cases, colon cancer develops from alterations in the adenoma-carcinoma sequence pathway. Currently, there are few studies regarding the effects of enteric viruses on the adenoma-carcinoma sequence pathway, and subsequently, the progression and development of the CRC. Here, fecal and tissue samples from a normal control group, an adenomatous polyp group, and a colorectal adenocarcinoma group were collected to gain a deeper understanding of the variations in enteric viruses in CRC patients and to analyze their significance. With the progression of CRC from adenoma to adenocarcinoma, the number of DNA viruses in the virus-like particles (VLPs) of fecal and tissue samples gradually increased, and there were distinct differences in the composition of enteric viruses among the different groups. Multiple species correlation analysis revealed extensive interactions among viruses, bacteria, and fungi in fecal and tissue samples. Functional analysis also revealed that the functional pathways in fecal and tissue samples also underwent significant changes. In conclusion, the changes in the composition and function of enteric viruses in the progression of CRC via adenoma-carcinoma sequence pathway were analyzed in this study, and these changes hold certain importance for exploring the role of enteric viruses in the occurrence of this disease; however, their mode of action and specific mechanisms require further investigation.},
}
@article {pmid39930907,
year = {2025},
author = {Doorenspleet, K and Jansen, L and Oosterbroek, S and Kamermans, P and Bos, O and Wurz, E and Murk, A and Nijland, R},
title = {The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14079},
doi = {10.1111/1755-0998.14079},
pmid = {39930907},
issn = {1755-0998},
support = {//European Regional Development Fund Interreg North Sea region GEANS/ ; TEWZ118017//Rijksdienst voor Ondernemend Nederland/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; North Sea ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; DNA Primers/genetics ; Biodiversity ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Fishes/genetics/classification ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; },
abstract = {To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.},
}
@article {pmid40180172,
year = {2025},
author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D},
title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.},
journal = {Molecular and cellular endocrinology},
volume = {},
number = {},
pages = {112534},
doi = {10.1016/j.mce.2025.112534},
pmid = {40180172},
issn = {1872-8057},
abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.},
}
@article {pmid40179782,
year = {2025},
author = {Chen, S and Xin, X and Wang, Z and Wang, H and Yan, W},
title = {Enhancing tetramethylammonium hydroxide degradation in anaerobic digestion: Neglected role of iron-based conductive materials in regulating degradation pathway.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138115},
doi = {10.1016/j.jhazmat.2025.138115},
pmid = {40179782},
issn = {1873-3336},
abstract = {The rapid expansion of TFT-LCD industry led to significant environmental challenges due to the highly corrosive and ecotoxic tetramethylammonium hydroxide (TMAH). This study explores a previously unrecognized role of iron-based conductive materials - nano magnetite (Fe3O4) and nano zero-valent iron (ZVI) - in enhancing TMAH degradation and regulating degradation pathways in anaerobic digestion systems. Results show these materials significantly enhance degradation efficiency as TMAH concentration increases. At the highest TMAH level (10 g/L), while the control group achieved only 78.41 % degradation efficiency, Fe3O4 and ZVI groups reached efficiencies of 97.36 % and 94.96 %, with methane yields increased by 89.00 % and 97.21 %. Mechanistic exploration revealed these materials promoted secretion of charged functional groups into extracellular polymeric substances that effectively shielded microbes from TMAH toxicity. Additionally, they stimulated flavin and riboflavin production, enhancing interspecies electron transfer rates by up to 46.14-fold for Fe3O4 and 9.00-fold for ZVI. Microbial and metagenomic analyses further uncovered these materials induced a shift in TMAH degradation from methylotrophic methanogenesis to syntrophic metabolism, facilitating a more efficient breakdown of TMAH through direct interspecies electron transfer. These findings unravel the effects of iron-based conductive materials in regulating degradation pathways, offering a promising approach to addressing environmental challenges posed by TFT-LCD industry.},
}
@article {pmid40179570,
year = {2025},
author = {Zhang, P and Liu, Y and Xu, M and Zhang, J and Xia, J and Shi, Y and Wang, J and Han, B and Feng, G},
title = {Gut microbiota characteristics and prognostic value in patients with aneurysmal subarachnoid hemorrhage: A clinical study.},
journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia},
volume = {136},
number = {},
pages = {111200},
doi = {10.1016/j.jocn.2025.111200},
pmid = {40179570},
issn = {1532-2653},
abstract = {BACKGROUND: This study aims to explore the characteristics of gut microbiota in the aneurysmal subarachnoid hemorrhage (aSAH) group and the healthy control group, as well as in the good prognosis group and the poor prognosis group. It also investigates the relationship between the severity of aSAH and gut microbiota, and the predictive value of gut microbiota for the prognosis outcome of patients with aSAH.<br><br>METHODS: Stool samples from 22 patients with aSAH and 11 healthy controls were subjected to metagenomic sequencing, and species annotations were obtained through the taxonomic information database corresponding to the NR database. The characteristics of the gut microbiota in the aSAH group versus the healthy control group, and the good prognosis group versus the poor prognosis group were analyzed.The correlations between differential microbiota and clinical hematology markers between the aSAH and control groups and between gut microbiota and aSAH severity were analyzed. The prognosis of patients with aSAH after three months was assessed. Finally, gut microbiota with significant effects were screened for potential as biomarkers, and the predictive value of gut microbiota for different prognostic outcomes in patients with aSAH was explored.<br><br>RESULTS: Gut microbiota composition, diversity, and abundance differed significantly between patients in the aSAH group and the control group. Additionally, the composition, diversity, and abundance differed between patients with good and poor prognosis. Five dominant genera--Bacillus, Eggerthia, Hominisplanchenecus, Carnobacterium, and Bifidobacterium were identified as potential biomarkers for predicting aSAH outcomes.<br><br>CONCLUSION: Patients with aSAH have altered gut microbiota composition, structure, and diversity compared with the healthy population. These alterations may be potential biomarkers for aSAH diagnosis and outcome prediction.},
}
@article {pmid40178790,
year = {2025},
author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W},
title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40178790},
issn = {1869-1889},
abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.},
}
@article {pmid40178526,
year = {2025},
author = {Contreras-de la Rosa, PA and De la Torre-Zavala, S and O Connor-Sánchez, A and Prieto-Davó, A and Góngora-Castillo, EB},
title = {Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001382},
pmid = {40178526},
issn = {2057-5858},
mesh = {*Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/metabolism ; Biotechnology ; Secondary Metabolism/genetics ; Metagenomics/methods ; *Geologic Sediments/microbiology ; Multigene Family ; Polyketide Synthases/genetics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.},
}
@article {pmid40178319,
year = {2025},
author = {Herzog, E and Ishida, K and Scherlach, K and Chen, X and Bartels, B and Niehs, SP and Cheaib, B and Panagiotou, G and Hertweck, C},
title = {Antibacterial Siderophores of Pandoraea Pathogens and their Impact on the Diseased Lung Microbiota.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202505714},
doi = {10.1002/anie.202505714},
pmid = {40178319},
issn = {1521-3773},
abstract = {Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a non-ribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.},
}
@article {pmid40177842,
year = {2025},
author = {Larnder, AH and Manges, AR and Murphy, RA},
title = {The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35427},
pmid = {40177842},
issn = {1097-0215},
support = {/CAPMC/CIHR/Canada ; //Weston Family Foundation/ ; },
abstract = {Increasing evidence links the gut microbiome to carcinogenesis. Disruptions in estrogen regulation by the estrobolome-gut microbiota with estrogen-related functions-may promote breast cancer. However, precise information on estrobolome targets and their underlying mechanisms is limited. This review identifies relevant targets for measuring the estrobolome, focusing on enzymes and microbial taxa involved in processing estrogens, precursors, metabolites, and phytoestrogens, to facilitate the exploration of potential links to breast cancer. Evidence from breast cancer case-control studies is synthesized to assess alignment with these targets, highlight gaps in the evidence, and suggest new paths forward. Findings from case-control studies were heterogeneous and showed limited alignment with estrobolome targets, with only Escherichia coli and Roseburia inulinivorans identified as differentially abundant and functionally relevant between cases and controls. The lack of compelling evidence for estrobolome-specific mechanisms may reflect measurement challenges or may suggest that broader ecological changes in the microbiome, which influence a network of interacting mechanisms, are more influential for carcinogenesis. To clarify the estrobolome's role in breast cancer, future research should use advanced sequencing techniques and methods such as metabolomics and transcriptomics, while considering clinical and behavioral factors that may modify estrobolome mechanisms.},
}
@article {pmid40177486,
year = {2025},
author = {Yang, S and Chen, J and Zheng, J and Mao, H and Deng, F and Wu, D and Chai, J},
title = {Feeding systems influence the rumen resistome in yaks by changing the microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1505938},
doi = {10.3389/fmicb.2025.1505938},
pmid = {40177486},
issn = {1664-302X},
abstract = {The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as Stomatobaculum longum and Succiniclasticum ruminis. Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW/N/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW/N/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes (Clostridium tepidiprofundi) carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.},
}
@article {pmid40177475,
year = {2025},
author = {Tenea, GN and Reyes, P and Flores, C},
title = {Crosslinking bacterial postbiotics for microbial and quality control of strawberries postharvest: bacteriological and 16S amplicon metagenome evidence.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570312},
doi = {10.3389/fmicb.2025.1570312},
pmid = {40177475},
issn = {1664-302X},
abstract = {INTRODUCTION: Strawberries are renowned for their exceptional flavor and nutritional properties but have a short shelf life due to rapid ripening and a high vulnerability to postharvest microbial decay. Postbiotic formulations (PBFs) derived from lactic acid bacteria (LAB) can be developed into effective preservation products, extending postharvest shelf life while maintaining fruit quality.<br><br>METHODS: This study aimed to assess the effects of postbiotic-based formulations (PBFs) consisting of two key components: (1) a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O, serving as the antimicrobial agent, and (2) an exopolysaccharide (EPS) from W. confusa UTNCys2-2, functioning as the biopolymer carrier. These formulations were tested against a multidrug-resistant Serratia liquefaciens P4StpC1 strain, isolated from ready-to-eat strawberries, and their potential mode of action was analyzed in vitro. Time-kill assays and electron microscopy were used to evaluate their impact on the target cells. Furthermore, the performance of PBFs was compared to a commercial disinfectant (C1) in terms of their effects on strawberry microbiota and fruit quality, employing bacteriological techniques and 16S amplicon metagenomic analysis.<br><br>RESULTS: The selected PBFs showed bacteriolytic effect on Serratia in vitro. The target cell viability was significantly reduced upon 1&#x202f;h co-cultivation by inducing several morphological and ultrastructural modifications. Dipping strawberries at the ripe stage four in PBFs indicated no increase in total cell counts, thus the microorganisms colonization was retained during storage with refrigeration. The 16S metagenome analysis showed that the treatment impacted the fruit microbiota, significantly increasing Lactobacillus abundance (p&#x202f;<&#x202f;0.001) by day eight compared to the disinfectant control. This suggests the formulation supports beneficial microbes, enhancing antimicrobial effects. Additionally, the postbiotic coating improved shelf-life, preserved fruit quality, and delayed deterioration in strawberries. The strawberries quality attributes were not affected by the treatment. Principal Component Analysis (PCA) revealed clear sample separation based on maturity stage, independent of the treatment.<br><br>CONCLUSION: The results highlight the potential of crosslinking of a peptide-protein fraction with EPS to prevent the colonization of undesirable microorganisms on postharvest strawberries while enhancing their safety and quality.},
}
@article {pmid40177465,
year = {2025},
author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE},
title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf030},
doi = {10.1093/ismeco/ycaf030},
pmid = {40177465},
issn = {2730-6151},
abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.},
}
@article {pmid40177421,
year = {2025},
author = {Tian, Y and Yang, X and Yang, Y and Lin, T and Wang, G and Zhang, Y and Wu, H and Wang, J},
title = {Aeromonas veronii-induced septic arthritis of the hip in a child with acute lymphoblastic leukemia.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20221042},
doi = {10.1515/biol-2022-1042},
pmid = {40177421},
issn = {2391-5412},
abstract = {Septic arthritis of the hip (SAH) is a prevalent form of infectious arthritis in children that can lead to serious complications if not promptly diagnosed and treated. A 6-year 4-month-old female child with a 1-year history of acute lymphoblastic leukemia chemotherapy was admitted to our hospital due to a 1-day fever. After 1 week, the child experienced right inguinal pain and exhibited severe restriction in the flexion of the right lower limb and hip. Consequently, edema was observed in the right lower extremity and foot. SAH was initially diagnosed using computed tomography and magnetic resonance imaging examinations of both hip joints. Subsequently, incision and irrigation procedure were performed on the hip joint. Following the surgery, pus metagenomic next-generation sequencing (mNGS) were conducted promptly, and the mNGS analysis indicated an Aeromonas veronii infection. The diagnosis of A. veronii SAH was subsequently confirmed through polymerase chain reaction. The child's condition was successfully treated with a combination of amikacin and imipenem-cilastatin, leading to improvement and subsequent discharge in a satisfactory state. SAH caused by A. veronii is a rare occurrence, and the utilization of mNGS holds significant potential for the early detection of uncommon infections in immunosuppressed children.},
}
@article {pmid40177267,
year = {2025},
author = {Yan, Z and Sun, C and Tang, W and Cao, W and Lv, J and Liang, Z and Wei, S and Zhong, W and Zhao, Z and Zhao, Z and Li, Y},
title = {Application of the metagenomic next-generation sequencing technology to identify the causes of pleural effusion.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1525100},
doi = {10.3389/fmed.2025.1525100},
pmid = {40177267},
issn = {2296-858X},
abstract = {BACKGROUND: Pleural effusion (PE), frequently encountered in clinical practice, can arise from a variety of underlying conditions. Accurate differential diagnosis of PE is crucial, as treatment and prognosis are heavily dependent on the underlying etiology. However, diagnosing the cause of PE remains challenging, relying on mycobacteriological methods that lack sensitivity and are time-consuming, or on histological examinations that require invasive biopsies. The recent advancements in metagenomic next-generation sequencing (mNGS) have shown promising applications in the diagnosis of infectious diseases. Despite this, there is limited research on the utility of mNGS as a comprehensive diagnostic tool for simultaneously identifying the causes of PE, particularly in cases of tuberculosis or malignancy.<br><br>METHODS: This study aimed to assess the efficacy of mNGS in detecting tuberculous pleural effusion (TPE) and malignant pleural effusion (MPE). A total of 35 patients with PE were included, and their PE samples were analyzed using mNGS.<br><br>RESULTS: Among the participants, 8 were ultimately diagnosed with TPE, and 10 were diagnosed with MPE, with lung adenocarcinoma being the most prevalent pathological type (50%, 5/10), according to established diagnostic criteria. Additionally, 7 patients were diagnosed with non-infectious PE. However, mNGS identified only 2 cases of TPE and 8 cases of MPE. The sensitivity of mNGS for detecting Mycobacterium tuberculosis was 25% (2/8), while the specificity was 100%. For tumor detection, mNGS demonstrated a sensitivity of 80%, a specificity of 92.6%, and an AUC of 0.882.<br><br>CONCLUSION: mNGS is effective in distinguishing MPE from non-MPE, but is not suitable for diagnosing TPE.},
}
@article {pmid40177264,
year = {2025},
author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, SE and Eren, AM and Bradley, PH},
title = {Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf039},
doi = {10.1093/bioadv/vbaf039},
pmid = {40177264},
issn = {2635-0041},
abstract = {MOTIVATION: Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.<br><br>RESULTS: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism.<br><br>Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.},
}
@article {pmid40176261,
year = {2025},
author = {Sim, BZ and Mah, JK and Heldman, MR and Stanly, KL and Hanson, KE and Caliendo, AM and Andes, D and Ostroskly-Zeichner, L and Wingard, JR and Alexander, BD},
title = {Plasma microbial cell-free DNA Metagenomic Sequencing for Diagnosis of Invasive Fungal Diseases Among High Risk Outpatient and Inpatient Immunocompromised Hosts.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf170},
pmid = {40176261},
issn = {1537-6591},
abstract = {BACKGROUND: New and minimally-invasive tools to aid the diagnosis of invasive fungal diseases (IFD) are urgently needed as the immunocompromised population at highest risk increases. Advancements in molecular technology have rendered new diagnostics more readily available for clinical use.<br><br>METHODS: This case-control study utilized prospectively collected, archived plasma specimens and data from the Aspergillus Technology Consortium (AsTeC) Repository to investigate the diagnostic performance of microbial cell free DNA (mcfDNA) sequencing as a minimally-invasive diagnostic for IFDs in a population of high-risk immunocompromised hosts including hematologic malignancy, stem cell and solid organ transplants patients. The 2008 Mycoses Study Group/European Organization for the Research and Treatment of Cancer diagnostic criteria served as the gold standard for test performance.<br><br>RESULTS: Sixty-five adult subjects with proven or probable IFD and 65 controls without IFD were included. Among IFD episodes Aspergillus was the most common pathogen (70.8%, 46/65), followed by Mucorales (10.8%, 7/65). Overall, sensitivity was 47.7% and specificity was 100%. Sensitivity varied based on disease certainty and pathogen; sensitivity was higher in proven versus probable IFD (60.0% vs 37.1%, respectively) and higher for subjects with invasive mucormycosis (100%) compared with aspergillosis (45.7%).<br><br>CONCLUSIONS: A positive result by mcfDNA sequencing may reduce the need for invasive sampling in patients with suspected IFD. In this exploratory analysis, its high sensitivity and specificity for invasive mucormycosis suggests it could be useful for early treatment and intervention of this IFD. Future studies should focus on understanding how specific factors impact the sensitivity of mcfDNA sequencing for invasive aspergillosis.},
}
@article {pmid40176190,
year = {2025},
author = {Xing, J and Niu, T and Yu, T and Zou, B and Shi, C and Wang, Y and Fan, S and Li, M and Bao, M and Sun, Y and Gao, K and Qiu, J and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, S and Hu, J and Zhang, D and Sun, W and Yang, G and Yang, W and Wang, C},
title = {Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {90},
pmid = {40176190},
issn = {2049-2618},
support = {U21A20261//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Swine ; *Porcine epidemic diarrhea virus/physiology ; *Gastrointestinal Microbiome ; *Swine Diseases/virology/microbiology ; *Faecalibacterium prausnitzii/metabolism/physiology ; *Coronavirus Infections/veterinary/virology/microbiology ; Probiotics/administration &amp; dosage ; Feces/microbiology ; *Bacterial Outer Membrane/metabolism ; },
abstract = {BACKGROUND: The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.<br><br>RESULTS: A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.<br><br>CONCLUSION: F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.},
}
@article {pmid40176137,
year = {2025},
author = {Sommer, F and Bernardes, JP and Best, L and Sommer, N and Hamm, J and Messner, B and López-Agudelo, VA and Fazio, A and Marinos, G and Kadibalban, AS and Ito, G and Falk-Paulsen, M and Kaleta, C and Rosenstiel, P},
title = {Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {91},
pmid = {40176137},
issn = {2049-2618},
support = {SO1141/10-1//Deutsche Forschungsgemeinschaft/ ; CRC1182//Deutsche Forschungsgemeinschaft/ ; miTARGET//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; RNA, Ribosomal, 16S/genetics ; *Fecal Microbiota Transplantation ; *Aging/physiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; *Intestinal Mucosa/microbiology/metabolism ; *Inflammation/microbiology ; Mice, Inbred C57BL ; *Rejuvenation ; Permeability ; *Intestines/microbiology ; Metagenomics ; Intestinal Barrier Function ; },
abstract = {BACKGROUND: Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.<br><br>RESULTS: Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.<br><br>CONCLUSIONS: Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.},
}
@article {pmid40175903,
year = {2025},
author = {Cao, L and Sun, H and Xu, Z and Xu, X and Shi, G and Zhang, J and Liang, C and Li, T and Liu, C and Wang, M and Tian, S and Li, E},
title = {Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {190},
pmid = {40175903},
issn = {1471-2180},
mesh = {*Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; China ; Food Microbiology ; *Metagenome ; Microbiota ; *Alcoholic Beverages/microbiology ; },
abstract = {BACKGROUND: The unique flavour and quality of Baijiu, a treasure of traditional Chinese culture, has attracted increasing attention. The pit mud is a key component for forming the unique flavour styles of different Baijiu brands. Hence, conducting in-depth research on the microbial colonies present in pit mud is paramount for enhancing the intricate bouquets of Baijiu flavours.<br><br>RESULTS: This study conducts a comprehensive metagenomic examination of the microbial ecosystem within Chinese&#xa0;Jiang-Nong Jianxiang Baijiu fermentation pit mud. Within the pit mud walls, six prominent species, each accounting for more than 1% of the average relative abundance, emerged as key contributors: Lentilactobacillus buchneri, Secundilactobacillus silagincola, Clostridium tyrobutyricum, Lentilactobacillus parafarraginis, Ligilactobacillus acidipiscis, and Lactobacillus acetotolerans. Conversely, at the pit mud bases, four species surpassed this threshold: Petrimonas sp. IBARAKI, Methanosarcina barkeri, Methanofollis ethanolicus, and Proteiniphilum propionicum. Notably, the abundance of Clostridium in the pit mud walls impart superior saccharifying capabilities compared with those at the bases. The consistently high relative abundance of enzymes belonging to the glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) across both the pit mud walls and the bases highlight their importance in fermentation.<br><br>CONCLUSIONS: The microbial composition analysis results underscore the important role of pit mud microorganisms in facilitating starch saccharification, ethyl caproate and ethyl butyrate production, among other aromatic compounds. Microbes residing in the pit mud walls may be exhibited a heightened propensity for lactic acid generation, whereas those inhabiting the bases may be displayed a stronger inclination towards caproic acid production. This research serves as a valuable reference for future endeavours aimed at harnessing microbial resources to refine and optimize Baijiu fermentation methodologies.},
}
@article {pmid40175854,
year = {2025},
author = {Abuzahrah, SS},
title = {Exploring the microorganisms biodiversity associated with sponge species in the red sea through 18S ribosomal RNA gene sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {60},
pmid = {40175854},
issn = {2191-0855},
abstract = {Around the world, sponges play a significant role in marine ecosystems, and a wide variety of sponge species can be found in the coast of Red Sea of Saudi Arabia. The unique environmental conditions of the Red Sea, including warm, oligotrophic water and high salinity, have encouraged the growth of abundant sponge fauna. Our study aims to investigate the biodiversity, taxonomic composition, and phylogenetic relationships of eukaryotic organisms linked with sponges in the Red Sea off the coast of Saudi Arabia and infer the possible ecological roles and functional contributions of the identified eukaryotic taxa to sponge health and ecosystem functioning. The study investigated the microbial diversity, focusing on the genera Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and other unclassified species. Our metagenomic analysis and phylogenetic evaluation revealed a deep and diverse microbial community, with each genus performing significant ecological roles, including nutrient cycling, primary production, and contributing to marine food networks. Moreover, these genera display promising biotechnological prospects, including uses in bioremediation, biofuel production, and the synthesis of high-value biomolecules. Comparative analysis with other marine regions has focused on both the similarities and unique aspects of the Red Sea microbial community, which are influenced by its distinct environmental conditions. The gained findings contribute to a deeper understanding of the ecological dynamics in the Red Sea and open new avenues for biotechnological exploration in marine ecosystems.},
}
@article {pmid40175821,
year = {2025},
author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W},
title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40175821},
issn = {1874-9356},
support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA&#x3000;2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; },
abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.},
}
@article {pmid40175737,
year = {2025},
author = {Sawhney, SS and Thänert, R and Thänert, A and Hall-Moore, C and Ndao, IM and Mahmud, B and Warner, BB and Tarr, PI and Dantas, G},
title = {Gut microbiome evolution from infancy to 8 years of age.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40175737},
issn = {1546-170X},
support = {R01AI155893//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD092414//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD092414//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T32GM007067//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; MD-FR-2013-292//Children's Discovery Institute (CDI)/ ; 5P30 DK052574//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
abstract = {The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.},
}
@article {pmid40175647,
year = {2025},
author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ},
title = {Increasing spatial working memory in mice with Akkermansia muciniphila.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {546},
pmid = {40175647},
issn = {2399-3642},
support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; },
abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.},
}
@article {pmid40175554,
year = {2025},
author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ},
title = {Bifidobacteria support optimal infant vaccine responses.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175554},
issn = {1476-4687},
abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.},
}
@article {pmid40175522,
year = {2025},
author = {Gichuki, BM and Van Camp, AG and Shao, Y},
title = {A new strain of thought in gut metagenomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40175522},
issn = {1740-1534},
}
@article {pmid40175313,
year = {2025},
author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B},
title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: A metagenomic perspective.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf035},
pmid = {40175313},
issn = {1574-6941},
abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic degrading capabilities.},
}
@article {pmid40174744,
year = {2025},
author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W},
title = {Thermal Environment Driving Specific Microbial Species to Form the Visible Biofilms on the UNESCO World Heritage Dazu Rock Carvings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121510},
doi = {10.1016/j.envres.2025.121510},
pmid = {40174744},
issn = {1096-0953},
abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4°C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.},
}
@article {pmid40174653,
year = {2025},
author = {Balasundaram, G and Gahlot, P and Hafyan, RH and Tyagi, VK and Gadkari, S and Sahu, A and Barber, B and Mutiyar, PK and Kazmi, AA and Kleiven, H},
title = {Anaerobic digestion of thermal hydrolysis pretreated sludge: Process performance, metagenomic analysis, techno-economic and life cycle assessment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132470},
doi = {10.1016/j.biortech.2025.132470},
pmid = {40174653},
issn = {1873-2976},
abstract = {This study assessed the potential of thermal hydrolysis process (THP) combined with anaerobic digestion (AD) for high solids sewage sludge treatment across various hydraulic retention times (HRTs). Optimal performance was achieved at a 10-day HRT (6 kg VS/m[3]·day), yielding 408 L CH4/kg VS added and 54 % volatile solids (VS) removal under THP conditions of 160 °C, 30 min, and 6 bar pressure. Microbial analysis revealed predominant acetoclastic and hydrogenotrophic methanogens. Four scenarios were designed and analyzed for environmental and economic performance: Scenario 1 (conventional AD-CHP), Scenario 2 (conventional AD-BioCNG), Scenario 3 (THP AD-BioCNG), and Scenario 4 (THP AD-CHP). The results showed that scenarios with CHP integration achieved better environmental performance by generating sufficient energy to meet demand, with energy consumption as a key factor. Notably, scenario 4 had the lowest global warming potential (GWP) at -0.0185 kg CO2-eq, outperforming conventional AD (Scenario 1) with CHP, which had a GWP of -0.00232 kg CO2-eq. However, profitability analysis showed that Scenario 3 was the most economically viable, with a net present value (NPV) of $4.3 million, an internal rate of return (IRR) of 10.21 %, and a 17-year payback period. Although it had higher capital ($58 million) and operational costs ($12.5 million/year) than Scenario 4 ($45 million and $8.6 million/year), its greater biomethane yield resulted in higher revenue ($20.7 million/year), making it the most profitable option. While Scenario 4 offered the best environmental benefits, Scenario 3 emerged as the most financially sustainable choice. These findings highlight the environmental and economic advantage of utilizing THP-AD process over conventional AD, suggesting that THP-AD optimizes methane production, solids reduction, and environmental impact, making the Bio CNG pathway a sustainable and economically viable option.},
}
@article {pmid40174641,
year = {2025},
author = {He, T and Zhang, X and Zhang, X},
title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.057},
pmid = {40174641},
issn = {2090-1224},
abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.<br><br>OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.<br><br>METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.<br><br>RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.<br><br>CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.},
}
@article {pmid40174574,
year = {2025},
author = {Zeng, S and Almeida, A and Mu, D and Wang, S},
title = {Embracing the unknown: Proteomic insights into the human microbiome.},
journal = {Cell metabolism},
volume = {37},
number = {4},
pages = {799-801},
doi = {10.1016/j.cmet.2025.02.003},
pmid = {40174574},
issn = {1932-7420},
abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.},
}
@article {pmid40174565,
year = {2025},
author = {Krohn, C and Khudur, L and Biek, SK and Elliott, JA and Tabatabaei, S and Jiang, C and Wood, JL and Dias, DA and Dueholm, MKD and Rees, CA and O'Carroll, D and Stuetz, R and Batstone, DJ and Surapaneni, A and Ball, AS},
title = {Microbial population shifts during disturbance induced foaming in anaerobic digestion of primary and activated sludge.},
journal = {Water research},
volume = {281},
number = {},
pages = {123548},
doi = {10.1016/j.watres.2025.123548},
pmid = {40174565},
issn = {1879-2448},
abstract = {Foaming during anaerobic digestion (AD) of sewage sludge is poorly understood and remains an uncontrollable operational obstacle for sewage treatment systems globally, causing mechanical damage, increased hazards and reduced biogas recovery. Foams during AD commonly occur after process disturbances, such as organic loading shocks. However, it is still unclear whether these foam events are biologically driven and linked to the abundance of organisms like filamentous or hydrophobic bacteria. A time-series study was conducted, comparing digestion performance, microbial community succession, metagenomes, and metabolomes in six anaerobic continuous stirred-tank reactors (CSTRs): a control group fed normally (n = 3), and one treated group inhibited through organic shock loading of more than twice the steady state loading rate with glycerol (treatment, n = 3). As soon as microbial activity and methanogenesis recovered after inhibition, significant volumes of foam accumulated simultaneously in the reactor headspace of the three treated CSTRs. Microbial abundance profiles (16S rRNA, V3-V4) from 165 days of operation showed that filamentous or mycolic acid-producing organisms were not associated with this foam event. Shock loading led to acidification, biomass decline and microbial imbalance, contributing indirectly to the foam event. During that period, metabolomes and functional pathway abundances indicated that the stressed microbial biomass was enriched in long-chain fatty acids prior to foaming. This biomass, combined with pH changes, may have modified the physicochemical properties of sludge, leading to the fractionation of organic mass once gas production resumed. More research is needed to understand how abiotic and biotic interactions contribute to foam formation.},
}
@article {pmid40174457,
year = {2025},
author = {Han, Q and Wang, Y and Shi, C and Qian, Y and Wang, X and Wang, S and Sun, X and Yu, Q and Li, H},
title = {Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138101},
doi = {10.1016/j.jhazmat.2025.138101},
pmid = {40174457},
issn = {1873-3336},
abstract = {The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.},
}
@article {pmid40174456,
year = {2025},
author = {Long, M and Zheng, CW and Zhou, C and Rittmann, BE},
title = {Mitigating chromate toxicity through concurrent denitrification in the H2-based membrane biofilm reactor.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138073},
doi = {10.1016/j.jhazmat.2025.138073},
pmid = {40174456},
issn = {1873-3336},
abstract = {High concentrations of hexavalent chromium (Cr(VI)) in industrial wastewaters pose significant environmental and health hazards. Biotranformation is a viable means to lower Cr(VI) toxicity, but research to date has focused on wastewaters with low concentrations (e.g., 2-5 mg/L Cr(VI)). This study evaluated the dynamics of biosorption and biotransformation of higher-concentration Cr(VI) by biofilms in the H2-based membrane biofilm reactor (MBfR). While the biofilm in an MBfR receiving Cr(VI) alone had limited capacity to remove Cr(VI) and Cr(VI) removal ceased in 30 days, an autotrophic denitrifying biofilms achieved 99 % reduction of over 20 mg/L Cr(VI) to less-toxic trivalent chromium (Cr(III)) in continuous long-term operation system over 4 months. Increasing the H2 pressure from 3 psig to 10 psig improved Cr(VI) removal from 87 % to 99 %, which occurred in parallel with over 95 % NO3[-] reduction to N2. Metagenomic analyses revealed the mechanisms of Cr(VI) bioreduction and highlighted the beneficial role of nitrate (NO3[-]) as the primary electron acceptor. For example, nitrite reductase NrfA could reduce Cr(VI), which lowered Cr(VI) caused oxidative stress. This research demonstrates the MBfR's effectiveness in reducing elevated levels of Cr(VI) and provides mechanistic understanding of the roles of denitrification in accelerating Cr(VI) reduction and detoxification.},
}
@article {pmid40174424,
year = {2025},
author = {Dai, Z and Li, Y and Zhang, Y and Xiang, T and Peng, J and Mao, X and Fan, Y and Wang, F and Yang, S and Cao, W},
title = {Nutrient enrichment by high aquaculture effluent input exacerbates imbalances between methane production and oxidation in mangrove sediments.},
journal = {Water research},
volume = {280},
number = {},
pages = {123552},
doi = {10.1016/j.watres.2025.123552},
pmid = {40174424},
issn = {1879-2448},
abstract = {Frequent aquaculture activities introduce substantial nutrients into mangrove ecosystems; however, the impact of this nutrient enrichment on methane (CH4) emissions and the associated microbial communities remains largely unexplored. In this study, we used the static chamber method, combined with 16S rRNA-based, metagenomic sequencing and binning techniques, to investigate the emission patterns of greenhouse gases (GHGs), with a particular focus on CH4, in mangroves subjected to different levels of effluents. The results showed that the effluent input decreased the mineral protection of sediment carbon (C) pools and increased C loss by more than double. In particular, high effluent input increased CH4 emissions by 243.3 %. Random forest analysis revealed that changes in methanogens were an important factor in explaining the variation of CH4 emissions. Amplicon data showed that the proportion of methylotrophic methanogens increased after effluent input, and metagenomic binning further attributed this change to the adaptability of methylotrophic methanogens to the substances transporting by the effluent. The enhanced hypoxia in sediments resulting from effluent input promoted the transition of methanotrophic communities from aerobic to anaerobic types and made anaerobic oxidation of CH4 more reliant on sulfur reduction rather than nitrate reduction. The PLS model further revealed that the nutrients brought by effluent input stimulated an increase in DOC content which induced an imbalance between CH4 production and oxidation in sediments by facilitating methanogens but inhibiting methanotrophs, ultimately resulting in an increase in CH4 fluxes. These findings underscore the significance of mangroves receiving effluent input as critical consequent reactors, highlighting the necessity to consider effects of high nutrient enrichment by aquaculture effluent input on GHG emissions and blue C potential in mangroves.},
}
@article {pmid40172536,
year = {2025},
author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR},
title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0056924},
doi = {10.1128/iai.00569-24},
pmid = {40172536},
issn = {1098-5522},
abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.},
}
@article {pmid40172519,
year = {2025},
author = {Chaves-Sierra, C and Botero-Rozo, D and Rodriguez-Cruz, MC and Montoya, C and Romero, HM},
title = {Detection and molecular characterization of 'Candidatus Liberibacter' in Colombian oil palms affected by Lethal Wilt Disease.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-24-2079-RE},
pmid = {40172519},
issn = {0191-2917},
abstract = {Lethal wilt (LW), also known as "Marchitez Letal (ML)" in Colombia, is an endemic disease affecting oil palms (Elaeis guineensis Jacq.) and is a leading cause of crop loss. The disease is characterized by the drying of leaflets from the tip to the base, primarily impacting the lower third of the plant and progressively moving upward. This progression leads to physiological disturbances, including necrosis at the tips of immature inflorescence bracts (spines) and the detachment of bunch fruits, ultimately causing wilting. As a phytosanitary measure, infected palms are eradicated to prevent further spread of the disease. The primary goal of this research was to identify the bacteria associated with LW and to validate a molecular detection method. A 16S amplicon-based analysis was employed to identify and compare the microbial diversity in LW-affected palm tissues with those of healthy plants. Among the 16 OTUs corresponding to different bacterial genera found in all LW samples, taxonomic classification and symptomatology suggested that the bacteria closely associated with LW belong to the genus Candidatus Liberibacter. Further phylogenetic analysis indicated that these bacteria are part of the Rhizobiaceae family, grouping closely with other species of the genus Candidatus. Liberibacter. The concentration of the pathogen in different oil palm tissues was determined using droplet digital PCR (ddPCR) and quantitative PCR (qPCR), expressed in copies/µL in the LW samples. This study represents the first report of 'Candidatus Liberibacter sp'. being associated with lethal wilt in oil palms of the Arecaceae family in Colombia. The findings from this research have the potential to contribute significantly to the development of effective management strategies to prevent crop losses.},
}
@article {pmid40172478,
year = {2025},
author = {Wang, H and Zhao, X and Li, D and Meng, L and Liu, S and Zhang, Y and Huo, L},
title = {Marine Metagenome Mining Reveals Lanthipeptides Colwesin A-C, Exhibiting Novel Ring Topology and Anti-inflammatory Activity.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00057},
pmid = {40172478},
issn = {2161-5063},
abstract = {Marine natural products are promising sources for drug discovery due to their unique structures and diverse biological activities. The establishment of the Global Marine Microbiome Genome Catalogue (GOMC) has significantly expanded the repository of natural products derived from marine-associated bacteria. In this study, we identified the Class I lanthipeptide biosynthetic gene cluster col from Colwellia_A sp. based on the GOMC database. Through heterologous expression in Escherichia coli and subsequent structural analysis, we characterized three novel lanthipeptides, colwesins A-C, which possess unique cyclic structures characterized by an exceptionally large number of thioether rings. To the best of our knowledge, colwesin C is the first lanthipeptide simultaneously containing locked, nonoverlapped, and nested ring topologies. These findings highlight the robust ring-forming capacity of Class I lanthipeptide synthetases. Colwesins A-C were found to exhibit anti-inflammatory activity in lipopolysaccharide-induced mouse macrophage RAW264.7 cell lines without detectable cytotoxicity. Overall, our results broaden our understanding of the structural diversity of marine-derived lanthipeptides.},
}
@article {pmid40172215,
year = {2025},
author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F},
title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2486511},
doi = {10.1080/19490976.2025.2486511},
pmid = {40172215},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology/metabolism ; *Metagenomics ; *Metabolomics ; *Disease Models, Animal ; Cricetinae ; *SARS-CoV-2/genetics ; Aging ; Age Factors ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Mesocricetus ; Metabolome ; },
abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.},
}
@article {pmid40172109,
year = {2025},
author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M},
title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0018423},
doi = {10.1128/mmbr.00184-23},
pmid = {40172109},
issn = {1098-5557},
abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.},
}
@article {pmid40171165,
year = {2025},
author = {Shi, H and Li, J},
title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1485048},
pmid = {40171165},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; *Bariatric Surgery ; Metagenome ; Metagenomics/methods ; Genomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Gastric Bypass ; Computational Biology/methods ; Adult ; },
abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.<br><br>METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota &#x3b1;-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling&#xa0;and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).<br><br>RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota &#x3b1;-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.<br><br>DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.},
}
@article {pmid40170926,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1546912},
pmid = {40170926},
issn = {1664-302X},
abstract = {Diet can influence the thermal performance of ectotherms, providing potential strategies for biological conservation in the context of global warming. The endangered Andrias davidianus is susceptible to heat stress due to energy deficiency in the liver when fed a worm-based diet rich in carbohydrates. A fish-based diet, rich in protein and lipids, improves their thermal performance, but the underlying physiological mechanisms remain unclear. In this study, we used metabolomics and metagenomics to examine the combined effects of temperature (15, 20, and 25°C) and diet (fish-based and worm-based) on liver metabolism and gut microbiota. Our results show that both temperature and diet shape liver metabolism, with several vital metabolic pathways (e.g., TCA cycle and sulfate metabolism) regulated by their combined effects. Notably, diet-dependent thermal responses in energy metabolism were observed, with fish-fed salamanders exhibiting a marked upregulation of the TCA cycle intermediates under heat stress, a response absent in worm-fed individuals. Given the role of TCA cycle in heat susceptibility of A. davidianus, these findings suggest that the TCA cycle likely mediates the interactive effects of temperature and diet on thermal performance. We then examined whether the gut microbiota is also a target of interactive effects or a mediator of the diet's influence on liver metabolism. While both temperature and diet shape microbiota composition, functional shifts occur only in response to temperature, indicating that the microbiota is not a major link between diet and liver metabolism. However, several bacterial groups (e.g., Thiosulfatimonas and Alcanivorax), jointly regulated by temperature and diet, correlate with liver metabolites, suggesting alternative, function-independent pathways through which dietary-related microbial changes may influence liver metabolism and even thermal tolerance. Overall, this study provides molecular insights into the dietary modulation of thermal performance in A. davidianus and highlight the potential of dietary microbial management strategies for amphibian conservation.},
}
@article {pmid40170918,
year = {2025},
author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T},
title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549128},
pmid = {40170918},
issn = {1664-302X},
abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.},
}
@article {pmid40170844,
year = {2025},
author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1539653},
pmid = {40170844},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/therapy/immunology/microbiology ; *Metagenomics/methods ; *Immunotherapy/methods ; *Machine Learning ; Male ; *Bacteria/genetics/classification/immunology ; Female ; Fungi/immunology ; Middle Aged ; Skin Neoplasms/immunology/therapy/microbiology ; Biomarkers ; Aged ; Adult ; Treatment Outcome ; },
abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.<br><br>METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.<br><br>RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.<br><br>CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.},
}
@article {pmid40170341,
year = {2025},
author = {Sorn, S and Matsuura, N and Honda, R},
title = {Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70087},
doi = {10.1111/1462-2920.70087},
pmid = {40170341},
issn = {1462-2920},
support = {19K22925//Japan Society for the Promotion of Science/ ; 22K19865//Japan Society for the Promotion of Science/ ; //Steel Foundation for&#xa0;Environmental&#xa0;Protection&#xa0;Technology/ ; },
mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; *Sewage/microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Biodegradation, Environmental ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Transcriptome ; Biotransformation ; Phylogeny ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) exhibit a widespread distribution across diverse global ecosystems throughout their lifecycle, posing substantial risks to human health. The persistence of PFAS makes biodegradation a challenging yet environmentally friendly solution for their treatment. In the authors' previous study, a bacterial consortium capable of reducing perfluorooctane sulfonate (PFOS) was successfully enriched from activated sludge. This study aimed to investigate the array of genes associated with PFOS reduction via biosorption and biotransformation to elucidate the metabolic pathways. Two metagenome-assembled genomes (MAGs) based on 16S rRNA sequences that share 99.86% and 97.88% similarity with Hyphomicrobium denitrificans and Paracoccus yeei, respectively were obtained. They were found to contain several genes encoding enzymes that potentially regulate biofilm formation of biosorption and facilitate the desulfonation and defluorination processes of biotransformation. Transcriptomic analysis demonstrated the high expression levels of these genes, including alkanesulfonate monooxygenase, catechol dioxygenase, (S)-2-haloacid dehalogenase and putative cytochrome P450, suggesting their involvement in PFOS biotransformation. The expression of these genes supports the presence of candidate metabolites of PFOS biotransformation detected in the previous study. These findings emphasise the significant potential of bacterial consortia and the crucial role played by genes encoding enzymes in facilitating the remediation of PFOS contaminants.},
}
@article {pmid40170118,
year = {2025},
author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P},
title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {89},
pmid = {40170118},
issn = {2049-2618},
support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; },
mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Temperature ; *RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/classification/genetics ; Carbon Dioxide/metabolism ; Carbon Cycle ; Metagenomics ; },
abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.<br><br>RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including &#x3b2;-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.<br><br>CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.},
}
@article {pmid40169660,
year = {2025},
author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE},
title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {547},
pmid = {40169660},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Metagenomics ; *Microbiota ; *Feces/microbiology ; Metagenome ; Saliva/microbiology ; Mouth/microbiology ; },
abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.},
}
@article {pmid40169555,
year = {2025},
author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P},
title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {115},
pmid = {40169555},
issn = {2158-3188},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Stress, Psychological/metabolism/microbiology ; *Feces/microbiology/chemistry ; Male ; *Social Defeat ; *Metabolome ; *Disease Models, Animal ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal ; *Anhedonia ; Humans ; Mice, Inbred C57BL ; Female ; RNA, Ribosomal, 16S/genetics ; Depression/metabolism/microbiology ; },
abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.},
}
@article {pmid40169141,
year = {2025},
author = {Zhang, J and Ying, X and Hu, R and Huang, Y and Wang, R and Wu, L and Han, D and Ma, R and He, K},
title = {Metagenomic and metabolomic analysis of gut microbiome's role in spinal cord injury recovery in rats.},
journal = {Biomolecules &amp; biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2025.12164},
pmid = {40169141},
issn = {2831-090X},
abstract = {Spinal cord injury (SCI) induces profound systemic changes, including disruptions in gut microbiome composition and host metabolism. This study aimed to investigate the impact of SCI on gut microbial diversity and serum metabolites in rats, and to explore potential microbiome-metabolite interactions that may influence recovery. Male Sprague-Dawley (SD) rats were assigned to either SCI or sham-operated groups. Fecal samples were collected for whole-genome metagenomic sequencing, and serum samples were analyzed using untargeted metabolomics. Gut microbial composition and diversity were assessed using α- and β-diversity indices, while Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa. Metabolomic pathway analysis was performed to detect significant changes in serum metabolites, and Spearman's correlation was used to evaluate associations between gut microbes and metabolites. SCI significantly altered gut microbiota composition, with increased proportions of Ligilactobacillus and Staphylococcus, and decreased proportions of Lactobacillus and Limosilactobacillus. Metabolomic analysis revealed disrupted energy metabolism and elevated oxidative stress in SCI rats, as indicated by increased serum levels of pyruvate and lactic acid. Correlation analysis further identified significant associations between specific gut bacteria and key metabolites, suggesting microbiome-driven metabolic dysregulation following SCI. These findings highlight significant interactions between the gut microbiota and host metabolism after SCI and suggest that microbiome-targeted interventions may hold therapeutic potential for improving recovery by modulating metabolic function and oxidative stress responses.},
}
@article {pmid40156868,
year = {2025},
author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L},
title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.},
journal = {Nucleic acids research},
volume = {53},
number = {6},
pages = {},
pmid = {40156868},
issn = {1362-4962},
support = {//New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; //Bill &amp; Melinda Gates Foundation/ ; },
mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Bacteriophages/genetics/enzymology ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/enzymology ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics ; Sequence Analysis, DNA/methods ; DNA, Viral/genetics/metabolism ; },
abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.},
}
@article {pmid40169073,
year = {2025},
author = {Sun, L and Yin, Y and Guo, Y and Chen, H and Wang, H},
title = {Metagenomic Next-Generation Sequencing Enhances the Diagnosis of Q Fever: A Retrospective Observational Study.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102845},
doi = {10.1016/j.tmaid.2025.102845},
pmid = {40169073},
issn = {1873-0442},
abstract = {BACKGROUND: Q fever, a global zoonosis, poses a significant challenge for public health due to its varied and nonspecific clinical presentations, making diagnosis difficult. Metagenomic next-generation sequencing (mNGS) is a potential tool for diagnosing Q fever.<br><br>METHODS: This retrospective observational study was conducted on patients with Q fever admitted to Peking University People's Hospital, from May 2023 to November 2024. mNGS was performed using the patient's peripheral blood, and the qPCR of Coxiella burnetii was also adopted. Subsequently, the clinical data of patients diagnosed with Q fever were systematically evaluated.<br><br>RESULTS: Twelve peripheral blood samples of 12 patients were detected Coxiella burnetii positive by mNGS. Most patients were male (10, 83.33%). Fever (12, 100%), muscle soreness (8, 66.7%), and headache (4, 33.3%) were the most common clinical manifestations. Specific qPCR of Coxiella burnetii was detected positive in 8 patients. Chronic Q fever was diagnosed in two patients, who had aortic valve replacement, and their immunological markers, like anti-nuclear were elevated. Once the diagnosis was clear, proper antibiotics were used, and all patients were discharged in better health.<br><br>CONCLUSION: Metagenomic next-generation sequencing enhances the diagnosis of Q fever, especially for patients displaying atypical and various clinical symptoms and having unclear epidemiological data or histories of antibiotic use.},
}
@article {pmid40169018,
year = {2025},
author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B},
title = {Making sense of the virome in light of evolution and ecology.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2044},
pages = {20250389},
doi = {10.1098/rspb.2025.0389},
pmid = {40169018},
issn = {1471-2954},
support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Virome ; *Viruses/genetics ; Biological Evolution ; Metagenomics ; Ecology ; Ecosystem ; Phylogeny ; },
abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.},
}
@article {pmid40168930,
year = {2025},
author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY},
title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138077},
doi = {10.1016/j.jhazmat.2025.138077},
pmid = {40168930},
issn = {1873-3336},
abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.},
}
@article {pmid40168814,
year = {2025},
author = {Harish, J and Prasannakumar, MK and Venkateshbabu, G and Karan, R and Mahesh, HB and Devanna, P and Sarangi, AN and Patil, SS and Tejashwini, V and Lohithaswa, HC and Kagale, S},
title = {Molecular and genomic insights into the pathogenicity of Sarocladium zeae causing maize stalk rot disease.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128146},
doi = {10.1016/j.micres.2025.128146},
pmid = {40168814},
issn = {1618-0623},
abstract = {Post-flowering stalk rot (PFSR) of maize has been traditionally associated with Fusarium verticillioides. Conversely, this study reveals Sarocladium zeae as a new phytopathogen responsible for the disease. This research was conducted to gain a comprehensive understanding of S. zeae by investigating its pathogenic mechanisms, profiling its metabolome, and deciphering its genomic characteristics. Maize stalks displaying stalk rot symptoms were collected from various regions of India. S. zeae was isolated and characterized using ITS and TEF-1α sequencing. Cultures of S. zeae exhibited slower growth on PDA medium compared to F. verticillioides, which dominated due to its rapid growth rate. Pathogenicity was confirmed through a toothpick inoculation assay. The symptoms induced by S. zeae was characterized by powdery, dry, pale brown-black discoloration, were distinct from the typical dark-brown lesions of Fusarium stalk rot. Enzymatic assays revealed increased activity of β-glucosidase, cellulase, and pectate lyase in infected stalks, while qPCR analysis showed the upregulation of endoglucanase and β-glucosidase genes in infected stalks underscored the critical roles of cellulase and β-glucosidase in pathogenicity Metagenomic analysis identified S. zeae as the predominant species in infected stalk samples. Genome assembly revealed the pathogen's complete genetic repertoire, including genes encoding effector proteins and CAZymes involved in cell wall degradation. Moreover, we have demonstrated that the S. zeae as a causal agent of maize stalk rot and further shedding light on its transition from an endophytic to a pathogenic lifestyle. Taken together, this research represents the first report to attribute maize stalk rot to S. zeae and to present its complete genome assembly, significantly advancing the understanding of its biology and pathogenic potential.},
}
@article {pmid40168753,
year = {2025},
author = {Ji, X and Yu, X and Xu, Y and Wu, Q and Madadi, M and Khaneghah, AM},
title = {Initial acidity regulates microbial sulfur metabolism in the spontaneous fermentation of sesame flavor-type baijiu.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111182},
doi = {10.1016/j.ijfoodmicro.2025.111182},
pmid = {40168753},
issn = {1879-3460},
abstract = {Volatile sulfur compounds play a crucial role in fermented foods, however, their metabolism during spontaneous food fermentation remains underexplored. With 3-(methylthio)-1-propanal as a case, we revealed the effect of initial acidity on the sulfur metabolism during sesame flavor-type baijiu fermentation. Results showed that the content of 3-(methylthio)-1-propanal reached 383.29 μg/kg with 1.8 mmol/10 g of the initial acidity, and it decreased to 320.54 μg/kg when the initial acidity increased to 2.4 mmol/10 g. Metagenomic analysis identified 11 core microbes associated with sulfur metabolism, characterized by gene abundance (> 0.5 %) and catalytic enzyme distribution frequency (> 10 %). Saccharomyces was the main producer of sulfur compounds. Lactobacillus was an important player in the methyl cycle pathway of sulfur metabolism. Low initial acidity increased the abundance of Lactobacillus and the content of genes associated with the methyl cycle pathway (P < 0.05). This resulted in a significant increase of methionine (253.26 mg/kg) (P < 0.05) and 3-(methylthio)-1-propanal contents (383.29 μg/kg) (P < 0.05). In simulated fermentation, the content of 3-(methylthio)-1-propanal significantly increased by 2.91 folds when Saccharomyces cerevisiae was cocultured with Lactobacillus acetotolerans (P < 0.05), and the transcription of genes related to sulfur metabolism significantly increased by 33.71 folds (P < 0.05). Results indicated that low initial acidity increased the abundance of Lactobacillus, which mediates the methyl cycle pathway in the sulfur metabolism, thereby increasing the contents of methionine and volatile sulfur compounds. This work provided insight into the regulation of metabolic mechanisms of volatile sulfur compounds in baijiu fermentation.},
}
@article {pmid40168325,
year = {2025},
author = {Yun, H and Seo, JH and Kim, YK and Yang, J},
title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320916},
doi = {10.1371/journal.pone.0320916},
pmid = {40168325},
issn = {1932-6203},
mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; },
abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.},
}
@article {pmid40167463,
year = {2025},
author = {Sun, C and Liu, H and Teng, J and Feng, W and Wang, D and Wang, X and Zhao, J and Wang, Q},
title = {Impact of Microplastic Exposure on Sand Crab Scopimera globosa Behavior: Implications for Microplastic Transport and Sulfur Cycling through Bioturbation.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01192},
pmid = {40167463},
issn = {1520-5851},
abstract = {The accumulation of microplastics (MPs) in estuarine regions and their ecological consequences have become global environmental concerns. Estuarine sediments function as major sinks for MPs and hotspots for critical biogeochemical processes, which are significantly influenced by benthic bioturbation. However, the impacts of MPs on the behavior of highly mobile benthic organisms and the ecological effects of bioturbation activities remain poorly understood. This study utilized laboratory simulation experiments, AI-based behavioral tracking, and metagenomic sequencing to systematically examine the effects of sand crab bioturbation on MPs migration, sediment physicochemical properties and sulfur cycling processes. Results demonstrated that sand crab bioturbation substantially enhanced the vertical migration of MPs, with fluxes to surface layers and the overlying water increasing by 27-fold compared to undisturbed conditions. Exposure to PE-MPs reduced sand crabs' surface foraging intensity and induced behavioral abnormalities. The crabs actively avoided MPs, exhibiting a preference for burrowing and residing in deeper sediment layers. This behavioral shift significantly altered microbial community distributions, with an increase of Pseudomonadota abundance and a decline of sulfate-reducing bacteria Thermodesulfobacteriota abundance. Furthermore, bioturbation accelerated sulfate oxidation in deeper sediments while inhibited dissimilatory sulfate reduction. This study is the first to identify the role of bioturbation in promoting the upward migration of MPs in sediments. Altered sand crab bioturbation will impact sediment biogeochemistry, estuarine function, and coastal resilience.},
}
@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14105},
doi = {10.1111/1755-0998.14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0069/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/BIA/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50027/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0048/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}
@article {pmid40166061,
year = {2025},
author = {Zhang, L and Guo, Y and Wang, X and Gai, W and Liu, L},
title = {Severe adenovirus pneumonia complicated by acute respiratory distress syndrome in immunocompetent patients: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1524783},
pmid = {40166061},
issn = {2296-858X},
abstract = {BACKGROUND: Human adenovirus (HAdV) is one of the most important pathogens detected in acute respiratory illness in pediatric and immunocompromised patients, but it is relatively rare to develop severe pneumonia in immunocompetent patients. We analyzed the clinical features, as well as the diagnosis and treatment processes, to provide a reference for clinical practice.<br><br>CASE PRESENTATION: We report a case of severe pneumonia caused by HAdV, complicated by acute respiratory distress syndrome (ARDS), in an immunocompetent patient with no underlying conditions. Chest computed tomography (CT) revealed consolidation in the right lower lung. Conventional microbial tests were negative, but metagenomic next-generation sequencing (mNGS) identified a large number of HAdV sequences in blood and sputum. Together with the clinical symptoms, this confirmed the diagnosis of severe pneumonia caused by HAdV. The patient was discharged after timely treatment with cidofovir.<br><br>CONCLUSION: In our study, we described a rare case of severe pneumonia caused by HAdV, complicated by ARDS, in an immunocompetent patient. mNGS proves to be an effective diagnostic tool for guiding treatment decisions.},
}
@article {pmid40165946,
year = {2025},
author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X},
title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1563225},
pmid = {40165946},
issn = {1664-3224},
mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration &amp; dosage ; Aquaporin 3 ; Aquaporin 4 ; },
abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.},
}
@article {pmid40165815,
year = {2025},
author = {Battur, M and Aaqil, M and Zheng, J and Lin, HX and Chuluunotgon, B and Zorigtbaatar, T and Zhao, C and Tian, Y},
title = {Exploring the effects of milk-enriched walnut soy sauce: Insights from GC-IMS and metagenomics approach to flavor and microbial shifts.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102364},
pmid = {40165815},
issn = {2590-1575},
abstract = {This study investigates the impact of milk addition on the fermentation of walnut soy sauce, using Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) and metagenomics to analyze flavor profiles and microbial dynamics. GC-IMS analysis showed significant increases in volatile compounds such as esters (ethyl acetate), aldehydes (hexanal), and alcohols (isoamyl alcohol), enhancing the aroma and taste. Metagenomic analysis revealed that milk increased microbial diversity, with Weissella and Lactobacillus dominating early fermentation. The milk-enriched soy sauce (SYM) exhibited higher amino acid nitrogen (2.67 g/L), and total nitrogen (7.18 g/L) compared to the control, indicating improved nutritional quality. Protease activity peaked at 2438.5 U/g for neutral protease, supporting efficient protein hydrolysis. Relative Odor Activity Value (ROAV) analysis identified 29 key flavor compounds, including 3-methyl butanol and ethyl 2-methyl butyrate, which contributed fruity and buttery notes to SYM. These results suggest that milk enhances microbial growth and improves both flavor and nutritional quality of walnut soy sauce.},
}
@article {pmid40165787,
year = {2025},
author = {Huang, Z and Wang, J and He, X and Zhang, M and Ren, X and Yu, W and Yao, S and Ji, K},
title = {Divergent profiles of rhizosphere soil carbon and nitrogen cycling in Pinus massoniana provenances with different types of carbon storage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537173},
pmid = {40165787},
issn = {1664-302X},
abstract = {INTRODUCTION: In subtropical China, P. massoniana is a timber tree species which have a great potential for carbon sequestration. However, few studies have investigated how varying levels of carbon storage in P. massoniana provenances affect the soil microbial functional potential related to nutrient cycling within the rhizosphere.<br><br>METHODS: In this investigation, metagenomic sequencing was employed to explore the differences in carbon and nitrogen cycling capabilities among rhizosphere microbial communities within P. massoniana provenances, categorized by high, medium, and low levels of carbon storage.<br><br>RESULTS: Our findings revealed a significant increase in the relative abundance of Acidobacteriota and Ascomycota by 23 and 61%, respectively, whereas Basidiomycota significantly decreased by 8% in the rhizosphere of P. massoniana provenances with high carbon storage compared with those with low carbon storage. The variability in carbon storage among P. massoniana provenances was linked to marked disparities in the presence of key genes essential for carbon and nitrogen cycling within their rhizosphere soils.<br><br>DISCUSSION: Notably, in P. massoniana provenances characterized by high carbon storage, the rhizosphere presented a significantly elevated presence of genes associated with carbon decomposition, carbon assimilation, methane generation, and denitrification, in stark contrast to provenances with medium and low carbon storage. Furthermore, P. massoniana provenances with high carbon storage rates presented increased transformation and availability of soil carbon and nitrogen, along with increased potential for ecological restoration. Moreover, the rhizosphere soil nitrification of P. massoniana provenances with low carbon storage surpassed that of other provenances, leading to increased available nitrogen content and elevated nitrate leaching risk. In the P. massoniana rhizosphere, critical soil factors, including soil organic carbon (SOC), total nitrogen (TN), pH, and nitrate nitrogen (NO3 [-]-N) content, significantly shape the functionality of genes associated with carbon and nitrogen cycling. In conclusion, our study lays a scientific foundation for establishing P. massoniana plantations and identifying P. massoniana provenances with superior ecological value and potential.},
}
@article {pmid40165255,
year = {2025},
author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J},
title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {141},
pmid = {40165255},
issn = {1466-609X},
support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization &amp; administration/statistics &amp; numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics &amp; numerical data ; },
abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.<br><br>METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.<br><br>RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.<br><br>CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.},
}
@article {pmid40165201,
year = {2025},
author = {Lin, L and Peng, X and Chen, L and Dong, L and Zhong, L},
title = {Case report: novel NFKB2 variant associated with pediatric eosinophilic granulomatosis with polyangiitis (EGPA) in the COVID-19 pandemic.},
journal = {Pediatric rheumatology online journal},
volume = {23},
number = {1},
pages = {35},
pmid = {40165201},
issn = {1546-0096},
mesh = {Humans ; Female ; *COVID-19/complications ; Child ; *NF-kappa B p52 Subunit/genetics ; SARS-CoV-2 ; Churg-Strauss Syndrome/genetics/diagnosis ; Granulomatosis with Polyangiitis/genetics/diagnosis ; },
abstract = {BACKGROUND: Childhood-onset eosinophilic granulomatosis with polyangiitis (cEGPA) is a rare type of systemic autoimmune disorder. Variants in the NFKB2 gene can manifest as common variable immunodeficiency or combined immunodeficiency, often accompanied by autoimmunity and ectodermal dysplasia. Here, we report a case of a Chinese patient who carries NFKB2 variants that coexist with cEGPA, a novel combination which, to our knowledge, has not been previously published.<br><br>CASE PRESENTATION: We reported a 9-year and 10-month-old girl who presented with cough, wheezing, dyspnea, hypereosinophilia, and vasculitis. Notably, she had significant bilateral pulmonary interstitial lesions. We performed metagenomic next-generation sequencing (mNGS), bronchoscopy and immunological analysis. She was considered to have refractory cEGPA after six months of corticosteroid and immunosuppressive treatment. Tapering off corticosteroids posed a challenge, and multiple immunosuppressive agents were ineffective. Our patient suffered from recurrent fever, wheezing, dyspnea and perianal abscess, along with life-threatening infections, including pneumocystis jirovecii pneumonia (PJP) and severe coronavirus disease 2019 (COVID-19) pneumonia during the pandemic. Her cytokines and inflammatory markers showed a profound collapse. She developed significant hypoxemia, which necessitated mechanical ventilation. Primary immunodeficiency gene panel testing revealed a novel de novo variant in NFKB2 (c.2578&#x2009;+&#x2009;2 dup) that was classified as pathogenic. Despite treatment with antibacterial, antiviral, and antifungal agents, biologics, and plasma exchange, she ultimately succumbed to respiratory failure.<br><br>CONCLUSIONS: This case report establishes a novel link between NFKB2 variants and EGPA, particularly in the context of the COVID-19 pandemic. This study expands the spectrum of NFKB2 variants and vividly illustrates the complex interrelationships among autoimmunity, infection, and immunodeficiency.},
}
@article {pmid40165140,
year = {2025},
author = {Trivett, H and Darby, AC and Oyebode, O},
title = {Academic and clinical perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {448},
pmid = {40165140},
issn = {1471-2334},
mesh = {Humans ; *Metagenome ; *Communicable Diseases/diagnosis ; *COVID-19/diagnosis ; Metagenomics/methods ; SARS-CoV-2/genetics ; England ; },
abstract = {BACKGROUND: Effective infectious disease diagnostics (IDD) are vital for informing clinical decision-making regarding the treatment and patient management of disease and infections. In England, conventional clinical methods rely upon culture-dependent techniques, and there has been little shift in the acceptance and integration of culture-independent sequencing methods into routine clinical IDD. This study explored stakeholders' experiences within IDD, including those working in clinical settings and those conducting research at the forefront of microbial genomics. From the participants' experiences, the study aimed to identify barriers and facilitators driving the development and implementation of metagenome sequencing as a routine diagnostic.<br><br>METHODS: Virtual semi-structured interviews were conducted with purposively selected individuals involved in IDD. The interviews explored the experiences of implementing metagenome sequencing as a diagnostic tool and decisions about which diagnostics are used for identifying bacteria-causing infections. Thematic analysis was used to analyse the data, and an Interpretive Phenomenological approach was used throughout.<br><br>RESULTS: Ten individuals were interviewed between July 2021 and October 2021, including clinical scientists, consultants, and professors in academia. Their experience ranged from limited knowledge of metagenome sequencing to an expert understanding of the phenomenon. The thoughts and perspectives of participants of the study could be grouped into five themes: Availability of diagnostics for infectious diseases; Clinical laboratory infrastructure; Ethical Data Sharing: Enhancing metagenomics through Open Access; Case study in action: COVID-19; and The importance of communication to improve developments of new diagnostics. Participants recognised the need for new diagnostics to be implemented to overcome the limitations of current diagnostic approaches but highlighted the barriers to integrating new diagnostics into clinical settings, such as the impact on clinical decision-making, accreditation, and cost. Further, participants felt that lessons could be learnt from using metagenomics in COVID-19 and how other diagnostic platforms have been integrated into clinical settings over the last 20 years.<br><br>CONCLUSIONS: The study provided insights into stakeholders' perspectives and opinions to address the knowledge gap in current literature and identified barriers and facilitators which drive the implementation of metagenome sequencing as a routine IDD in clinical settings. Knowledge of new and upcoming genomic diagnostic testing is not equally distributed throughout the UK, impacting the understanding and drive to integrate metagenome sequencing into routine clinical diagnostics. Improvements in access to new diagnostics could improve patient treatment and management and positively impact population health.},
}
@article {pmid40165002,
year = {2025},
author = {Wang, H and Su, Q and Sun, H and Meng, Y and Xing, X and Zheng, H and Li, Y},
title = {Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12976},
pmid = {40165002},
issn = {1749-4877},
abstract = {The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.},
}
@article {pmid40164980,
year = {2025},
author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM},
title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2484385},
doi = {10.1080/19490976.2025.2484385},
pmid = {40164980},
issn = {1949-0984},
mesh = {Animals ; *Diet ; *Hominidae/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Life Style ; Humans ; Adaptation, Physiological ; Pan troglodytes/microbiology ; Metagenome ; Phylogeny ; Africa ; },
abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.},
}
@article {pmid40164860,
year = {2025},
author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG},
title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.},
journal = {Tropical animal health and production},
volume = {57},
number = {3},
pages = {148},
pmid = {40164860},
issn = {1573-7438},
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Amino Acids/metabolism ; *Animal Feed/analysis ; Male ; *Metabolome ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage/pharmacology ; Cross-Over Studies ; Dietary Supplements/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.},
}
@article {pmid40164832,
year = {2025},
author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA},
title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40164832},
issn = {2058-5276},
abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.},
}
@article {pmid40164697,
year = {2025},
author = {Jia, L and Ke, Y and Zhao, S and Liu, J and Luo, X and Cao, J and Liu, Y and Guo, Q and Chen, WH and Chen, F and , and Wang, J and Wu, H and Ding, J and Zhao, XM},
title = {Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40164697},
issn = {1476-5578},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.},
}
@article {pmid40164638,
year = {2025},
author = {Mills, S and Ijaz, UZ and Lens, PNL},
title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {54},
pmid = {40164638},
issn = {2055-5008},
support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; 15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification ; Microbiota ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics ; Methane/metabolism ; Metagenome ; Phylogeny ; },
abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.},
}
@article {pmid39812462,
year = {2025},
author = {Kamel, K and Sardo Infirri, S and Riddell, A and Chowdary, P and Batty, P},
title = {Factor VIII Antibodies Demonstrate Type I or Type II Kinetics in Acquired Haemophilia A.},
journal = {Haemophilia : the official journal of the World Federation of Hemophilia},
volume = {31},
number = {2},
pages = {313-318},
pmid = {39812462},
issn = {1365-2516},
mesh = {*Hemophilia A/immunology/blood ; Humans ; *Factor VIII/immunology ; Kinetics ; Male ; Retrospective Studies ; *Autoantibodies/immunology/blood ; Aged ; Middle Aged ; Female ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Acquired haemophilia A (AHA) is an acquired bleeding disorder resulting from autoantibodies against Factor VIII (FVIII). Previous studies have reported differences in FVIII inhibitor kinetics (type I or type II) in AHA compared to severe haemophilia A.<br><br>AIM: To characterise inhibitor kinetics in AHA and evaluate the proportions displaying type I, II or indeterminate kinetics.<br><br>METHODS: Single-centre retrospective study of inhibitor kinetics in adults with AHA. Type I kinetics were defined as linear FVIII inhibition with &#x2265; 97% FVIII inactivation. Type II kinetics were defined as non-linear kinetics and inability to completely neutralise FVIII. Inhibitor titres were calculated using two methods outlined by the International Council for Standardisation in Haematology.<br><br>RESULTS: Baseline samples from 34 patients were included. Fifteen samples (44.1%) exhibited type I kinetics, 16 samples (47.1%) exhibited type II kinetics and 3 (8.8%) were indeterminate. Plateau mean residual FVIII:C was higher for inhibitors displaying type II compared to type I kinetics (18.6&#xa0;vs. 2.9&#xa0;IU/dL, p < 0.0001). Non-linear regression using a dose-response curve without categorisation for kinetics type yielded a poor fit (R[2] = 38%), which improved with refitting using categories of type I or II kinetics that explained 87% and 85% of the variability. The median difference in inhibitor titre between the two reporting methods was 5% and 15% in the type I and II kinetics groups, respectively.<br><br>CONCLUSION: FVIII autoantibodies demonstrate either type I or type II kinetics. Greater discrepancy in reported inhibitor titres depending on the method used is seen for inhibitors with type II kinetics.},
}
@article {pmid40164558,
year = {2025},
author = {Zhou, HY and Zhang, J and Weng, DD},
title = {[One case of recurrent infection with chlamydia psittaci pneumonia].},
journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases},
volume = {43},
number = {3},
pages = {237-240},
doi = {10.3760/cma.j.cn121094-20240109-00008},
pmid = {40164558},
issn = {1001-9391},
mesh = {Humans ; *Chlamydophila psittaci/isolation &amp; purification ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; Psittacosis/microbiology ; Recurrence ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {This paper analyzed the clinical data of a patient with recurrent infection of chlamydia psittaci pneumonia within 7 months. The patient had a clear history of contact with live poultry, and the clinical manifestations were dry cough, persistent fever, and respiratory failure. Chest CT imaging changes showed lobar consolidation of infected lung lobes, ground-glass shadows, bronchial air-filling signs, and pleural effusion. The two infections were detected in bronchoalveolar lavage fluid by metagenomic next-generation sequencing (mNGS) and pathogen targeted next-generation sequencing (tNGS), respectively, to achieve early diagnosis of chlamydia psittaci pneumonia. New tetracycline drugs were used as the core of treatment for both infections, and rapid improvement was achieved after anti-infection treatment.},
}
@article {pmid40163992,
year = {2025},
author = {Lei, H and Zhou, N and Zhang, J and Lin, R and Chen, T and Wu, J and Su, L and Liu, S and Liu, T},
title = {Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138075},
doi = {10.1016/j.jhazmat.2025.138075},
pmid = {40163992},
issn = {1873-3336},
abstract = {Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.},
}
@article {pmid40163955,
year = {2025},
author = {Du, R and Cui, L and Feng, Y and Lv, X and Gao, Y and Li, A and Wang, Q and Ma, Y},
title = {Enhancing the decomposition and composting of food waste by in situ directional enzymatic hydrolysis: performance, ARGs removal and engineering application.},
journal = {Waste management (New York, N.Y.)},
volume = {200},
number = {},
pages = {114774},
doi = {10.1016/j.wasman.2025.114774},
pmid = {40163955},
issn = {1879-2456},
abstract = {This research utilized food waste (FW) as substrate, innovatively developed a directional multienzyme applied for accelerating FW hydrolysis and composting, and an in situ enzymatic hydrolysis combining in composting has been developed to manage FW. Results showed that the composting was achieved at 4 days and the humification index was increased by 2.60 compared with that of without enzymatic hydrolysis. FTIR analysis revealed that following multienzyme pretreatment, the primary constituents of FW, including protein, starch and lipid, underwent structural breakdown, among which protein exhibited the higher susceptibility to multienzyme action and was the first to disintegrated, and the structure also became looser. Moreover, the total antibiotic resistance gene (ARGs) was reduced more than 90 % in the proposed composting process. Analysis of microbial communities and metagenomes showed that multienzyme pretreatment reshaped microbial communities towards favoring FW hydrolysis and humification. The engineering application analysis further implied that the proposed composting approach is scale flexible, engineering applicable, economic viability and environmentally sustainability. It was anticipated that this study has the potential to trigger a paradigm shift in future in-situ treatment of FW to achieve full resource recovery towards zero solid discharge.},
}
@article {pmid40163458,
year = {2025},
author = {Vendrell-Fernández, S and Beamud, B and Abou Haydar, Y and Am de Sousa, J and Burlaud-Gaillard, J and Kornobis, E and Raynal, B and Vinh, J and Bikard, D and Ghigo, JM},
title = {Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles.},
journal = {PLoS biology},
volume = {23},
number = {3},
pages = {e3002787},
doi = {10.1371/journal.pbio.3002787},
pmid = {40163458},
issn = {1545-7885},
mesh = {*Bacteriophages/physiology/genetics ; *Virion/ultrastructure ; *Bacteroides/virology/genetics ; *Lysogeny ; Phylogeny ; Retroelements/genetics ; DNA, Viral/genetics ; Genome, Viral ; },
abstract = {Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.},
}
@article {pmid40163416,
year = {2025},
author = {Tordoff, J and Alfonse, LE and Makarova, KS and Ornstein, A and Garrity, AJ and Yan, WX and Scott, DA and Koonin, EV and Cheng, DR},
title = {Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems.},
journal = {The CRISPR journal},
volume = {},
number = {},
pages = {},
doi = {10.1089/crispr.2024.0100},
pmid = {40163416},
issn = {2573-1602},
abstract = {Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.},
}
@article {pmid40162776,
year = {2025},
author = {Haft, DH and Tolstoy, I},
title = {Novel selenoprotein neighborhoods suggest specialized biochemical processes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0141724},
doi = {10.1128/msystems.01417-24},
pmid = {40162776},
issn = {2379-5077},
abstract = {UNLABELLED: Prokaryotic genomes encode selenoproteins sparsely, roughly one protein per 5,000. Finding novel selenoprotein families can expose unknown biological processes that are enabled, or at least enhanced, by having a selenium atom replace a sulfur atom in some cysteine residues. Here, we report the discovery of 18 novel selenoprotein families or second selenocysteine sites in previously unrecognized extensions of protein translations. Most of these families had some confounding factors-too small a family, too few selenoproteins in the family, selenocysteine (U) too close to one end, a skew toward understudied or uncultured lineages, and consequently were missed previously. Discoveries were triggered by observations during the ongoing construction of protein family models for the National Center for Biotechnology Information's RefSeq and Prokaryotic Gene Annotation Pipeline or made by targeted searches for novel selenoproteins in the vicinity of known ones, rather than by any broadly applied genome mining method. Unrelated families TsoA, TsoB, TsoC, and TsoX are adjacent in tso (three selenoprotein operon) loci in the bacterial phylum Thermodesulfobacteriota. TrsS (third radical SAM selenoprotein) occurs strictly in the context of a molybdopterin-dependent aldehyde oxidoreductase. A short carboxy-terminal motif, U-X-X-stop (UXX-star), occurs in selenoproteins with various architectures, usually providing the second U in the protein. The multiple new selenocysteine insertion sites, selenoprotein families, and selenium-dependent operons we curated manually suggest that many more proteins and pathways remain to be discovered; once improved computational methods are applied comprehensively to the latest collections of microbial genomes and metagenomes, they may reveal surprising new biochemical processes.<br><br>IMPORTANCE: Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast "dark matter" of hard-to-decipher protein sequences. Selenoproteins, optimized by natural selection to encode selenocysteine where cysteine might have been encoded much more easily, carry a strong clue to their function-some specialized aspect of binding or catalysis. Operons with multiple adjacent, but otherwise unrelated, selenoproteins should provide even more vivid information. In this study, efforts in protein family construction and curation, aimed at improving the PGAP genome annotation pipeline, generated multiple novel selenoprotein-containing genomic contexts that may lead to the future characterization of several systems of proteins. Past observations suggest roles in the metabolic handling of trace elements (mercury, tungsten, arsenic, etc.) or of organic compounds refractory to simpler enzymatic pathways. In addition, the work significantly expands the truth set of validated selenoproteins, which should aid future, more automated genome mining efforts.},
}
@article {pmid40162769,
year = {2025},
author = {Dickter, JK and Zhao, Y and Parekh, V and Ma, H and Modi, BG and Li, W-Y and Armenian, SH and Wu, X and Abdulla, FR},
title = {Mining metagenomes and metatranscriptomes unveils viruses associated with cutaneous squamous cell carcinoma in hematopoietic stem cell transplant recipients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0005325},
doi = {10.1128/spectrum.00053-25},
pmid = {40162769},
issn = {2165-0497},
abstract = {UNLABELLED: We investigated the presence of viral DNA and RNA in cutaneous squamous cell carcinoma (cSCC) tumor and normal tissues from nine individuals with a history of hematopoietic stem cell transplantation (HCT). Microbiome quantification through DNA and RNA sequencing (RNA-seq) revealed the presence of 18 viruses in both tumor and normal tissues. DNA sequencing (DNA-seq) identified Torque teno virus, Saimiriine herpesvirus 1, Merkel cell polyomavirus, Human parvovirus B19, Human gammaherpesvirus-4, Human herpesvirus-6, and others. RNA-seq revealed additional viruses such as Tobamovirus, Pinus nigra virus, Orthohepadnavirus, Human papillomavirus-5, Human herpesvirus-7, Human gammaherpesvirus-4, Gammaretrovirus, and others. Notably, DNA-seq indicated that tumor samples exhibited low levels of Escherichia virus in three out of nine subjects and elevated levels of Human gammaherpesvirus-4 in one subject, while normal samples frequently contained Gammaretrovirus and occasionally Escherichia virus. A comparative analysis using both DNA- and RNA-seq captured three common viruses: Abelson murine leukemia virus, Murine type C retrovirus, and Human gammaherpesvirus-4. These findings were corroborated by an independent data set, supporting the reliability of the viral detection methods utilized. The study provides insights into the viral landscape in post-HCT patients, emphasizing the need for comprehensive viral monitoring in this vulnerable population.<br><br>IMPORTANCE: This study is important because it explores the potential role of viruses in the development of cSCC in individuals who have undergone allogeneic HCT. cSCC is common in this population, particularly in those with chronic graft-versus-host disease on long-term immunosuppression. By using advanced metagenomic and metatranscriptomic next-generation sequencing, we aimed to identify viral pathogens present in tumor and adjacent normal tissue. The results could lead to targeted preventive or therapeutic interventions for these high-risk people, potentially improving their outcomes and management of cSCC.},
}
@article {pmid40162572,
year = {2025},
author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y},
title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2502743},
doi = {10.1002/advs.202502743},
pmid = {40162572},
issn = {2198-3844},
support = {2024YFD1700500//National Key R&amp;D Program&#xa0;of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&amp;D Program&#xa0;of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&amp;F University Young Talent Project/ ; },
abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.},
}
@article {pmid40162034,
year = {2025},
author = {Huang, L and Zheng, D and Li, T and Li, X and Kong, J and Wang, K and Wang, S and Cao, C},
title = {Disseminated Histoplasmosis Due to Anti-IFN-γ Autoantibodies-Associated Immunodeficiency.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1605-1609},
doi = {10.2147/IDR.S513750},
pmid = {40162034},
issn = {1178-6973},
abstract = {BACKGROUND: Disseminated histoplasmosis caused by the temperature-dependent dimorphic fungus Histoplasma capsulatum is an invasive fungal disease rarely reported in southern China. Here, we report a case of disseminated histoplasmosis due to anti-IFN-γ autoantibodies (AIGA)- associated immunodeficiency.<br><br>CASE PRESENTATION: We present the case of a 57-year-old HIV-negative female patient with disseminated histoplasmosis in southern China. The patient showed progressively enlarging multiple clavicular, neck, and upper chest skin nodules and dyspnea, which led to the initial suspicion of pulmonary tuberculosis or lung cancer. Bacterial cultures results were negative. Histopathology of a skin tissue showed infectious granulomas. Disseminated histoplasmosis was diagnosed via next-generation sequencing (mNGS) and fungal culture. Furthermore, enzyme-linked immunosorbent assay results from a peripheral blood confirmed that the patient had a high-titer of AIGA.<br><br>CONCLUSION: This case prompts clinicians to consider histoplasmosis an important differential diagnosis in a region where talaromycosis is highly endemic. This case report emphasizes that clinicians should be vigilant for immunodeficiency and consider testing for AIGA in HIV-negative patients who are suspected of having complex opportunistic infections.},
}
@article {pmid40161798,
year = {2025},
author = {Zeamer, AL and Lai, Y and Sanborn, V and Loew, E and Tracy, M and Jo, C and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP},
title = {Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641911},
pmid = {40161798},
issn = {2692-8205},
abstract = {Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.},
}
@article {pmid40161742,
year = {2025},
author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.11.642547},
pmid = {40161742},
issn = {2692-8205},
abstract = {UNLABELLED: Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.<br><br>IMPORTANCE: Human microbiota-associated (HMA) mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effect of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, MET4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbour a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.},
}
@article {pmid40161675,
year = {2025},
author = {Secaira-Morocho, H and Jiang, X and Zhu, Q},
title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.13.643052},
pmid = {40161675},
issn = {2692-8205},
abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes evenly distributed across major microbial phyla, covering only a small fraction of gene families. And yet, most microbial diversity is found in metagenome-assembled genomes that are unevenly distributed and harbor gene families that do not fit the criteria of universal orthologous genes. To address these limitations, we systematically evaluate the phylogenetic signal of gene families annotated from KEGG and EggNOG functional databases for deep microbial phylogenomics. We show that markers selected from an expanded pool of gene families and tailored to the input genomes improve the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes. The improved accuracy of trees compared to previous markers persists even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. We introduce TMarSel, a software tool for automated, systematic, free-from-expert opinion, and tailored marker selection that provides flexibility in the number of markers and annotation databases while remaining robust against uneven taxon sampling and incomplete genomic data.},
}
@article {pmid40161639,
year = {2025},
author = {Williams, A and Ravel, J and Kaul, R and Armstrong, E and Huibner, S and Holm, JB},
title = {Temporal Dynamics of the Vaginal Microbiome and Host Immune Markers Before, During, and After Metronidazole Treatment for Bacterial Vaginosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.13.643085},
pmid = {40161639},
issn = {2692-8205},
abstract = {UNLABELLED: This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment, variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.<br><br>IMPORTANCE: Bacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections among others, is characterized by a dysbiotic vaginal microbiome associated with dominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at initiation of treatment as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during and after metronidazole treatment.},
}
@article {pmid40160274,
year = {2025},
author = {Naushad, S and Gao, R and Duceppe, MO and Dupras, AA and Reiling, SJ and Merks, H and Dixon, B and Ogunremi, D},
title = {Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1566579},
doi = {10.3389/fmicb.2025.1566579},
pmid = {40160274},
issn = {1664-302X},
abstract = {INTRODUCTION: Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.<br><br>MATERIALS AND METHODS: We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of Cryptosporidium parvum oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with C. hominis, C. muris, Giardia duodenalis and Toxoplasma gondii individually or together.<br><br>RESULTS: The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 &#x3bc;g of DNA (median = 4.10 &#x3bc;g), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of C. parvum in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of C. parvum, C. hominis, C. muris, G. duodenalis and T. gondii.<br><br>DISCUSSION: Our metagenomic procedure led to the identification of C. parvum present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.},
}
@article {pmid40160273,
year = {2025},
author = {Liu, Y and Ying, Y and Li, Y and Zhang, W and Shu, J},
title = {Symbiotic bacteria associated with different species of Curculio (Coleoptera: Curculionidae) and their host plants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531847},
doi = {10.3389/fmicb.2025.1531847},
pmid = {40160273},
issn = {1664-302X},
abstract = {Bacteria often play important roles in the host adaptation of phytophagous insects. Beetles of the genus Curculio (Coleoptera: Curculionidae) include pest species that bore into the seeds of trees in the family Fagaceae and damage the cotyledons. At present, there are few studies of the taxonomic diversity and functional effects of symbiotic bacteria involved in changes in host ranges and host adaptation of Curculio. Here, we used 16S rRNA gene Illumina and metagenomic sequencing to compare the composition and functions of the bacterial communities of three species of host plants and several Curculio species combinations: Curculio bimaculatus feeding on Castanopsis sclerophylla, C. bimaculatus feeding on Castanopsis tibetana, and Curculio davidi feeding on Ca. tibetana. The host plants influenced the diversity of symbiotic bacteria, while the Curculio species influenced the community structure of the symbiotic bacteria. Functional predictions showed that symbiotic bacteria contributed to the metabolism of the hosts. However, consistent with the variation in bacteria, the major metabolism-related bacterial genera varied among the treatment groups. Comparisons of metabolic enzymes based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed differences in the enzymes involved in insect development and detoxification of plant secondary compounds among the three groups, and the patterns were influenced by the dominance of the Curculio species on the host plants. This study provides valuable insights into the possible role of symbiotic bacteria in Curculio as host insects.},
}
@article {pmid40160271,
year = {2025},
author = {Yang, B and Feng, C and Jiang, H and Chen, Y and Ding, M and Dai, H and Zhai, Z and Yang, M and Liang, T and Zhang, Y},
title = {Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496385},
doi = {10.3389/fmicb.2025.1496385},
pmid = {40160271},
issn = {1664-302X},
abstract = {As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.},
}
@article {pmid40160267,
year = {2025},
author = {Kragh, ML and Scheel, NH and Leekitcharoenphon, P and Truelstrup Hansen, L},
title = {Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542193},
doi = {10.3389/fmicb.2025.1542193},
pmid = {40160267},
issn = {1664-302X},
abstract = {There is a concern about the development of microbial tolerance and resistance to biocides due to their repeated use within the food industry. This study aimed to develop a floor drain biofilm model and test whether repeated biocide treatment would result in increased tolerance to biocides. Culturomics and shotgun metagenomic analysis of 14 drains and 214 bacterial isolates from three industrial food production environments revealed microbiomes with great diversity and complexity, but with the dominance of a few highly abundant taxa, including Pseudomonas. A representative drain biofilm was created (3 days, 15°C) using 31 whole genome sequenced bacterial isolates from 24 genera. The biofilm model represented 47-58% and 76-81% of the microbial abundance observed in the metagenome and viable microbiota, respectively. The biofilm model was exposed on days 3 and 6 to water or different industrial concentrations of benzalkonium chloride (BC), peracetic acid (PAA), or sodium hypochlorite (SH). Analysis of the viable survivors using MALDI-TOF MS and the regrowing biofilms using 16S rRNA amplicon sequencing showed how the diversity of the biofilm decreased but without any change in biocide tolerance as seen in log reductions (CFU/cm[2]). The use of different biocides did, however, exert significantly different selective pressures on the microbiomes as Citrobacter, Acinetobacter, Aeromonas, and Pseudomonas dominated the biofilm after treatments with SH or PAA, while Serratia and Moraxella dominated after treatments with BC. The dominance of Serratia marcescens could be explained by the carriage of a BC efflux pump (oqxB) and the highest (20 mg/L BC) minimum inhibitory concentration (MIC) result of the drain isolates. In contrast, despite carrying a BC efflux pump (qacH), Listeria monocytogenes ST121 did not show increased survival or presence in the biofilm after BC treatments. Only the highest tested concentration of PAA was able to completely eradicate L. monocytogenes. The developed biofilm model and the repeated biocide treatments enabled a better understanding of how biocides affect the biofilm microbiome. Future research should involve testing biocide rotation strategies to control biofilm regrowth and inactivation of persistent foodborne pathogens in floor drains.},
}
@article {pmid40159059,
year = {2025},
author = {Shang, SY and Li, XP and Xu, J and Li, Y and Cao, LQ and Ye, H},
title = {[A case of acute pseudomembranous necrotizing tracheobronchitis in an adult].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {4},
pages = {385-388},
doi = {10.3760/cma.j.cn112147-20240828-00510},
pmid = {40159059},
issn = {1001-0939},
mesh = {Humans ; *Tracheitis/diagnosis/microbiology ; *Bronchitis/microbiology/diagnosis ; *Staphylococcal Infections/diagnosis ; Male ; Staphylococcus aureus/isolation &amp; purification ; Bronchoscopy ; Influenza B virus/isolation &amp; purification ; Adult ; Necrosis ; Influenza, Human/complications ; Middle Aged ; Linezolid/therapeutic use ; },
abstract = {This study presented a rare case of secondary Staphylococcus aureus (S. aureus) infection following influenza B virus infection, resulting in diffuse airway injury and hemorrhagic pneumonia. The patient initially underwent bronchial artery embolization (BAE) due to persistent hemoptysis refractory to conventional hemostatic therapy. Although the hemoptysis was resolved postoperatively, severe hypoxemia persisted. Bronchoscopy revealed diffuse yellow plaques with mucosal erosion and necrosis in the airways. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified S. aureus harboring the Panton-Valentine leukocidin (PVL) genes. Histopathological examination revealed severe acute inflammatory changes consistent with necrotizing airway pathology. A diagnosis of IBV-associated S. aureus infection leading to acute pseudomembranous necrotizing tracheobronchitis and hemorrhagic pneumonia was made. The patient responded favorably to linezolid therapy. Follow-up bronchoscopy revealed multiple granulation tissues in the airways, which were subsequently removed under endoscopic guidance. After ruling out persistent infection, the patient was treated with low-dose oral prednisone, which resulted in significant clinical improvement.},
}
@article {pmid40158829,
year = {2025},
author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G},
title = {Huang-qin Decoction alleviates Deoxycholic Acid-induced Colorectal Cancer in Mice by Regulating Gut Microbiota.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119715},
doi = {10.1016/j.jep.2025.119715},
pmid = {40158829},
issn = {1872-7573},
abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.<br><br>AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.<br><br>METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2% deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.<br><br>RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.<br><br>CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.},
}
@article {pmid40158299,
year = {2025},
author = {Borkakoti, N and Ribeiro, AJM and Thornton, JM},
title = {A structural perspective on enzymes and their catalytic mechanisms.},
journal = {Current opinion in structural biology},
volume = {92},
number = {},
pages = {103040},
doi = {10.1016/j.sbi.2025.103040},
pmid = {40158299},
issn = {1879-033X},
abstract = {In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing 'Catalysis in silico' are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.},
}
@article {pmid40158160,
year = {2025},
author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J},
title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {50},
pmid = {40158160},
issn = {1475-2891},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; },
abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.},
}
@article {pmid40158141,
year = {2025},
author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY},
title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {87},
pmid = {40158141},
issn = {2049-2618},
support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; },
mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; },
abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.},
}
@article {pmid40157594,
year = {2025},
author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D},
title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115419},
doi = {10.1016/j.fct.2025.115419},
pmid = {40157594},
issn = {1873-6351},
abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70% non-GM maize (Corn group), and diet formulation containing 70% GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.},
}
@article {pmid40157532,
year = {2025},
author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA},
title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108322},
doi = {10.1016/j.jip.2025.108322},
pmid = {40157532},
issn = {1096-0805},
abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.},
}
@article {pmid40157487,
year = {2025},
author = {Li, J and Zhu, L and Li, X and Han, X and Yi, J and Wu, Y and Wang, M},
title = {Characterization and Risk-quantification of Antibiotic Resistome in Grain-based and Non-grain Cropping Soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126147},
doi = {10.1016/j.envpol.2025.126147},
pmid = {40157487},
issn = {1873-6424},
abstract = {Microbial contamination in soils, encompassing human bacterial pathogens (HBPs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs), poses a significant threat to human health via the food chain. Currently, there is a lack of comprehensive assessments of microbial contamination and associated health risks of ARGs in agricultural soils. In this study, metagenomic sequencing was used to evaluate microbial contamination in grain-based cropping soils (rice cultivation) and non-grain cropping soils (vegetable cultivation and aquaculture). The results showed that the diversity and abundance of HBPs and VFGs were significantly higher in non-grain soils. Further resistome analysis revealed higher abundances of high-risk (from 0.014 to 0.018 - 0.023) and "last-resort" ARGs (from 0.007 to 0.034 - 0.046) in non-grain soils. Besides ARGs abundance, health risk quantification revealed that non-grain soils exhibited 1.49 to 2.14-fold greater ARG-related risks than grain-based soils. Additionally, stronger network associations were found between HBPs, ARGs, and mobile genetic elements (MGEs) in non-grain soils. This study indicated that the non-grain cropping pattern of soils elevated the risk of microbial contamination and ARGs health risk, which provided an important basis for accurately quantifying the risk of microbial contamination in different agricultural soils.},
}
@article {pmid40157184,
year = {2025},
author = {Qiao, X and Kong, X and Zhou, H and Fan, X and Yuan, J and Zhang, Y},
title = {Deciphering the inhibitory mechanisms of polystyrene microplastics on thermophilic methanogens from the insights of microbial metabolite profiling and metagenomic analyses.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138054},
doi = {10.1016/j.jhazmat.2025.138054},
pmid = {40157184},
issn = {1873-3336},
abstract = {Due to the utilization of food packaging bags, a substantial amount of polystyrene microplastics (PS MPs) are introduced into the food waste (FW) treatment system during the pre-treatment process, potentially impacting the subsequent biochemical treatment system. In order to investigate the mechanism by which PS MPs affect anaerobic methanogenesis metabolism in thermophilic condition, this study analyzed the characteristics of methanogenesis in thermophilic anaerobic digestion (AD) of FW under different concentrations of PS MPs (100 μm, 10-200 mg/L). The results revealed a negative correlation between PS MPs concentration and methane (CH4) yield from FW. When the concentration of PS MPs reached 200 mg/L, CH4 yield decreased by 47.8 %. Further mechanistic investigations revealed that while the presence of PS MPs at lower concentrations could alleviate its adverse impact on methanogenesis by enhancing EPS content, the accumulation of reactive oxygen species (ROS) persisted with increasing PS MPs concentration, thereby inhibiting the activities of key enzymes involved in solubilization and acidification metabolisms (e.g., acetate kinase and F420). Metagenomics analysis indicated that the presence of PS MPs down-regulate abundance of genes for quorum sensing and CH4 metabolism pathways. These findings not only unveil potential detrimental effects of PS MPs on AD systems but also provide novel insights into comprehending and controlling the impact of MPs pollution on environmental preservation and energy recovery processes.},
}
@article {pmid40157173,
year = {2025},
author = {Weiting, S and Chen, W and Xiao, L and Yanqiu, H},
title = {Enhanced acid reduction in lactic acid bacteria: Breeding through irradiation-induced mutation and functional assessment.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111161},
doi = {10.1016/j.ijfoodmicro.2025.111161},
pmid = {40157173},
issn = {1879-3460},
abstract = {High concentrations of citric acid (CA), malic acid (MA), and tartaric acids (TA) are the primary contributors to the sour taste of fruit and fruit products. However, lactic acid bacteria that are capable of efficiently degrading these organic acids are scarce. Here, three brands of sauerkraut (Xinxi, X; Yuyuan, Y; and Zou Youcai, Z) with various doses of [60]Co γ-irradiation could be treated to induce mutations in their associated lactic acid bacteria and then the abilities of the resulting microbial communities to degrade CA, MA, and TA were evaluated. Sauerkraut X treated with 0.4 kGy irradiation demonstrated the greatest ability of acid reduction. Metagenomic analyses of irradiated (0.4 kGy) and non-irradiated bacterial communities from sauerkraut X revealed a slight decrease in microbial diversity due to irradiation, with a substantial decline in the relative abundance of Lactiplantibacillus xiangfangensis. Concurrently, the relative abundance of dominant acid-reducing lactic acid bacteria such as Levilactobacillus brevis, Pediococcus ethanolidurans, and Lentilactobacillus parafarraginis increased. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed an increase in metabolism-related genes after irradiation, indicating that fatty acid synthesis and aspartate metabolism might be key pathways involved in the enhanced degradation of CA, MA, and TA. Analysis using the Carbohydrate-Active enzymes Database (CAZy) database revealed that glycoside hydrolase (GH) and glycosyltransferase (GT) genes were the most abundant carbohydrate-associated enzyme genes in the bacterial community of sauerkraut X. This finding proved that the oligosaccharides and monosaccharides produced by GH and GT might indirectly affect rates of organic acid degradation. Three highly effective acid-reducing lactic acid bacteria from the microbial community of irradiated sauerkraut X a were isolated and identified via 16S rRNA sequencing as Pediococcus ethanolidurans, Levilactobacillus brevis, and Loigolactobacillus coryniformis. The individual strains showed degradation rates as high as 92.02 % for citric acid (Pediococcus ethanolidurans), 83.04 % for malic acid (Levilactobacillus brevis), and 90.33 % for TA (Loigolactobacillus coryniformis). This study provides a theoretical basis and technical support for the development of enhanced microbial strains that can reduce the acid content of fruit materials.},
}
@article {pmid40156973,
year = {2025},
author = {Zhong, S and Li, B and Chen, Q and Zhang, J and Cai, H and An, R and Liu, G and Zhou, S},
title = {Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake.},
journal = {Water research},
volume = {280},
number = {},
pages = {123544},
doi = {10.1016/j.watres.2025.123544},
pmid = {40156973},
issn = {1879-2448},
abstract = {Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.},
}
@article {pmid40156579,
year = {2025},
author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D},
title = {Revealing Microbial Functionalities and Ecological Roles in Rajpardi Lignite Mine: Insights from Metagenomics Analysis.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf048},
pmid = {40156579},
issn = {1472-765X},
abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10,071,318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance (AMR) and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasising the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.},
}
@article {pmid40156577,
year = {2025},
author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S},
title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf032},
pmid = {40156577},
issn = {1574-6941},
abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.},
}
@article {pmid40156536,
year = {2025},
author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ},
title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.},
journal = {Australian veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/avj.13442},
pmid = {40156536},
issn = {1751-0813},
support = {DE200100367//Australian Research Council/ ; },
abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.},
}
@article {pmid40156205,
year = {2025},
author = {Huyghe, CET and Fages, A and Ronco, F and Indermaur, A and Schedel, FDB and Kimirei, I and Makasa, L and Tschopp, P and Salzburger, W},
title = {Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17743},
doi = {10.1111/mec.17743},
pmid = {40156205},
issn = {1365-294X},
support = {189970//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
abstract = {Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet-such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods-were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.},
}
@article {pmid40155949,
year = {2025},
author = {Song, J and Lin, LA and Tang, C and Chen, C and Yang, Q and Zhang, D and Zhao, Y and Wei, HC and Linghu, K and Xu, Z and Chen, T and He, Z and Liu, D and Zhong, Y and Zhu, W and Zeng, W and Chen, L and Song, G and Chen, M and Jiang, J and Zhou, J and Wang, J and Chen, B and Ying, B and Wang, Y and Geng, J and Lin, JW and Chen, L},
title = {DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {76},
pmid = {40155949},
issn = {1474-760X},
mesh = {*Metagenomics/methods ; Humans ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; COVID-19/virology/genetics ; Gene Expression Profiling/methods ; Transcriptome ; Glioma/genetics ; High-Throughput Nucleotide Sequencing/methods ; SARS-CoV-2/genetics ; Software ; Malaria ; },
abstract = {Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m[6]A's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.},
}
@article {pmid40155846,
year = {2025},
author = {Zhang, Z and Tian, L},
title = {Validation of mNGS results using extensive lab and clinical data.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {173},
pmid = {40155846},
issn = {1471-2180},
mesh = {Humans ; Retrospective Studies ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Mycoplasma pneumoniae/genetics/isolation &amp; purification ; Male ; Adult ; Middle Aged ; Female ; Tuberculosis/microbiology/diagnosis ; Aged ; Adolescent ; Young Adult ; Child ; },
abstract = {PURPOSE: Interpreting the results of metagenomic next-generation sequencing (mNGS) presents a significant challenge in both clinical and laboratory contexts.<br><br>METHODS: A retrospective analysis was conducted to validate mNGS findings, with a particular emphasis on Mycobacterium tuberculosis, Mycoplasma pneumoniae, and Pneumocystis jirovecii as representative pathogens, examined from both clinical and laboratory perspectives.<br><br>RESULTS: Based on a comprehensive clinical analysis, the mNGS demonstrated detection accuracies for M. tuberculosis, M. pneumoniae, and P. jirovecii of 87.0% (60 out of 69; 95% confidence interval [CI], 77.04%-92.99%), 97.6% (81 out of 83; 95% CI, 91.63%-99.34%), and 78.9% (45 out of 57; 95% CI, 66.72%-87.53%), respectively. Conversely, when incorporating laboratory confirmation from a variety of detection methodologies, the accuracy rates for mNGS in identifying M. tuberculosis, M. pneumoniae, and P. jirovecii were 92.7% (51 out of 55; 95% CI, 82.74%-97.14%), 82.3% (51 out of 62; 95% CI, 70.96%-89.80%), and 83.9% (26 out of 31; 95% CI, 67.36%-92.91%), respectively. Additionally, our analysis revealed no statistically significant difference in read counts and relative abundances between mNGS results deemed clinically as false positives and those considered true positives (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In contemporary clinical practice, the detection of positive results from mNGS is notably high from both laboratory and clinical standpoints. Nonetheless, the interpretation of results with low read counts presents significant challenges for both clinical and laboratory environments under current conditions.},
}
@article {pmid40155693,
year = {2025},
author = {Refahi, M and Sokhansanj, BA and Mell, JC and Brown, JR and Yoo, H and Hearne, G and Rosen, GL},
title = {Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {517},
pmid = {40155693},
issn = {2399-3642},
support = {1936791//National Science Foundation (NSF)/ ; 1919691//National Science Foundation (NSF)/ ; 2107108//National Science Foundation (NSF)/ ; },
mesh = {*Genomics/methods ; Sequence Analysis, DNA/methods ; Base Sequence ; Algorithms ; Metagenomics/methods ; },
abstract = {Analysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio (Sequence Contrastive Optimization for Representation and Predictive Inference on DNA), a versatile framework designed for nucleotide sequences that employ contrastive learning to improve embeddings. By leveraging pre-trained genomic language models and k-mer frequency embeddings, Scorpio demonstrates competitive performance in diverse applications, including taxonomic and gene classification, antimicrobial resistance (AMR) gene identification, and promoter detection. A key strength of Scorpio is its ability to generalize to novel DNA sequences and taxa, addressing a significant limitation of alignment-based methods. Scorpio has been tested on multiple datasets with DNA sequences of varying lengths (long and short) and shows robust inference capabilities. Additionally, we provide an analysis of the biological information underlying this representation, including correlations between codon adaptation index as a gene expression factor, sequence similarity, and taxonomy, as well as the functional and structural information of genes.},
}
@article {pmid40155620,
year = {2025},
author = {Kazarina, A and Wiechman, H and Sarkar, S and Richie, T and Lee, STM},
title = {Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {521},
pmid = {40155620},
issn = {2052-4463},
support = {2020-67019-31803//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2238633//National Science Foundation (NSF)/ ; OIA-1656006//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Metagenome ; Metagenomics ; Bacteria/genetics/classification ; Kansas ; Soil/chemistry ; Archaea/genetics ; },
abstract = {Soil contains a diverse community of organisms; these can include archaea, fungi, viruses, and bacteria. In situ identification of soil microorganisms is challenging. The use of genome-centric metagenomics enables the assembly and identification of microbial populations, allowing the categorization and exploration of potential functions living in the complex soil environment. However, the heterogeneity of the soil-inhabiting microbes poses a tremendous challenge, with their functions left unknown, and difficult to culture in lab settings. In this study, using genome assembling strategies from both field core samples and enriched monolith samples, we assembled 679 highly complete metagenome-assembled genomes (MAGs). The ability to identify these MAGs from samples across a precipitation gradient in the state of Kansas (USA) provided insights into the impact of precipitation levels on soil microbial populations. Metabolite modeling of the MAGs revealed that more than 80% of the microbial populations possessed carbohydrate-active enzymes, capable of breaking down chitin and starch.},
}
@article {pmid40155586,
year = {2025},
author = {Bebawy, AS and Saad, BT and Saad, MT and Mosaad, GS and Gomaa, FAM and Alshahrani, MY and Aboshanab, KM},
title = {Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {40155586},
issn = {2190-3883},
abstract = {Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.},
}
@article {pmid40154870,
year = {2025},
author = {Yang, JT and Zhang, Y and Xiong, SY and Wei, HJ and Zhang, WT and Lian, XL and Xu, XL and Jiang, HX and Sun, J},
title = {Microplastics Reduced the Natural Attenuation of Antibiotic Resistance Genes in Fertilized Soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126144},
doi = {10.1016/j.envpol.2025.126144},
pmid = {40154870},
issn = {1873-6424},
abstract = {The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.},
}
@article {pmid40154751,
year = {2025},
author = {Jiang, X and Zhao, Y and Zhang, W and Zheng, Q and Li, D and Zhang, G and Zhou, T},
title = {Chlorotetracycline-driven modulation of substrate utilization and metabolic traits in sludge anaerobic fermentation for optimized methane production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132449},
doi = {10.1016/j.biortech.2025.132449},
pmid = {40154751},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a highly efficient and promising method for treating waste activated sludge (WAS). Nevertheless, the presence of chlortetracycline (CTC) in WAS introduced uncertainty into the AD process. This study revealed thatthe cumulative methane yield was increased by 27.5 % with the CTC concentration at 50 mg/kg dry sludge by enhancing hydrolysis, acidification and methanogenesis during which specific microbial communities were enriched and related functional genes were enhanced. Subsequent investigations foundthe accumulation of extracellular polymeric substances (EPS) was improved and methane-producing microorganisms (e.g., Bacteroidetes and Euryarchaeota) were also enriched under CTC exposure. Metagenomic analysis further elucidated thatCTC significantly increased functional genes related to bacterial secretion system and metabolism of organic matter for methane production (e.g., pyruvate metabolism and methane metabolism). This study shed light on the substantial impact of CTC on the AD of WAS and provided a promising strategy for improvements in anaerobic fermentation.},
}
@article {pmid40154110,
year = {2025},
author = {Alameer, RM and Tayeb, H and Magrashi, A and Alqasabi, A and Nazmi, A and Yamani, A and Almaghrabi, RS},
title = {Diagnosis of donor-derived Malassezia restricta &amp;Aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - A report of 2 cases and literature review.},
journal = {Journal of infection and public health},
volume = {18},
number = {5},
pages = {102742},
doi = {10.1016/j.jiph.2025.102742},
pmid = {40154110},
issn = {1876-035X},
abstract = {Diagnosing donor-derived fungal infection in solid organ transplant recipients can be particularly challenging and is associated with high mortality. Here, we report two cases of Malassezia restricta and Aspergillus spp donor-derived fungal infection in renal transplant recipients leading to graft loss. Fortunately, both patients achieved full recovery with the administration of antifungal therapy.},
}
@article {pmid40154057,
year = {2025},
author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y},
title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.},
journal = {Food chemistry},
volume = {481},
number = {},
pages = {143980},
doi = {10.1016/j.foodchem.2025.143980},
pmid = {40154057},
issn = {1873-7072},
abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.},
}
@article {pmid40154039,
year = {2025},
author = {Li, J and Huang, Z and Zhang, R},
title = {Unmasking Prototheca wickerhamii: A rare case of cutaneous infection and its implications for clinical practice.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {29},
number = {3},
pages = {104525},
doi = {10.1016/j.bjid.2025.104525},
pmid = {40154039},
issn = {1678-4391},
abstract = {Prototheca, an opportunistic pathogenic algae widely found in nature, has emerged as a potential public health concern. Most cases occur in immunocompromised individuals, with infections in immunocompetent patients being relatively rare. Due to their non-specific clinical presentation and limited awareness among clinicians, Prototheca infections are often misdiagnosed, resulting in delayed treatment. Recent advances in species identification and antifungal susceptibility testing have provided important tools for diagnosis and therapy. Here, we report a case of recurrent facial infection in a 76-year-old immunocompetent man. Skin biopsy revealed an infectious granuloma, and fungal culture identified yeast-like colonies. Fluorescence staining and scanning electron microscopy revealed abundant spores, while metagenomic sequencing confirmed the infection as Prototheca wickerhamii. The patient was successfully treated with long-term itraconazole and dipotassium glycyrrhizinate capsules. This case highlights the importance of early and accurate diagnosis in the management of Prototheca skin infections and reviews the therapeutic strategies used.},
}
@article {pmid40153957,
year = {2025},
author = {Huang, M and Mu, G and Mai, F and Zhou, Y and Li, X and Yang, Q and Shao, B and Wang, J and Tong, Y},
title = {Methane cycling in typical emerging proglacial lakes on the Tibetan Plateau: Insights into the metabolic mechanisms mediated by microorganisms.},
journal = {Water research},
volume = {280},
number = {},
pages = {123533},
doi = {10.1016/j.watres.2025.123533},
pmid = {40153957},
issn = {1879-2448},
abstract = {A large number of high-latitude emerging proglacial lakes have formed on the Tibetan Plateau (TP) due to the global warming and deglaciation. These lakes have the potential to emit methane (CH4) because of the exposure of cryopreserved organic carbon, leading to their significance in regional carbon turnover and cycling. However, previous studies have focused more on human-impacted lakes (e.g., eutrophic lakes), resulting in limited research on the mechanisms of CH4 cycling in the proglacial lakes. In this study, we demonstrated that three typical emerging high-latitude proglacial lakes (∼5500 m a.s.l.) on the TP exhibited a diffusive emission flux of 32.39 ± 11.66 μmol/m[2]/d during the summer. The δ[13]C-CH4 values (-50.10 ± 0.56‰) suggested a biogenic origin of CH4 through the acetoclastic pathway in the lakes. Metagenome sequencing further showed that microbes involved in methanogenesis were dominated by Methanosarcina (36.74 ± 0.07 % of total methanogens). Significant CH4 consumption was observed in the proglacial lakes. The microbes involved in the CH4 consumption were dominated by Methylobacter (48.50 ± 0.17 % of total methanotrophs). A Mantel test demonstrated that dissolved iron (Fe) was a key factor controlling the structure of the CH4 cycling microbial communities. Functional gene and co-occurrence network analyses indicated that members of Pseudomonadota, Bacteroidota, and Actinomycetota may be involved in CH4 cycling by providing methanogenic substrates (i.e., acetyl coenzyme A) and consuming CH4 oxidative intermediates (i.e., methanol, formaldehyde, and formic acid). This study emphasized the ecological significance of emerging proglacial lakes in CH4 releases. It broadened the current understanding of cryophilic CH4 cycling microbes and their mechanisms, that enhances our knowledge of the carbon cycle on the TP.},
}
@article {pmid40153355,
year = {2025},
author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T},
title = {Bacterial consortia of ewes´ whey in the production of bryndza cheese in Slovakia.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf047},
pmid = {40153355},
issn = {1472-765X},
abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza-cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characterisitics of final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes´ milk-based bryndza-cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3 - 8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, Lactobacillus diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus gasseri and Lentilactobacillus otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.},
}
@article {pmid40153196,
year = {2025},
author = {Erickson, I and Davidson, S and Choi, H and Rho, S and Guignet, M and Peagler, K and Thummel, K and Ericsson, A and Barker-Haliski, M},
title = {Intestinal dysbiosis alters acute seizure burden and antiseizure medicine activity in Theiler's virus model of encephalitis.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18395},
pmid = {40153196},
issn = {1528-1167},
support = {//University of Washington/ ; },
abstract = {OBJECTIVE: Brain infection with Theiler's murine encephalomyelitis virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.<br><br>METHODS: Male C57BL/6J mice (4-5&#x2009;weeks old) received oral ABX or saline (SAL) once daily beginning on arrival through day 7 after TMEV infection (postinfection [p.i.]). Mice were infected with TMEV or phosphate-buffered saline on day 0. Mice received intraperitoneal (20&#x2009;mg/kg) CBZ or vehicle (VEH) twice daily on days 3-7 p.i. and were assessed for handling-induced seizures 30&#x2009;min after treatment. Plasma was collected on day 7 p.i. at 15 and 60&#x2009;min after CBZ administration for bioanalysis.<br><br>RESULTS: TMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX-CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment&#x2009;&#xd7;&#x2009;ASM interaction (p&#x2009;=&#x2009;.0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p&#x2009;=&#x2009;.004). CBZ significantly increased latency to seizure presentation, an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.<br><br>SIGNIFICANCE: ABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV-induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an underrecognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.},
}
@article {pmid40152616,
year = {2025},
author = {Yao, J and Zeng, Y and Hong, X and Wang, M and Zhang, Q and Chen, Y and Gou, M and Xia, Z-Y and Tang, Y-Q},
title = {Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0020025},
doi = {10.1128/msystems.00200-25},
pmid = {40152616},
issn = {2379-5077},
abstract = {The dynamics of the structure of polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, five PHA-MMCs were enriched, and biological samples were sampled temporally to study the interactions between phage and bacterial members by combining metagenomics and metatranscriptomics. A total of 963 metagenome-assembled genomes (MAGs) and 4,294 phage operational taxonomic units (pOTUs) were assembled from bulk metagenomic data. The dynamic changes in the structure of phage and bacterial communities were remarkably consistent. Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated. Seven key auxiliary metabolic genes (AMGs), phaC, fadJ, acs, ackA, phbB, acdAB, and fadD, potentially contributing to PHA synthesis were identified from phage sequences. Importantly, these AMGs were transcribed, indicating that they were in an active expression state. The meta-analysis provides the first catalog of phages in PHA-MMCs and the AMGs they carry, as well as how they affect the dynamic changes in bacterial communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of open microbial systems.IMPORTANCEThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., Azomonas, Paracoccus, and Thauera) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.},
}
@article {pmid40152185,
year = {2025},
author = {Allos, H and Hasbun, R},
title = {Aseptic meningitis: a foundation review.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001105},
pmid = {40152185},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review addresses the multifaceted nature of aseptic meningitis, a condition with diverse infectious and noninfectious etiologies. Despite its common presentation in clinical settings, over half of the cases remain without an identified cause, necessitating a comprehensive examination of diagnostic and management strategies. The increasing availability of advanced molecular diagnostics and the challenge of distinguishing bacterial from nonbacterial cases make this an opportune time to explore its implications for clinical practice.<br><br>RECENT FINDINGS: The literature highlights the pivotal role of advanced molecular diagnostics, such as multiplex PCR and metagenomic sequencing, in improving the identification of pathogens in aseptic meningitis. Enteroviruses remain the leading cause, but pathogens like Herpesviridae, arboviruses, and nonviral agents such as fungi and spirochetes also contribute significantly. New diagnostic algorithms and clinical models are emerging to distinguish bacterial from viral meningitis, reducing unnecessary treatments.<br><br>SUMMARY: Aseptic meningitis management is evolving with advancements in diagnostic technologies that allow for earlier pathogen identification, improving patient outcomes and minimizing healthcare costs. These findings underscore the importance of timely and accurate diagnostics and tailored therapeutic strategies in both clinical and research settings. Enhanced awareness of noninfectious causes is also crucial for comprehensive care.},
}
@article {pmid40152095,
year = {2025},
author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q},
title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06308b},
pmid = {40152095},
issn = {2042-650X},
abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.},
}
@article {pmid40151642,
year = {2025},
author = {Cai, X and Cho, JY and Chen, L and Liu, Y and Ji, F and Salgado, K and Ge, S and Yang, D and Yu, H and Shao, J and Futreal, PA and Sepesi, B and Gibbons, D and Chen, Y and Wang, G and Cheng, C and Wu, M and Zhang, J and Hsiao, A and Xia, T},
title = {Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112162},
pmid = {40151642},
issn = {2589-0042},
abstract = {Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.},
}
@article {pmid40151403,
year = {2025},
author = {Otsuki, A and Inoue, R and Imai, T and Miura, H and Nishida, A and Inatomi, O and Andoh, A},
title = {Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission.},
journal = {Journal of clinical biochemistry and nutrition},
volume = {76},
number = {2},
pages = {202-209},
pmid = {40151403},
issn = {0912-0009},
abstract = {This study aimed to analyze the gut phageome in Japanese patients with ulcerative colitis (UC) in endoscopic remission. Fecal samples were collected from 35 UC patients and 22 healthy controls. The gut microbiome was analyzed using 16S rRNA amplicon sequencing, and the phageome was profiled through shotgun metagenomic sequencing. Compared to healthy controls, UC patients showed a significant reduction in phageome richness (observed species and Chao1 index). Principal coordinate analysis revealed a significant difference in beta-diversity between UC and healthy controls (p = 0.001). The abundance of temperate phages was higher in UC (15.2%) compared to healthy controls (5.9%), although this was not statistically significant (p = 0.088). Temperate phages associated with Coprococcus sp., Bacteroides sp. KFT8, and Faecalibacterium prausnitzii, as well as virulent phages associated with Ruminococcus gnavus and Lactobacillus farciminis, were increased in UC patients. Conversely, phages associated with Thermosipho affectus, Bacteroides sp. OF03-11BH, and Odoribacter splanchnicus were decreased in UC patients. Phages associated with the genera Odoribacter (p = 0.0004), Ruminococcus (p = 0.009), and Veillonella (p = 0.013) were significantly reduced in UC patients. The gut phageome of inactive UC patients exhibited notable alterations in viral composition compared to healthy controls. These results suggest that changes in the gut phageome might be involved in the pathogenesis of UC.},
}
@article {pmid40151093,
year = {2025},
author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J},
title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e024},
doi = {10.1002/jobm.70024},
pmid = {40151093},
issn = {1521-4028},
support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; },
abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.},
}
@article {pmid40150979,
year = {2025},
author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN},
title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {1},
pages = {25725},
doi = {10.31083/FBE25725},
pmid = {40150979},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Rectum/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metabolic Networks and Pathways ; Metagenomics ; Dairying ; },
abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.<br><br>METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.<br><br>RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).<br><br>CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.},
}
@article {pmid40150359,
year = {2025},
author = {Liu, Y and Dong, X and Sun, L and Cui, H and Kang, J and Bu, N and Zhang, Y and Qi, Z and Li, Z and Zhang, Z and Zhao, L},
title = {Analysis of the Microbial Community Structure of Ixodes persulcatus at Each Developmental Stage.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/ani15060830},
pmid = {40150359},
issn = {2076-2615},
support = {32260887//National Natural Science Foundation of China/ ; },
abstract = {Ticks are the second most significant vector of pathogens worldwide. Ixodes persulcatus is one of the dominant tick species in Inner Mongolia that can carry and transmit various pathogenic microorganisms. However, only one specific pathogen has been detected in a particular developmental stage of I. persulcatus, moreover metagenomic analysis has been conducted only in the adult tick stage. In this study, we used I. persulcatus at different developmental stages (first-generation female adult ticks, eggs, larval ticks, engorged larval ticks, nymphal ticks, engorged nymphal ticks, and second-generation adult ticks) from Inner Mongolia as materials for nucleic acid extraction. Subsequently, we constructed Illumina PE250 and Illumina PE150 libraries and sequenced them on the Illumina NovaSeq 6000 platform. Finally, we used molecular biology software and sequence analysis platform to analyze microbial community structures. Illumina PE250 sequencing revealed that the seven developmental stages of I. persulcatus were annotated to 21 phyla, 43 classes, 104 orders, 188 families, 391 genera, and 556 species of bacteria. Among them, 4 phyla and 14 genera were present at all developmental stages, with Proteobacteria being the dominant phylum and Rickettsia spp. being the dominant genus. In addition, Rickettsia had the highest relative abundance in the seven developmental stages. All developmental stages were annotated to a certain abundance of Brucella spp. Illumina PE150 sequencing revealed that the three samples (X-I-YDCP: first-generation adult ticks; X-I-MIX: mixed samples of eggs, larval ticks, and nymphal ticks; X-I-EDCP: second-generation adult ticks) of I. persulcatus were annotated to six orders, 28 families, 72 genera, and 158 species of viruses, of which 46 genera and 80 species were found in all three sample species. To the best of our knowledge, this is the first study that comprehensively analyzed the microbial community composition of I. persulcatus at different developmental stages. Based on the study outcomes, certain abundance of Rickettsia japonica, bovine viral diarrhea virus, and African swine fever virus were annotated to I. persulcatus.},
}
@article {pmid40149936,
year = {2025},
author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C},
title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.},
journal = {Biomolecules},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/biom15030400},
pmid = {40149936},
issn = {2218-273X},
mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; Colitis, Ulcerative/microbiology/drug therapy ; Mice ; Bacteria/drug effects/genetics/classification ; Male ; Butyric Acid/pharmacology ; Disease Models, Animal ; },
abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}
@article {pmid40149684,
year = {2025},
author = {Zhao, X and Xu, J and Wu, D and Chen, N and Liu, Y},
title = {Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course.},
journal = {Biomedicines},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biomedicines13030708},
pmid = {40149684},
issn = {2227-9059},
support = {(No. RDJP2022-15 to X.Z., No. RDJP2023-22 to J.X.)//Scientific Research Development Funds of Peking University 401 People's Hospital/ ; No. CFH2024-4-4089 to J.X.//the Capital Health Research and Development of Special/ ; (82370555 to J.X., 400 No. 82370537, 82341228 to Y.L.)//the National Natural Science Foundation of China/ ; (No. XZ2024ZR-ZY012(Z) to X.Z.//the Xizang Autono- 402 mous Region Natural Science Foundation Group Medical Aid Project/ ; },
abstract = {Background and Aims: Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with a globally increasing prevalence, partially driven by alterations in gut microbiota. Although biological therapy is the first-line treatment for CD, a significant proportion of patients experience a primary non-response or secondary loss of response over time. This study aimed to explore the differences in gut microbiota among CD patients with divergent long-term responses to biological therapy, focusing on a long disease course. Methods: Sixteen CD patients who applied the biological agents for a while were enrolled in this study and were followed for one year, during which fecal specimens were collected monthly. Metagenomic analysis was used to determine the microbiota profiles in fecal samples. The response to biological therapy was evaluated both endoscopically and clinically. Patients were categorized into three groups based on their response: R (long-term remission), mA (mild active), and R2A group (remission to active). The differences in the gut microbiota among the groups were analyzed. Results: Significant differences in fecal bacterial composition were observed between the groups. The R2A group exhibited a notable decline in gut microbial diversity compared to the other two groups (p < 0.05). Patients in the R group had higher abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and Megasphaera elsdenii. In contrast, Veillonella parvula, Veillonella atypica, and Klebsiella pneumoniae were higher in the R2A group. Conclusions: Gut microbial diversity and specific bacterial significantly differed among groups, reflecting distinct characteristics between responders and non-responders.},
}
@article {pmid40149628,
year = {2025},
author = {Kaczka, A and Błońska, A and Chojnacki, C and Gąsiorowska, A and Błasiak, J and Popławski, T and Chojnacki, J},
title = {Periodic Changes in the Gut Microbiome in Women with the Mixed Type of Irritable Bowel Syndrome.},
journal = {Biomedicines},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biomedicines13030652},
pmid = {40149628},
issn = {2227-9059},
abstract = {Background: The mixed type of irritable bowel syndrome (IBS-M) is characterized by recurrent constipation and diarrhea. The cause of the variability of these symptoms is not sufficiently understood. The aim of this study was to perform metagenomic and metabolic assessment of the gut microbiome in constipation and diarrheal period of IBS-M. Methods: This study included 30 women, aged 28-47 years old, with the symptoms which aligned with those of IBS-M, according to the Rome IV Criteria. Results: In both periods of the disease, the dysbiosis index (DI), the Shannon diversity index (SDI), the hydrogen-methane and ammonia breath tests, as well as the selected bacterial metabolites (-p-hydroxyphenyl acetic acid (HPA), 3-indoxyl sulfate (Indican, 3-IS)), and hippuric acid (A) in urine, were determined. The dysbiosis index (DI) in the period of constipation was 3.73 ± 0.90 points, and in the diarrheal period it did not change significantly 3.93 ± 0.75 points (p > 0.05). During the diarrheal period, the diversity of bacteria increases from 2.16 ± 0.59 to 2.74 ± 0.50 points on the Shannon dietary index (p < 0.001). The gut microbiome profile also changed, especially during the diarrheal period where an abundance of Bifidobacterium spp. and Lactobacillus spp. decreased significantly. In addition, during this period, the levels of hydrogen and ammonia in breath air increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. During the diarrheal period, the levels of hydrogen and ammonia ions increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. Conclusions: In patients with IBS-M, periodic changes in the profile and metabolism of the gut microbiome occur, which coexist with recurrent symptoms such as constipation and diarrhea.},
}
@article {pmid40149502,
year = {2025},
author = {Hailu, G and Legesse, M and Mulu, A and Medhin, G and Tsegaye, MM and Alemayehu, DH and Ayele, A and Gebreegziabxier, A and Tayachew, A and Aguine, A and Dejene, H and Tessema, SK and Onywera, H and Stanislas, AE and Abate, E and Marcello, A and Bitew, M},
title = {SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19.},
journal = {Genes},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/genes16030351},
pmid = {40149502},
issn = {2073-4425},
mesh = {Humans ; Ethiopia/epidemiology ; *COVID-19/virology/epidemiology/transmission ; *SARS-CoV-2/genetics/pathogenicity ; Male ; Female ; Adult ; *Whole Genome Sequencing/methods ; *Genome, Viral ; Middle Aged ; Phylogeny ; Genetic Variation ; Young Adult ; Adolescent ; },
abstract = {BACKGROUND: The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.<br><br>METHOD: From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.<br><br>RESULTS: Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.<br><br>CONCLUSION: Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.},
}
@article {pmid40149437,
year = {2025},
author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A},
title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.},
journal = {Genes},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/genes16030285},
pmid = {40149437},
issn = {2073-4425},
mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics/classification ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; Ecosystem ; Microbiota/genetics ; Plant Roots/microbiology ; Fungi/genetics/classification ; },
abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.},
}
@article {pmid40149106,
year = {2025},
author = {Olsen, NS and Riber, L},
title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antibiotics14030296},
pmid = {40149106},
issn = {2079-6382},
support = {NNF23OC0086264//Novo Nordisk Foundation/ ; },
abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.},
}
@article {pmid40148934,
year = {2025},
author = {de Campos, GM and Clemente, LG and Lima, ARJ and Cella, E and Fonseca, V and Ximenez, JPB and Nishiyama, MY and de Carvalho, E and Sampaio, SC and Giovanetti, M and Elias, MC and Slavov, SN},
title = {Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {88},
pmid = {40148934},
issn = {1743-422X},
support = {2022/00910-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/11944-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/11944-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/11944-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/23205-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 403075/2023-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Anelloviridae/genetics/classification/isolation &amp; purification ; *Torque teno virus/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; DNA Virus Infections/virology/blood ; Plasma/virology ; Algorithms ; Metagenome ; Genome, Viral/genetics ; },
abstract = {BACKGROUND: Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.<br><br>METHODS: In this study, we propose using the identification of Torque Teno Viruses (TTVs), from the Anelloviridae family, as indicators to evaluate the performance of four short-read-based metagenomic classifiers: Kraken2, Kaiju, CLARK and DIAMOND, when evaluating human plasma samples.<br><br>RESULTS: Our results show that each classifier assigns TTV species at different abundance levels, potentially influencing the interpretation of diversity within samples. Specifically, nucleotide-based classifiers tend to detect a broader range of TTV species, indicating higher sensitivity, while amino acid-based classifiers like DIAMOND and CLARK display lower abundance indices. Interestingly, despite employing different algorithms and data types (protein-based vs. nucleotide-based), Kaiju and Kraken2 performed similarly.<br><br>CONCLUSION: Our study underscores the critical impact of classifier selection on diversity indices in metagenomic analyses. Kaiju effectively assigned a wide variety of TTV species, demonstrating it did not require a high volume of reads to capture diversity. Nucleotide-based classifiers like CLARK and Kraken2 showed superior sensitivity, which is valuable for detecting emerging or rare viruses. At the same time, protein-based approaches such as DIAMOND and Kaiju proved robust for identifying known species with low variability.},
}
@article {pmid40148927,
year = {2025},
author = {Feng, Z and Lorenc, N and O'Brien, B and Sun, G and Li, Z and Jung, D and Ronholm, J},
title = {Deep culturing the fecal microbiota of healthy laying hens.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {32},
pmid = {40148927},
issn = {2524-4671},
abstract = {BACKGROUND: The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.<br><br>RESULTS: In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.<br><br>CONCLUSIONS: Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.},
}
@article {pmid40148567,
year = {2025},
author = {Austin, GI and Brown Kav, A and ElNaggar, S and Park, H and Biermann, J and Uhlemann, AC and Pe'er, I and Korem, T},
title = {Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40148567},
issn = {2058-5276},
support = {R01HD106017//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD114715//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T15LM007079//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; U54DK104309//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
abstract = {Every step in common microbiome profiling protocols has variable efficiency for each microbe, for example, different DNA extraction efficiency for Gram-positive bacteria. These processing biases impede the identification of signals that are biologically interpretable and generalizable across studies. 'Batch-correction' methods have been used to address these issues computationally with some success, but they are largely non-interpretable and often require the use of an outcome variable in a manner that risks overfitting. We present DEBIAS-M (domain adaptation with phenotype estimation and batch integration across studies of the microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using diverse benchmarks including 16S rRNA and metagenomic sequencing, classification and regression, and a variety of clinical and molecular targets, we demonstrate that using DEBIAS-M improves cross-study prediction accuracy compared with commonly used batch-correction methods. Notably, we show that the inferred bias-correction factors are stable, interpretable and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M facilitates improved modelling of microbiome data and identification of interpretable signals that generalize across studies.},
}
@article {pmid40147547,
year = {2025},
author = {Liu, H and Sun, R and Wu, Y and Feng, J and Fan, G and Chen, S and Li, L},
title = {Molecular detection and identification of goose astrovirus in GuangDong Province, China.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105745},
doi = {10.1016/j.meegid.2025.105745},
pmid = {40147547},
issn = {1567-7257},
abstract = {In recent years, Goose Astrovirus (GAstV) has become a major pathogen in China, afflicting geese with significant clinical manifestations like gout and urate deposits in organs. Notably, similar symptoms have emerged in ducks. From 2023 to 2024, 126 liver samples were collected from ducks in Guangdong Province, where farms reported emaciation, paralysis, and deaths. Metagenomic analysis pinpointed GAstV as the primary pathogen, with a 43.65 % confirmed positive rate via qPCR. A new strain, GD2406, was identified, showing 97.5 %-98.8 % similarity to 30 GAstV-2 strains in GenBank. GD2406 displayed 98.3 % and 97.7 % identity with the duck strains HNNY0620 and SDTA, and 98.3 % and 98.4 % identity with highly virulent GAstV strains HNKF-1 and HNSQ-6. Phylogenetic analysis indicated a genetic closeness between GD2406 and the goose strain HB01. There were 13 amino acid mutations, mainly within ORF2, and a single mutation differing from HNKF-1 and HNSQ-6, hinting at significant pathogenic potential for both ducks and geese. This study is the first to report GAstV causing severe symptoms and mortality in Muscovy ducks in Guangdong Province, suggesting ducks could be key hosts and underscoring the risk of cross-species transmission.},
}
@article {pmid40147421,
year = {2025},
author = {Goswami, P and Ji, R and Shen, J and Roberts, AP and Lin, W},
title = {Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov. from an acidic peatland.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {3},
pages = {126605},
doi = {10.1016/j.syapm.2025.126605},
pmid = {40147421},
issn = {1618-0984},
abstract = {Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1[Ts], a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1[Ts] provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.},
}
@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}
@article {pmid40147232,
year = {2025},
author = {Wang, J and Ge, Y},
title = {Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content.},
journal = {The Science of the total environment},
volume = {974},
number = {},
pages = {179224},
doi = {10.1016/j.scitotenv.2025.179224},
pmid = {40147232},
issn = {1879-1026},
abstract = {Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.},
}
@article {pmid38630846,
year = {2024},
author = {Phan, HV and Tsitsiklis, A and Maguire, CP and Haddad, EK and Becker, PM and Kim-Schulze, S and Lee, B and Chen, J and Hoch, A and Pickering, H and van Zalm, P and Altman, MC and Augustine, AD and Calfee, CS and Bosinger, S and Cairns, CB and Eckalbar, W and Guan, L and Jayavelu, ND and Kleinstein, SH and Krammer, F and Maecker, HT and Ozonoff, A and Peters, B and Rouphael, N and , and Montgomery, RR and Reed, E and Schaenman, J and Steen, H and Levy, O and Diray-Arce, J and Langelier, CR},
title = {Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.},
journal = {Science translational medicine},
volume = {16},
number = {743},
pages = {eadj5154},
pmid = {38630846},
issn = {1946-6242},
support = {U19 AI090023/AI/NIAID NIH HHS/United States ; U19 AI118608/AI/NIAID NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; S10 OD026880/OD/NIH HHS/United States ; U19 AI077439/AI/NIAID NIH HHS/United States ; U19 AI118610/AI/NIAID NIH HHS/United States ; U19 AI167891/AI/NIAID NIH HHS/United States ; U19 AI167903/AI/NIAID NIH HHS/United States ; U19 AI128913/AI/NIAID NIH HHS/United States ; R01 AI132774/AI/NIAID NIH HHS/United States ; S10 OD030463/OD/NIH HHS/United States ; R01 AI135803/AI/NIAID NIH HHS/United States ; U19 AI089992/AI/NIAID NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; U19 AI128910/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Aged ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged, 80 and over ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Multiomics ; Chemokines ; },
abstract = {Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.},
}
@article {pmid40146796,
year = {2025},
author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S},
title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.},
journal = {Polish journal of microbiology},
volume = {74},
number = {1},
pages = {71-81},
doi = {10.33073/pjm-2025-006},
pmid = {40146796},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Aged ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; },
abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.},
}
@article {pmid40146759,
year = {2025},
author = {Guan, Y and Guo, H and Xia, D and Liu, Y and Wang, X},
title = {Migration of heavy metals and microbial metabolic regulation mechanisms in the co-fermentation of coal slime and sawdust.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/09593330.2025.2482966},
pmid = {40146759},
issn = {1479-487X},
abstract = {Heavy metals (HMs) significantly affect the anaerobic fermentation of coal slime (CS), while sawdust serves as a promising substrate for methane bioconversion and an effective adsorbent for HMs. To explore the migration of HMs and improve the conversion efficiency of CS and sawdust to biomethane, experiments were conducted on the co-fermentation of CS and sawdust with different mass ratios. FT-IR, ICP-MS, SEM-EDS, and metagenomic sequencing were employed to elucidate the regulation mechanism of microorganisms after adding sawdust in altering the toxicological environment. The results revealed that the optimum mass ratio of CS to sawdust was 2:1. Oxygen-containing functional groups in CS were removed, and the fatty structure was degraded. Addition of sawdust promoted the further degradation of CS and migration of various HMs. Metal elements such as Fe, Mg, Co, and Cd had also been detected on its surface. Bacillota (39.05%) was significantly enriched, which effectively improved the microbial community structure. The abundance of species with metal detoxification functions increased. The types and abundance of transporters related to toxic metal ions increased in families such as ATP-binding Cassette Superfamily (ABC) and Resistance-Nodulation-Cell Division Superfamily (RND), which would further aid in cellular homeostasis. Moreover, the addition of sawdust promoted the expression of metal resistance genes (MRGs). Multi-MRGs were primarily linked to Cu, As, and Zn, with an increased abundance of bacterial species contributing to key MRGs such as copA, ziaA, and actP. These findings offer valuable insights that support the clean and efficient utilization of CS and sawdust.},
}
@article {pmid40145240,
year = {2025},
author = {Zhou, Y and Oba, K and Xu, T and Kuroiwa, M and Hori, T and Terada, A},
title = {Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12732},
pmid = {40145240},
issn = {1520-5851},
abstract = {Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. [15]N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass[-1]·h[-1]. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min[-1]) and low (0.08 mmol·min[-1]) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.},
}
@article {pmid40144527,
year = {2025},
author = {Wang, J and Ren, W and Sun, Z and Liu, S and Han, Z and Wang, Y and Zeng, Y and Meng, J and Yao, X},
title = {Impact of intragastric administration of donkey milk on mouse immunity utilizing gut microbiomics and plasma metabolomics.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1486406},
pmid = {40144527},
issn = {2297-1769},
abstract = {INTRODUCTION: Donkey milk demonstrates closer compositional resemblance to human milk compared to bovine milk, positioning it as an optimal nutritional substitute for infants with cow's milk allergy. Furthermore, its rich profile of bioactive compounds suggests potential immunomodulatory properties. This study systematically investigated the effects of donkey milk supplementation on murine immune function and gut microbiome dynamics, thereby providing mechanistic insights to support its clinical development in functional food applications.<br><br>METHODS: Following daily intragastric administration of 10 mL/kg of body weight of donkey milk (DM) or distilled water (DW) to the mice for 28 consecutive days, liver tissues were harvested for immunological profiling, with concurrent collection of blood samples for plasma metabolomic analysis and fecal specimens for gut microbiome characterization. Subsequently, the modulatory effects of donkey milk supplementation on immune parameters, intestinal microbiota composition, and plasma metabolic profiles were systematically evaluated.<br><br>RESULTS: Immunity analysis revealed that intragastric administration of DM raised the levels of IL-6 and TNF-&#x3b1; cytokines in mouse liver. In addition, DM modulated the composition of both the murine gut microbiome and plasma metabolites. One-hundred and forty-five differentially-produced metabolites were identified, most prominently nicotinamide, L-valine, and &#x3b2;-estradiol, that are primarily associated with valine, leucine, and isoleucine biosynthesis and degradation, nicotinate and nicotinamide metabolism, and unsaturated fatty acid biosynthesis. Alterations at phylum, genus, and species levels were evident in the fecal microbiota of mice after intragastric administration of DM. In particular, an increased abundance of the Lactobacillus bacterium was observed. Correlation analysis of differential metabolites and microbiomes indicated a correspondence between Falsiroseomonas and Salipiger species and the antioxidant coenzyme Q that has the potential to activate the immune system.<br><br>CONCLUSION: The data collectively suggest that DM may adjust the murine gut microbiome and plasma metabolites thereby potentially improving immunity in mice.},
}
@article {pmid40144403,
year = {2025},
author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X},
title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf042},
pmid = {40144403},
issn = {2730-6151},
abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.},
}
@article {pmid40143870,
year = {2025},
author = {Hu, Y and Zhou, J and Lin, X},
title = {Akkermansia muciniphila helps in the recovery of lipopolysaccharide-fed mice with mild intestinal dysfunction.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1523742},
pmid = {40143870},
issn = {1664-302X},
abstract = {BACKGROUND: Mild intestinal dysfunction, linked to subtle yet significant health issues, can be induced by lipopolysaccharide (LPS), a Gram-negative bacterial component that disrupts gut function and triggers inflammation. Akkermansia muciniphila has shown promise as a probiotic for gut health due to its roles in mucin degradation and short-chain fatty acid production. This study explores the therapeutic effects of Akkermansia muciniphila on LPS-induced mild intestinal dysfunction in mice.<br><br>METHODS: Thirty-eight 6-week-old C57BL/6 mice were split into control (n&#x202f;=&#x202f;19) and LPS-treated (n&#x202f;=&#x202f;19) groups. LPS-treated mice received 300&#x202f;&#x3bc;g/kg/day of LPS for 4&#x202f;weeks, followed by Akkermansia muciniphila supplementation at 41&#x202f;mg/kg/day (Akk1) or 82&#x202f;mg/kg/day (Akk2) for another 4&#x202f;weeks. Gut microbiota was analyzed via metagenomic sequencing, and gene expression was evaluated through transcriptomics.<br><br>RESULTS: LPS significantly altered gut microbiota, reducing diversity and increasing pathogenic genera like Lachnoclostridium. Akkermansia muciniphila supplementation, particularly at higher doses, partially restored gut microbiota by increasing beneficial genera such as Muribaculum. Transcriptomics showed that LPS induced immune and inflammatory responses, while Akkermansia muciniphila reduced these effects by modulating pathways like TNF and NF-kappa B signaling.<br><br>CONCLUSION: Akkermansia muciniphila mitigates LPS-induced gut dysfunction by restoring microbiota balance and modulating immune responses, highlighting its potential as a therapeutic agent for gut health.},
}
@article {pmid40143862,
year = {2025},
author = {Sujatha, S and Sindhura, KAV and Koti, PS and Hiremath, S and Muttappagol, M and Vinay Kumar, HD and Shankarappa, KS and Venkataravanappa, V and Reddy, KMS and Reddy, CNL},
title = {Influence of weather and seasonal factors on whitefly dynamics, associated endosymbiotic microbiomes, and Begomovirus transmission causing tomato leaf curl disease: insights from a metagenomic perspective.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1555058},
pmid = {40143862},
issn = {1664-302X},
abstract = {INTRODUCTION: Bemisia tabaci (Gennadius) is a globally significant agricultural pest, responsible for transmitting over 120 plant viruses, including those from the Begomovirus genus, which contribute to considerable crop losses. The species complex comprises cryptic species, associated with a diverse array of bacterial endosymbionts that play essential roles in host nutrition, virus transmission, and overall host adaptability. These endosymbionts are classified into primary and secondary categories, with primary endosymbionts forming obligatory, long-term associations, and secondary endosymbionts influencing factors such as biotype differentiation and vector competency. Notably, these microbial communities enhance B. tabaci's capacity to transmit viruses, including the tomato leaf curl virus (ToLCuV), which poses a significant threat to tomato production.<br><br>METHODS: In this study, we examined the population dynamics of B. tabaci across three major tomato-growing regions in Karnataka, South India, focusing on their seasonal associations with endosymbionts and the incidence of tomato leaf curl disease (ToLCuD). Multiple regression analysis was employed to assess the influence of weather parameters on whitefly populations and disease prevalence. Additionally, we constructed a metagenomic profile to evaluate the effects of geographical location, seasonality, environmental factors, and agricultural practices on the bacterial communities associated with B. tabaci. Species-specific primers were used to validate the presence and diversity of these bacterial communities.<br><br>RESULTS: Meteorological data revealed a positive correlation between temperature and B. tabaci populations, which corresponded with an increased incidence of ToLCuD. Genetic characterization of the whitefly identified Asia II-5 and Asia II-7 cryptic species as the dominant forms in the surveyed regions, with Portiera emerging as the most prevalent endosymbiont. A more in-depth analysis of the microbial communities associated with B. tabaci, utilizing 16S rRNA metagenomic sequencing, revealed a dominance of the Proteobacteria phylum. The endosymbiotic bacterial consortium was primarily composed of Candidatus Portiera, Candidatus Hamiltonella, Candidatus Rickettsia, and Candidatus Arsenophonus.<br><br>DISCUSSION: The metagenomic analysis revealed a highly diverse array of bacterial communities, with 92% of sequences classified under Proteobacteria, representing a spectrum of microbial types associated with B. tabaci ranging from parasitic and pathogenic to mutualistic. Within this phylum, Alphaproteobacteria were predominant, known for their role as facultative symbionts, while Gammaproteobacteria provided essential nutrients to arthropods, enhancing their survival and fitness. The interplay of continuous and intensive tomato cultivation, elevated temperatures, favorable host plants, and abundant viral inoculum creates an ideal environment for the proliferation of B. tabaci and the widespread transmission of ToLCuD. The presence of diverse cryptic species of B. tabaci, which are efficient viral vectors, further complicates the situation. These findings underscore the urgent need for integrated management strategies globally to control both whitefly populations and ToLCuD, ensuring the protection of tomato crops and the sustainability of farmer livelihoods.},
}
@article {pmid40143285,
year = {2025},
author = {Popov, N and Sonets, I and Evdokimova, A and Molchanova, M and Panova, V and Korneenko, E and Manolov, A and Ilina, E},
title = {AliMarko: A Pipeline for Virus Identification Using an Expert-Guided Approach.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/v17030355},
pmid = {40143285},
issn = {1999-4915},
support = {122030900069-4//Russian State/ ; },
mesh = {*Phylogeny ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; *Feces/virology ; Animals ; *Genome, Viral ; Humans ; Metagenome ; Chiroptera/virology ; Computational Biology/methods ; Software ; Sequence Analysis, RNA/methods ; },
abstract = {Viruses are ubiquitous across all kingdoms of cellular life, posing a significant threat to human health, and analyzing viral communities is challenging due to their genetic diversity and lack of a single, universally conserved marker gene. To address this challenge, we developed the AliMarko pipeline, a tool designed to streamline virus identification in metagenomic data. Our pipeline uses a dual approach, combining mapping reads with reference genomes and a de novo assembly-based approach involving an HMM-based homology search and phylogenetic analysis, to enable comprehensive detection of viral sequences, including low-coverage and divergent sequences. We applied our pipeline to total RNA sequencing of bat feces and identified a range of viruses, quickly validating viral sequences and assessing their phylogenetic relationships. We hope that the AliMarko pipeline will be a useful resource for the scientific community, facilitating the interpretation of viral communities and advancing our understanding of viral diversity and its impact on human health.},
}
@article {pmid40143275,
year = {2025},
author = {Sarana da Silva, A and de Campos, GM and Altizani, GM and de Carvalho, E and Barros, AC and Cella, E and Kashima, S and Sampaio, SC and Elias, MC and Giovanetti, M and Scrideli, CA and Slavov, SN},
title = {Utilizing Viral Metagenomics to Characterize Pathogenic and Commensal Viruses in Pediatric Patients with Febrile Neutropenia.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/v17030345},
pmid = {40143275},
issn = {1999-4915},
support = {17/23205-8; 21/11944-6; 2022/10278-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 403075/2023-8; 305111/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Humans ; *Metagenomics/methods ; Child ; Male ; Female ; Child, Preschool ; *Febrile Neutropenia/virology ; Adolescent ; Viruses/classification/genetics/isolation &amp; purification ; Infant ; Herpesviridae/genetics/classification/isolation &amp; purification ; Oropharynx/virology ; Neoplasms/virology/complications ; Metagenome ; },
abstract = {Febrile neutropenia (FN) is one of the most common complications in pediatric oncology patients. It has a complex etiologic nature, which in the majority of cases remains unclear. Intervention often follows empirical treatment protocols, mainly using broad-spectrum antibiotics. To evaluate potential viral etiologic agents, this study applied viral metagenomics to paired plasma and oropharyngeal samples obtained from pediatric patients with oncological diseases diagnosed with FN. Metagenomic sequencing was performed on 15 pediatric patients with oncological diseases and FN at the outpatient clinic of Pediatric Oncology at the University Hospital of the Faculty of Medicine of Ribeirão Preto, University of São Paulo. As a control group, we included 15 pediatric patients with oncological diseases in remission or undergoing treatment. Clinically relevant viruses identified by metagenomics in FN patients predominantly included herpesviruses and viruses found in the respiratory tract, like adenoviruses. Direct molecular confirmation was performed on all of them. Anelloviruses, represented by various genera and species in all groups, were also highly prevalent. The data obtained in this study show that viruses might also have possible implications for the etiology of FN. However, due to the complex nature of this disease, more studies are necessary to evaluate their causal relationship. The results obtained in our study may serve to improve patient treatment and ensure adequate management.},
}
@article {pmid40142589,
year = {2025},
author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M},
title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030697},
pmid = {40142589},
issn = {2076-2607},
support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; },
abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.},
}
@article {pmid40142582,
year = {2025},
author = {Peng, Y and Jiang, L and Wu, J and Yang, J and Guo, Z and Miao, M and Peng, Z and Chang, M and Miao, B and Liu, H and Liang, Y and Yin, H and He, Q and Liu, X},
title = {Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030690},
pmid = {40142582},
issn = {2076-2607},
support = {Grant No. 2018YFC1800400//the National Key Research and Development Program of China/ ; Grant No. 51909282//the National Natural Science Foundation of China/ ; Grant No. 2022JJ40583//the Natural Science Foundation of Hunan Province of China/ ; Grant No. 2022WK2017//the Hunan Provincial Key Research and Development Plan/ ; Grant No. 2023NK2030//the Hunan Provincial Key Research and Development Plan/ ; },
abstract = {Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria-phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.},
}
@article {pmid40142572,
year = {2025},
author = {Yi, Q and Zhang, G and Wang, T and Li, J and Kang, W and Zhang, J and Liu, Y and Xu, Y},
title = {Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030682},
pmid = {40142572},
issn = {2076-2607},
support = {2022-PUMCH-B-074//National High Level Hospital Clinical Research Funding/ ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.},
}
@article {pmid40142491,
year = {2025},
author = {Kioukis, A and Camargo, AP and Pavlidis, P and Iliopoulos, I and Kyrpides, NC and Lagkouvardos, I},
title = {Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030598},
pmid = {40142491},
issn = {2076-2607},
support = {710//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; },
abstract = {The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the 'Global Archaea Diversity' (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.},
}
@article {pmid40142462,
year = {2025},
author = {Hadian, S and Smith, DL and Supronienė, S},
title = {Modulating the Plant Microbiome: Effects of Seed Inoculation with Endophytic Bacteria on Microbial Diversity and Growth Enhancement in Pea Plants.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030570},
pmid = {40142462},
issn = {2076-2607},
abstract = {Understanding plant microbe interactions is crucial for achieving sustainable agriculture. This study investigated the effects of inoculating pea plants (Pisum sativum) with two endophytic Bacillus strains, AR11 and AR32, isolated from Artemisia species and characterized by phosphate solubilization, nitrogen fixation, and pathogen antagonism. Utilizing cutting-edge methods such as rarefaction curves, rank abundance modeling, and metagenomic analysis, this research provides a detailed understanding of how these bacterial strains influence plant associated microbiomes. AR11 significantly enhanced microbial diversity, while AR32 showed a moderate effect. Beta diversity analyses revealed distinct shifts in microbial community composition, with AR11-treated samples enriched with beneficial taxa such as Paenibacillus, Flavobacterium, and Methylotenera, known for their roles in nutrient cycling, pathogen suppression, and plant health promotion. This innovative methodological framework surpasses traditional approaches by offering a comprehensive view of ecological and functional microbiome shifts. The study highlights the potential of nonhost bacteria as biostimulants and their role in developing microbiome engineering strategies to enhance plant resilience. These findings contribute to sustainable agriculture by demonstrating how microbial inoculants can be employed to enhance crop productivity and environmental resilience in diverse agricultural systems.},
}
@article {pmid40142456,
year = {2025},
author = {Zhu, S and Guo, Z and Liu, L and Gao, Y and Bai, L and Chen, Y and Zha, M},
title = {Complex Probiotics Relieve Constipation Through Regulation of the Intestinal Microbiota in Kittens.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030563},
pmid = {40142456},
issn = {2076-2607},
support = {2024LHMS03043//The Natural Science Foundation of Inner Mongolia, China/ ; 2022 - Science and Technology Xing Meng - Quality improvement - 02//Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; SPYQ202001//The Cultivation Project for Excellent Youth of Inner Mongolia Agricultural University/ ; },
abstract = {The early developmental phase is a critical window for feline growth, during which immature digestive systems are susceptible to microbiome imbalances caused by environmental stressors. Our research employed macrogenomic analysis to evaluate how complex probiotic formulations influence growth metrics and gastrointestinal flora in juvenile felines. Two dozen healthy kittens were equally divided into the control group and the probiotics group following a 5-day environmental adaptation phase. Fecal scores were recorded daily for all kittens. Fresh fecal samples were collected on days 1 and 14 for macrogenomic analysis. The results showed a significantly lower rate of constipation in the probiotics group compared to the control group (p < 0.05). However, no significant differences were observed in intestinal microbial diversity or structure between the two groups. Metagenomic analysis revealed a higher relative abundance of Bifidobacterium animalis in the probiotics group compared to the control group (p < 0.05). Additionally, the probiotics group exhibited lower relative abundances of Lachnospiraceae bacterium 2 1 58FAA, Lachnospiraceae bacterium 1 1 57FAA, and Acidaminococcus intestini compared to the control group (p < 0.05). These results suggest that complex probiotics can regulate the intestinal microbiota, improve constipation, and promote intestinal health in kittens.},
}
@article {pmid40142431,
year = {2025},
author = {Aires, C and Maioto, R and Inês, A and Dias, AA and Rodrigues, P and Egas, C and Sampaio, A},
title = {Microbiome and Microbiota Within Wineries: A Review.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030538},
pmid = {40142431},
issn = {2076-2607},
abstract = {The main goal of this work is to review the winery's microbiota, from the grape to the winery's microbial niches (fermentation tanks, surfaces, air), and their risks to wine and human health. The impact of climate change on the winery microbiome and related challenges are also discussed. Microbial diversity in wineries depends on several factors, such as the grape variety and its ripeness, temperature, relative humidity and the diverse activities of the winemaking process. Winery surfaces and equipment allow the establishment of a microbial community that can impact wine quality, the health of winery workers and visitors and even wine consumers. In the context of climate change, changes in the sugar content, phenolic compounds and the profile of hexoses and amino acids are already evident. These changes interfere with the fermentation microbiota and the quality of the wines, which are more alcoholic and less acidic. Furthermore, periods of drought or heavy rain favor species associated with berry diseases, including some capable of producing mycotoxins or harmful biogenic amines. In order to understand the impact of these changes on microbial communities, the use of various techniques will be discussed, such as flow cytometry, fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (qPCR) and metagenomic methods.},
}
@article {pmid40142426,
year = {2025},
author = {Needle, DB and Reboul, G and Mitchell, PK and Rothenheber, D and Marra, NJ and Cronk, BD and Patel, NG and Goodman, LB},
title = {Application of Amplicon Metagenomics to Identify Fungal Pathogens in Formalin-Fixed Paraffin-Embedded Samples: Proof of Concept in Animals with Fungal Pathologies.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030533},
pmid = {40142426},
issn = {2076-2607},
support = {1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN)/ ; 1R03DE033304-01A1/NH/NIH HHS/United States ; },
abstract = {The identification of fungal pathogens in formalin-fixed paraffin-embedded (FFPE) tissues is an unmet need in human and animal medicine, and sequence-agnostic approaches are needed to identify emerging pathogens. Eleven FFPE biopsy specimens with etiologic diagnoses of fungal disease based on standard testing of paired fresh tissue samples were utilized here to evaluate metabarcoding approaches. The cases included tissues from three dogs, three cats, one box turtle, one goat, one common loon, and one gray tree frog. The diagnoses from the fresh tissues in these cases were Microsporum canis, Penicillium sp., Exophiala sp. (likely E. jeanselmei), Verticillium sp., Rhizopus sp., atypical Cryptococcus neoformans, Conidiobolus spp., Aspergillus fumigatus, Cryptococcus neoformans var grubii, Batrachochytrium dendrobatidis, Fusarium solani, Blastomyces dermatitidis, Coccidiodes immitis, and Histoplasma capsulatum. We compared the ITS1 and 28S D1 rRNA gene genetic markers in combination with several bioinformatic strategies to identify fungal pathogens in the FFPE tissue samples, with a success rate of 9/11. These methods could allow diagnosticians who receive only FFPE tissues and see fungal pathogens to speciate the pathogens and could be of value in retrospective studies wherein FFPE tissue is the only archived tissue. Furthermore, these techniques could be of use to researchers investigating polymicrobial communities where DNA preservation is suboptimal.},
}
@article {pmid40142417,
year = {2025},
author = {Chao, S and Chen, Y and Wu, J and Zhang, Y and Song, L and Li, P and Sun, Y and Hu, Y and Wang, H and Jiang, Y and Lv, B},
title = {Exserohilum turcicum Alters Phyllosphere Microbiome Diversity and Functions-Implications for Plant Health Management.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030524},
pmid = {40142417},
issn = {2076-2607},
support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; },
abstract = {The phyllosphere represents the largest biological surface on Earth and serves as an untapped reservoir of functional microbiota. The phyllosphere microbiome has the potential to mitigate plant diseases; however, limited information exists regarding its role in maintaining plant health. In this study, metagenomic sequencing was employed to analyze the microbiomes of the adaxial and abaxial leaf surfaces of healthy (CKWT) and diseased (EWT) maize, with the aim of dissecting the influence of Exserohilum turcicum on phyllosphere microbiome function. E. turcicum altered the alpha and beta diversity of the phyllosphere microbiome, with the Shannon diversity and Chao1 index values significantly reduced in EWT. More beneficial microbes accumulated in the CKWT phyllosphere, whereas pathogenic microbes decreased. E. turcicum may have altered the balance between commensal and pathogenic microorganisms. The species and abundances of microorganisms on the two sets of leaf surfaces were also altered after inoculation with E. turcicum. Further analysis of disease-resistance-related metabolic pathways and abundances of antibiotic-resistance genes revealed that E. turcicum altered the abundance of the functional microbiome and modified the microbiome differences between adaxial and abaxial leaf surfaces. In conclusion, the results reveal that microbial diversity in the maize phyllosphere can influence the microbiome and regulate microbial functions to support plant health. These findings enhance our understanding of how E. turcicum affects the phyllosphere microbiome and provide a theoretical basis for biological control of E. turcicum.},
}
@article {pmid40142410,
year = {2025},
author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL},
title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030518},
pmid = {40142410},
issn = {2076-2607},
support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; },
abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).},
}
@article {pmid40141768,
year = {2025},
author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM},
title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/life15030423},
pmid = {40141768},
issn = {2075-1729},
support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; },
abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.},
}
@article {pmid40140988,
year = {2025},
author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W},
title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {30},
pmid = {40140988},
issn = {1756-994X},
mesh = {Humans ; *Virome/genetics ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; China ; Female ; Feces/virology ; Male ; Metagenomics/methods ; Genome, Viral ; Asian People/genetics ; East Asian People ; },
abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.<br><br>METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.<br><br>RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC&#x2009;=&#x2009;0.698) and high-risk patients from controls (AUC&#x2009;=&#x2009;0.761), and its predictive ability was also validated in external cohorts.<br><br>CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.},
}
@article {pmid40140753,
year = {2025},
author = {Yan, Z and Wang, Y and Zeng, W and Hui, J and Yang, B and Xu, J and Miao, Y and Xia, R},
title = {Antibiotic-driven pathogen replacement events in a kidney transplant recipient with ADPKD: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {423},
pmid = {40140753},
issn = {1471-2334},
support = {82270784//National Natural Science Foundation of China/ ; 2023A1515012276//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2024CL-GX03//Clinical High-tech and Major Technology Projects in Guangzhou Area/ ; },
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Polycystic Kidney, Autosomal Dominant/complications/surgery ; *Anti-Bacterial Agents/therapeutic use ; Male ; Transplant Recipients ; Middle Aged ; Nephrectomy ; Enterococcus faecium/isolation &amp; purification/drug effects ; },
abstract = {BACKGROUND: Retaining the native bilateral kidneys after transplantation is a common treatment for patients with end-stage autosomal dominant polycystic kidney disease. However, this strategy poses the risks of potential complications from polycystic kidney infection. The efficiency of antibiotic therapy and the optimal time for native nephrectomy in managing these infections remain uncertain.<br><br>CASE PRESENTATION: We report a case of a kidney transplant recipient with retained bilateral polycystic kidneys who experienced recurrent cyst and bloodstream infections, accompanied by antibiotic-driven pathogen replacement. After multiple failed attempts at antibiotic therapy, the patient subsequently underwent unilateral polycystic kidney resection. Subsequently, a new infection episode occurred, leading to the other native nephrectomy. Cystic tissue and fluid samples were collected from both shallow and deep layers of the polycystic kidneys, along with peripheral blood and urine samples. These samples were analyzed using microbial culture, metagenome sequencing, and digital polymerase chain reaction to identify infectious pathogens. Pathogen replacement occurred across different infection episodes, with the dominant bacterial species being Escherichia coli, Klebsiella aerogenes, and Enterococcus faecium, in succession.<br><br>CONCLUSIONS: This case highlights the replacement of dominant pathogens under antibiotic selection pressure in polycystic kidney infections, primarily involving gram-negative bacilli. When initial and subsequent antibiotic therapy fail, re-evaluation of the cyst infection definition is necessary, and preemptive native nephrectomy should be considered.},
}
@article {pmid40140741,
year = {2025},
author = {Zhao, X and Liu, X and Wang, Z and Wei, S and Wu, Z},
title = {Metagenomic next-generation sequencing for the diagnosis of Corynebacterium striatum meningitis: case report and literature review.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {127},
pmid = {40140741},
issn = {1471-2377},
support = {20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; [2023]14-73//Shanxi Provincial Department of Education/ ; },
mesh = {Humans ; Male ; Aged ; *Corynebacterium/isolation &amp; purification/genetics ; *Corynebacterium Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Meningitis, Bacterial/diagnosis/drug therapy/microbiology ; },
abstract = {OBJECTIVE: To report a case of Corynebacterium striatum meningitis and conduct a comprehensive literature review to determine the clinical presentation, microbiology, and treatment approaches for these patients.<br><br>MATERIALS AND METHODS: A 75-year-old male patient presented with headache and fever; however, bacterial cultures of cerebrospinal fluid (CSF) yielded negative results. Metagenomic next-generation sequencing (mNGS) of CSF subsequently identified Corynebacterium striatum meningitis as the causative agent for meningitis. A systematic search was performed across various databases encompassing systematic reviews, cohort studies, case series, and case reports involving patients diagnosed with Corynebacterium striatum meningitis regardless of age. Clinical presentation characteristics and the most frequently employed diagnostic technologies were obtained. A narrative summary of the findings is presented.<br><br>RESULTS: Corynebacterium striatum meningitis patients do not exhibit any specific age or sex predisposition or distinctive symptoms or signs. In patients with Corynebacterium striatum meningitis, CSF tests typically reveal an increased number of white blood cells (predominantly polymorphonuclear cells), elevated protein levels, and decreased glucose levels. Notably, the prevalence of antibiotic-resistant strains of Corynebacterium striatum has increased in recent years, leading to a gradual rise in antibiotic treatment failure rates. It is predicted that by 2030, vancomycin may be the sole effective drug available.<br><br>CONCLUSION: The possibility of Corynebacterium striatum infection should be considered during clinical diagnosis and laboratory testing procedures for bacterial meningitis. mNGS can serve as a supplementary gold standard in the diagnosis of bacterial meningitis, effectively enhancing the detection rate of rare pathogens.},
}
@article {pmid40140706,
year = {2025},
author = {Best, L and Dost, T and Esser, D and Flor, S and Gamarra, AM and Haase, M and Kadibalban, AS and Marinos, G and Walker, A and Zimmermann, J and Simon, R and Schmidt, S and Taubenheim, J and Künzel, S and Häsler, R and Franzenburg, S and Groth, M and Waschina, S and Rosenstiel, P and Sommer, F and Witte, OW and Schmitt-Kopplin, P and Baines, JF and Frahm, C and Kaleta, C},
title = {Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40140706},
issn = {2058-5276},
support = {859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; FOR5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 416 418087534//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice with metabolic modelling to characterize host-microbiome interactions during aging. Reconstructing integrated metabolic models of host and 181 mouse gut microorganisms, we show a complex dependency of host metabolism on known and previously undescribed microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These changes coincided with increased systemic inflammation and the downregulation of essential host pathways, particularly in nucleotide metabolism, predicted to rely on the microbiota and critical for preserving intestinal barrier function, cellular replication and homeostasis. Our results elucidate microbiome-host interactions that potentially influence host aging processes. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies.},
}
@article {pmid40140705,
year = {2025},
author = {Garrido-Sanz, D and Keel, C},
title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40140705},
issn = {2058-5276},
abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.},
}
@article {pmid40140473,
year = {2025},
author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA},
title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10378},
pmid = {40140473},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adolescent ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism ; *Attention Deficit Disorder with Hyperactivity/metabolism/microbiology ; *Biomarkers ; *Depression/metabolism ; Anxiety/microbiology ; Mental Health ; Stress, Psychological/metabolism ; Feces/microbiology ; },
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.},
}
@article {pmid40140149,
year = {2025},
author = {Ananda, A and Brigiyanti, LN and Widhiastuty, MP and Haryati, T and Suharti, and Ma'ruf, IF and Akhmaloka, },
title = {Characterization and molecular dynamics simulation of Lk2 lipase expressed in Pichia pastoris.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {342},
pmid = {40140149},
issn = {1573-4978},
support = {12/II.7/HK/2023//RIIM Research Project Program, National Research and Innovation/ ; },
mesh = {*Lipase/genetics/metabolism/chemistry/isolation &amp; purification ; *Molecular Dynamics Simulation ; Substrate Specificity ; Pichia/genetics/metabolism ; Hydrogen-Ion Concentration ; Fungal Proteins/genetics/metabolism/chemistry ; Recombinant Proteins/metabolism/genetics/isolation &amp; purification/chemistry ; Molecular Docking Simulation ; Hydrolysis ; Saccharomycetales ; },
abstract = {BACKGROUND: Lipase is a versatile enzyme that serves as a biocatalyst in various industries. lk2 was successfully isolated from household waste compost through a metagenomic approach.<br><br>MATERIALS AND METHODS: lk2 from plasmid pPICZ&#x3b1;A- lk2 was integrated into chromosomes of Pichia. pastoris GS115 using the electroporation method. Lk2 was expressed on Pichia. pastoris by methanol induction. The enzyme was purified through Ion Metal Affinity Chromatography Ni-NTA. The purified enzyme was characterized based on hydrolytic activity and in silico analysis.<br><br>RESULTS: Lk2 was successfully expressed as an extracellular protein in Pichia pastoris. The cell-free supernatant exhibited hydrolysis activity to para-nitro phenyl laurate. The purified protein showed 15 times activity compared to cell-free supernatant and the size at around 35&#xa0;kDa following gel electrophoresis. The enzyme showed optimum activity at 60[o]C and pH 8. Lk2 preferred para nitro phenyl laurate as substrate. The enzyme's preference for medium-long carbon chains was corroborated by in silico analysis, which revealed favorable interactions between the enzyme and substrate, including affinity binding energy and optimal orientation of catalytic pocket to the substrate. Furthermore, the radius of gyration analysis of the Lk2 showed that the best structural compactness of Lk2 was at 60[o]C. This is in line with the optimal temperature of Lk2 activity. In addition, docking analysis found important substrate binding residues, including Tyr30, Ser85, Leu121, Leu163, Leu166, Leu 233, and Leu254 beside Ser85, Asp231, and His253 as triad catalytic.<br><br>CONCLUSION: Lk2 belongs to a thermotolerant and alkaline lipase, prefers a medium-length carbon chain as substrate and is confirmed by in silico analysis. Several amino acid residues were probed to be important for substrate binding residues. The data give valuable information to develop the possibility of Lk2 as an industry's enzyme.},
}
@article {pmid40139349,
year = {2025},
author = {Bilton, TP and Hickey, SM and Jonker, A and McRae, K and Hess, MK and Perry, BJ and Bryson, B and Henry, H and Bain, W and Booker, F and Veenvliet, B and Peers-Adams, J and Pile, G and Waller, E and Janssen, PH and Tiplady, KM and Reid, P and Muetzel, S and Agnew, M and Dodds, KG and McEwan, JC and Rowe, SJ},
title = {Milk fatty acids and rumen composition as proxy measures of enteric methane.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25876},
pmid = {40139349},
issn = {1525-3198},
abstract = {Genomic selection is a powerful tool to reduce methane emissions in ruminants. However, it requires large-scale on-farm phenotypic measures of methane. Current technologies to measure methane emissions have several limitations and may not be suitable for lactating animals. Because enteric methane is closely linked to the fermentation process in the rumen, which in turn affects milk composition, breeding for low-methane ruminants may change the rumen microbial and milk composition. Consequently, these compositions may provide proxy measures of methane for use in selective breeding of low-methane ruminants. We investigated the effect on rumen and milk composition in sheep bred for divergent methane yield and the potential for generating proxy measures of methane emissions from rumen or milk samples in lactating ewes. Four hundred genotyped lactating ewes from a sheep research flock bred specifically for high and low-methane emissions had methane measured and rumen and milk samples collected approximately 6 wk post-lambing across 4 lactation years. Rumen samples were processed to generate VFA and metagenomic profiles of the rumen microbial community, and fatty acid profiles and mid-infrared spectra were generated for the milk samples. Although no differences in total fat, protein, and lactose percentages in the milk were found, the milk fatty acid profiles differed between methane selection lines, with higher PUFA and branched-chain fatty acids levels, and lower total SFA contents in ewes from the low-methane line. Higher proportions of acetate relative to propionate were found in the rumen samples from the low-methane ewes. Predictions of methane were obtained from the rumen VFA and metagenomic profiles and the fatty acid profiles and mid-infrared spectra from milk. These predictions formed the proxy methane measures and were heritable (between 0.12 to 0.36) and correlated (between 0.29 and 0.42) with the measured methane values. The genetic correlation between proxies and measured methane was between 0.52 and 0.71. The estimated efficiency of indirect selection for methane was higher for the milk sample proxies (49%-75%) than the rumen metagenomic profiles (45%-47%) and rumen VFA profiles (12%-38%). These results suggest that milk fatty acid, MIR spectroscopic, and rumen microbial composition phenotypes have the potential to be used as proxy measures of methane in lactating ruminants, with the milk-based proxies showing greater promise. Results show that the number of animals with methane proxy measures could be increased substantially and will enable access to breeding technology in countries with limited methane measurement infrastructure.},
}
@article {pmid40139294,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Sun, W and Li, B and Zhu, J},
title = {Integrated rice-fish farming dynamically altered the metal resistances and microbial-mediated iron, arsenic, and mercury biotransformation in paddy soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126107},
doi = {10.1016/j.envpol.2025.126107},
pmid = {40139294},
issn = {1873-6424},
abstract = {Given the global concern over heavy metal contamination in agricultural soil, comprehensive and in-depth investigations into the microbial ecological impacts of different agricultural practices on soil heavy metals and their biotransformation processes are both urgent and necessary. We employed metagenomic sequencing to investigate the impacts of integrated rice-fish farming on metal concentrations, metal resistance genes (MRGs), and microbial-mediated Fe, As, and Hg biotransformation processes within rice field. Our findings revealed that integrated rice-fish farming significantly reduced both the diversity and total abundance of MRGs. It also reduced the soil Al, Cd, Cu, Fe, Hg, Ni, Se, V, and Zn levels, with a marked correlation observed between metal concentration and MRGs profiles. Furthermore, integrated rice-fish farming markedly altered the microbial-mediated biotransformation processes for Fe, As, and Hg. It notably upregulated the abundance of Fe biotransformation genes, particularly those involved in the Fe gene regulation, oxidation, reduction, and storage. Biotransformation genes responsible for the As (III) oxidation and As methylation also exhibited increased abundances, along with mercury methylation and demethylation genes. Through metagenome assembled genomes (MAGs), we identified the Mycobacterium aubagnese from paddy soil which contained As oxidation genes and other multiple MRGs, exhibiting strong As remediation potential. Our findings demonstrated the potential of integrated rice-fish farming to reduce soil metal concentrations and mitigate soil metal pollution.},
}
@article {pmid40139249,
year = {2025},
author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL},
title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.},
journal = {Journal of wildlife diseases},
volume = {},
number = {},
pages = {},
doi = {10.7589/JWD-D-24-00115},
pmid = {40139249},
issn = {1943-3700},
abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.},
}
@article {pmid40139192,
year = {2025},
author = {Munneke, MJ and Yuan, Y and Preisner, EC and Shelton, CD and Carroll, DT and Kirchoff, NS and Dickson, KP and Cantu, JO and Douglass, MV and Calcutt, MW and Gibson-Corley, KN and Nicholson, MR and Byndloss, MX and Britton, RA and de Crécy-Lagard, V and Skaar, EP},
title = {A thiouracil desulfurase protects Clostridioides difficile RNA from 4-thiouracil incorporation, providing a competitive advantage in the gut.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.03.001},
pmid = {40139192},
issn = {1934-6069},
abstract = {Nucleotides are essential building blocks for major cellular macromolecules and are critical for life. Consequently, bacterial pathogens must acquire or synthesize nucleotides during infection. Clostridioides difficile is the most common hospital-acquired gastrointestinal infection, and nutrient acquisition is critical for pathogenesis. However, the impact of nucleotide metabolism on C. difficile infection remains unclear. Here, we discover that 4-thiouracil (4-TU), a pyrimidine analog present in the human gut, is toxic to commensal bacteria. 4-TU hijacks the uracil salvage pathway for incorporation into RNA through the uracil phosphoribosyltransferase activity encoded by PyrR and Upp. C. difficile can salvage 4-TU as a pyrimidine source through the enzymatic action of a thiouracil desulfurase (TudS), thereby contributing to C. difficile fitness in mice fed 4-TU or MiniBioreactor models of infection containing exogenous 4-TU. Collectively, these results reveal a molecular mechanism for C. difficile to utilize a poisonous pyrimidine analog in the vertebrate gut to outcompete commensal microbes.},
}
@article {pmid40138989,
year = {2025},
author = {Uprety, T and Swan, M and Kennedy, L and Bryant, U and Cassone, L and Loynachan, A and Janes, J and Evely, MM and Calvaruso, FC and Quick, M and Morgan, J and Abdelrazek, S and Lahmers, K and Carter, C and Erol, E},
title = {Retrospective investigation of 43 necropsy cases of Tyzzer disease in foals and partial genome sequence of Clostridium piliforme by shotgun metagenomics.},
journal = {Veterinary microbiology},
volume = {304},
number = {},
pages = {110489},
doi = {10.1016/j.vetmic.2025.110489},
pmid = {40138989},
issn = {1873-2542},
abstract = {Clostridium piliforme is an obligate intracellular filamentous bacterium that causes Tyzzer disease (TD) in many animals. The disease manifests as severe, multifocal necrotizing hepatitis, with a high fatality rate in foals. Through retrospective investigation, we detected C. piliforme in 43 equine necropsy cases from 2012 to 2024. Positive cases were diagnosed from February to July, peaking in May. The age of affected foals ranged from 4 days to 2 months. Histologically, all cases had necrotizing hepatitis with multifocal, coalescing pinpoint, tan or reddish foci. Since only a partial 16S rRNA gene sequence was available for the horse strain of C. piliforme, we used shotgun metagenomics to obtain its genome sequence from the liver of a necropsied foal with TD. The sequences obtained were compared against the NCBI NT/NR database with the highest number of reads and contigs aligning to Clostridium species. A complete 16S rRNA gene was obtained, showing the highest identity to a 16S rRNA gene of the horse strain of C. piliforme (99.05 %), followed by 98.02-96.71 % identities to rabbit and rodent strains of C. piliforme, indicating cross-species variation. Additional identified genes included alveolysin, exo-α-sialidase, flagellar and spore formation/vegetation, providing the first genetic evidence of virulence factors for C. piliforme. Furthermore, presence of genes encoding multidrug export and multidrug resistance proteins suggested C. piliforme could develop resistance to beta-lactams and fluoroquinolones. This study provides the first partial genome sequence of C. piliforme using a shotgun metagenomics hepatic sampling approach on a foal with TD.},
}
@article {pmid40138908,
year = {2025},
author = {Díaz-García, C and Sánchez-Osuna, M and Serra-Compte, A and Karakatsanidou, I and Gómez-Sánchez, I and Fidalgo, B and Barbuzana-Armas, C and Fittipaldi, M and Rosselli, R and Vinyoles, J and González, S and Pich, OQ and Espasa, M and Yáñez, MA},
title = {Mapping antimicrobial resistance landscape at a city scale sewage network.},
journal = {The Science of the total environment},
volume = {974},
number = {},
pages = {179127},
doi = {10.1016/j.scitotenv.2025.179127},
pmid = {40138908},
issn = {1879-1026},
abstract = {Wastewater is a valuable source for monitoring contaminants of biotic or abiotic origin. Antimicrobial resistance (AMR) has emerged as a public health threat that consists of the ability of microorganisms to resist the effects of antimicrobial compounds, rendering them very difficult or impossible to eradicate in case of infection. Considering the dissemination of antimicrobial resistance genes (ARGs) to a wide number of ecosystems, there is a need for the identification of hotspots that concentrate antimicrobial resistance determinants. A comprehensive investigation conducted at a city-scale in Sabadell (Barcelona, Spain) has integrated both phenotypic and genotypic methodologies, including metagenomics and culture-based techniques coupled with whole-genome sequencing (WGS), to monitor ARG presence in seven different spots of the sewage system. Metagenomics approach identified 262 ARG variants across analyzed sampling sites, grouped into 15 resistance categories. The most prevalent ARGs were macrolides-lincosamides-class B streptogramins (MLSB) (35.1 %) and beta-lactams (28.7 %), including carbapenems (5.9 %) and cephalosporins (5.3 %). MLSB resistance featured dominant msr(E) and mph(E) genes, the most abundant ARGs in our study. ARGs conferring resistance to beta-lactam were dominated by blaOXA-464, blaOXA-491, and blaNPS. Key genes for carbapenem (blaOXA-372, blaKPC-2) and cephalosporin (blaOXA-10, blaOXA-1) resistance were identified. The hospital sector exhibited the highest relative abundance of ARGs, dominated by beta-lactams, MLSB, and aminoglycosides. Wastewater treatment plant (WWTP) entrance points and residential areas displayed similar ARG profiles, while WWTP effluent and industrial zones had the lowest ARG levels. WWTP significantly reduced ARG presence (93.3 %). The characterization of antibiotic-resistant bacterial isolates found that most abundant ARGs were predominantly plasmid-borne, favoring ARG spread across bacterial genera. This finding confirmed the significant role of plasmids in ARG dissemination, increasing both diversity and prevalence within waterborne bacterial communities. City-scale surveillance programs can play a pivotal role in guiding effective measures to reduce the dissemination of AMR and mitigate their environmental impact.},
}
@article {pmid40138872,
year = {2025},
author = {Liang, T and Jiang, T and Liang, Z and Li, L and Chen, Y and Chen, T and Yang, L and Zhang, N and Dong, B and Xie, X and Gu, B and Wu, Q},
title = {Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128145},
doi = {10.1016/j.micres.2025.128145},
pmid = {40138872},
issn = {1618-0623},
abstract = {An increase in branched-chain amino acid (BCAA) levels can result in insulin resistance at different stages of type 2 diabetes (T2D), however, the causes of this increase are unclear. We performed metagenomics and metabolomics profiling in patients with prediabetes (PDM), newly diagnosed diabetes (NDDM), and post-medication type 2 diabetes (P2DM) to investigate whether altered gut microbes and metabolites could explain the specific clinical characteristics of different disease stages of T2D. Here we identify acetolactate synthase (ALS) a BCAA biosynthesis enzyme in Staphylococcus aureus as a cause of T2D insulin resistance. Compared with healthy peoples, patients with PDM, NDDM, and P2DM groups, especially in P2DM group, have increased faecal numbers of S. aureus. We also demonstrated that insulin administration may be a risk factor for S. aureus infection in T2D. The presence of ALS-positive S. aureus correlated with the levels of BCAAs and was associated with an increased fasting blood glucose (FBG) and insulin resistance. Humanized microbiota transplantation experiment indicated that ALS contributes to disordered insulin resistance mediated by S. aureus. We also found that S. aureus phage can reduced the FBG levels and insulin resistance in db/db mice. The ALS-positive S. aureus are associated with insulin resistance in T2D, opening a new therapeutic avenue for the prevention or treatment of diabetes.},
}
@article {pmid40138860,
year = {2025},
author = {Li, G and Srinivasan, V and Tooker, NB and Wang, D and Onnis-Hayden, A and Bott, C and Dombrowski, P and Pinto, A and Gu, AZ},
title = {Metagenomic analysis revealed community-level metabolic differences between full-scale EBPR and S2EBPR systems.},
journal = {Water research},
volume = {280},
number = {},
pages = {123509},
doi = {10.1016/j.watres.2025.123509},
pmid = {40138860},
issn = {1879-2448},
abstract = {Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) has emerged as a promising technology addressing certain challenges of conventional Enhanced Biological Phosphorus Removal (EBPR), notably stability in phosphorus removal, yet the underlying mechanisms are not fully understood. Metagenomic analysis presents a powerful approach to elucidate community-level metabolic differences between EBPR and S2EBPR configurations. In this study, we compared three EBPR and three S2EBPR activated sludge communities using metagenomic analysis at taxonomy, key functional pathways/genes, and polyphosphate-metabolism marker genes. Our analysis revealed larger genus-level diversity variance in S2EBPR communities, indicating distinct microbial community compositions influenced by different operational configurations. A higher diversity index in the S2EBPR than the EBPR was observed, and a higher Ca. Accumulibacter abundance was detected in EBPRs, whereas the fermentative candidate PAOs genera, including Ca. Phosphoribacter and Ca. Promineifilum, were more abundant in S2EBPR systems. EBPR and S2EBPR groups displayed similar gene and pathway abundance patterns related to core metabolisms essential for carbon and nitrogen metabolism. PolyP-metabolism marker gene phylogeny analysis suggested that exopolyphosphatase gene (ppx) showed better distinctions between EBPR and S2EBPR communities than polyphosphate kinase gene (ppk). This also highlighted the needs in fine-cale microdiversity analysis and finding novel Ca. Accumulibacter clades and species as resolved using the ppk gene. These findings provide valuable insights into AS community dynamics and metabolic functionalities, paving the way for further research into optimizing phosphorus removal processes in wastewater treatment systems.},
}
@article {pmid40138725,
year = {2025},
author = {Stachler, E and Gnirke, A and McMahon, K and Gomez, M and Stenson, L and Guevara-Reyes, C and Knoll, H and Hill, T and Hill, S and Messer, KS and Arizti-Sanz, J and Albeez, F and Curtis, E and Samani, P and Wewior, N and O'Connor, DH and Vuyk, W and Khoury, SE and Schnizlein, MK and Rockey, NC and Broemmel, Z and Mina, M and Madoff, LC and Wohl, S and O'Connor, L and Brown, CM and Ozonoff, A and Park, DJ and MacInnis, BL and Sabeti, PC},
title = {Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA.},
journal = {Emerging infectious diseases},
volume = {31},
number = {13},
pages = {},
doi = {10.3201/eid3113.250087},
pmid = {40138725},
issn = {1080-6059},
abstract = {Highly pathogenic avian influenza A(H5N1) virus has caused a multistate outbreak among US dairy cattle, spreading across 16 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk samples from 20 states for methods development, we found that H5N1 virus concentrations by digital PCR strongly correlated with quantitative PCR cycle threshold values; digital PCR exhibited greater sensitivity. Metagenomic sequencing after hybrid selection was best for higher concentration samples, whereas amplicon sequencing performed best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to perform monthly testing of bulk milk samples from all dairy cattle farms in Massachusetts, USA, which remain negative to date. The methods, workflow, and recommendations described provide a framework for others aiming to conduct H5N1 surveillance efforts.},
}
@article {pmid40138143,
year = {2025},
author = {Ali, KA and He, LX and Gao, F and Xia, ZA and Huang, H and Zeng, H and Hu, WH},
title = {Pathogen Detection in Spinal Infections: Next-Generation Sequencing Versus Conventional Microbiological Methods.},
journal = {Current medical science},
volume = {},
number = {},
pages = {},
pmid = {40138143},
issn = {2523-899X},
support = {(2023AFB646)//Hubei Provincial Natural Science Foundation of China/ ; (No. 2023020201010155)//Innovation Program of Wuhan Basic Research/ ; (2022135)//Educational Research Program of Huazhong University of Science and Technology/ ; },
abstract = {OBJECTIVE AND BACKGROUND: Early and accurate diagnosis of spinal infections, including spinal tuberculosis, is pivotal for effective treatment but remains challenging. This study aims to assess the diagnostic yield of metagenomic next-generation sequencing (mNGS) compared with that of conventional microbiological tests (CMTs) in identifying pathogens associated with spinal pathologies, with a special focus on infections leading to surgical interventions.<br><br>METHODS: We enrolled 85 patients who underwent spinal surgery, comprising 63 patients with clinically diagnosed spinal infections, including patients with spinal tuberculosis, and 22 patients with noninfectious spinal conditions. The procedures involved irrigation and debridement for persistent wound drainage, with subsequent DNA extraction from plasma and joint fluid for mNGS and CMT analysis.<br><br>RESULTS: Significantly increased C-reactive protein (CRP) levels were observed in patients with infections. The mNGS approach showed greater diagnostic sensitivity (92.06%) for detecting pathogens, including Mycobacterium tuberculosis, than did CMTs (36.51%). Despite its low specificity, mNGS had considerable negative predictive value (70.59%), underscoring its utility in ruling out infections.<br><br>CONCLUSIONS: The mNGS offers superior sensitivity over CMTs in the diagnosis of a variety of spinal infections, notably spinal tuberculosis. This study highlights the potential of mNGS in enhancing the diagnosis of complex spinal infections, thereby informing targeted treatment strategies.},
}
@article {pmid40138008,
year = {2025},
author = {Davasaz Tabrizi, E and Sevil, M and Arican, E},
title = {Bioinformatic strategies in metagenomics of chronic prostatitis.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {188},
pmid = {40138008},
issn = {1433-8726},
mesh = {Male ; *Prostatitis/microbiology ; Humans ; Adult ; *Metagenomics ; *Computational Biology ; Chronic Disease ; Young Adult ; Middle Aged ; Microbiota/genetics ; },
abstract = {PURPOSE: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent urological condition in young men, significantly affecting quality of life due to persistent discomfort and neuropsychological symptoms. Despite its high prevalence, the etiology of CP/CPPS remains poorly understood. This study investigated urinary microbiota differences between CP/CPPS patients and healthy controls to identify microbial contributors, antibiotic resistance genes (ARGs), and virulence factors of dominant bacteria, as well as to explore potential therapeutic targets.<br><br>METHODS: Urine samples were collected from 58 CP/CPPS patients and 25 controls. Symptom severity was assessed by a specialist urologist using the NIH Chronic Prostatitis Symptom Index and UPOINT classification. Bacterial-specific 16&#xa0;S rRNA sequencing was performed using nanopore technology, with bioinformatics analyses conducted via ONT guppy 5.0.11, NCBI and SLV 16&#xa0;S bacterial taxonomic databases, UPGMA hierarchical clustering, and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pairwise comparisons were analyzed using the Mann-Whitney U test.<br><br>RESULTS: Distinct microbial diversity patterns were observed between patients and controls. Bacillus species were significantly enriched in CP/CPPS patients, while Enterococcus species predominated in controls. Younger patients exhibited unique microbiome profiles compared to older groups. Bioinformatics analyses identified ARGs and virulence factors associated with Bacillus species, implicating them in localized inflammation. Antibiotics like pleuromutilin or vancomycin were identified as potential therapeutic options, though experimental validation was beyond the study's scope.<br><br>CONCLUSION: These findings highlight microbial imbalances and provide a foundation for microbiome-targeted therapeutic strategies for CP/CPPS management in the future. Additionally, the identification of bacterial virulence factors and ARG provides insights into the potential mechanisms driving persistent symptoms. Future research with larger cohorts and experimental validation of the suggested therapeutic options may contribute to more effective treatment for CP/CPPS.},
}
@article {pmid40137749,
year = {2025},
author = {Mao, W and Wang, J and Li, T and Wu, J and Wang, J and Wen, S and Huang, J and Shi, Y and Zheng, K and Zhai, Y and Li, X and Long, Y and Lu, J and Guo, C},
title = {Hybrid Capture-Based Sequencing Enables Highly Sensitive Zoonotic Virus Detection Within the One Health Framework.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/pathogens14030264},
pmid = {40137749},
issn = {2076-0817},
support = {2023YFVA1005//National Natural Science Foundation of China International (Regional) Cooperation and Ex-change Project/ ; 51000-12240016//Startup Fund for Young Researchers of Sun Yat-sen University/ ; z1-2023005//Discipline Cluster of Oncology, Wenzhou Medical University/ ; },
mesh = {Animals ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *One Health ; *SARS-CoV-2/genetics/isolation &amp; purification ; Cattle ; Metagenomics/methods ; Genome, Viral/genetics ; Zoonoses/virology/diagnosis ; COVID-19/diagnosis/virology ; Viruses/genetics/isolation &amp; purification ; Sensitivity and Specificity ; Limit of Detection ; },
abstract = {Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized probe set consisting of 149,990 probes, targeting 663 viruses associated with humans and animals. The detection performance was initially assessed using viral reference materials in a background of human nucleic acids. Compared to standard metagenomic next-generation sequencing (mNGS), our method achieved substantial read enrichment, with increases ranging from 143- to 1126-fold, and enhanced detection sensitivity by lowering the limit of detection (LoD) from 10[3]-10[4] copies to as few as 10 copies based on whole genomes. This method was further validated using infectious samples from both animals and humans, including bovine rectal swabs and throat swabs from SARS-CoV-2 patients across various concentration gradients. In both sample types, our hybrid capture-based sequencing method exhibited heightened sensitivity, increased viral genome coverage, and more comprehensive viral identification and characterization. Our method bridges a critical divide between diagnostic detection and genomic surveillance. These findings illustrate that our hybrid capture-based sequencing method can effectively enhance sensitivity to as few as 10 viral copies and genome coverage to >99% in medium-to-high viral loads. This dual capability is particularly impactful for emerging pathogens like SARS-CoV-2, where early detection and genomic characterization are equally vital, thereby addressing the limitations of metagenomics in the surveillance of emerging infectious diseases in complex samples.},
}
@article {pmid40137713,
year = {2025},
author = {Shaw, CA and Soltero-Rivera, M and Profeta, R and Weimer, BC},
title = {Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/pathogens14030228},
pmid = {40137713},
issn = {2076-0817},
support = {UL1 TR001860/NH/NIH HHS/United States ; },
mesh = {Animals ; Cats ; *Microbiota/genetics ; *Cat Diseases/microbiology/diagnosis ; *Aggressive Periodontitis/microbiology ; Stomatitis/microbiology/veterinary ; Bacteria/genetics/classification/isolation &amp; purification ; Disease Progression ; Mouth/microbiology ; Metagenomics ; Male ; },
abstract = {Aggressive Periodontitis (AP) and Feline Chronic Gingivostomatitis (FCGS) are two oral inflammatory diseases in cats with unknown etiology. Both conditions present with severe inflammation of the oral cavity and in FCGS it is found with additional deterioration of the non-keratinized mucosa. The oral microbiome is increasingly implicated in disease progression, but little is known about shifts in the microbial community during the AP and FCGS progression. To that end, we used deep metagenomic sequencing with total RNA on three longitudinal samples of the oral microbiome in a cat first diagnosed with AP that progressed to FCGS. This deep sequencing approach revealed that increased diversity at both the genus and species levels marked the shift from AP to FCGS, including increases in Porphyromonas and Treponema species, and decreased Streptobacillus species. The metatranscriptomes were then probed for expression of antimicrobial resistance genes and virulence factors. Disease-related genes that include cheY, and ompP5 were expressed in early AP and FCGS, while others like galU were only expressed in one or the other disease state. Both genus and species-level shifts were observed along the longitudinal microbiome samples with a noted increase in species diversity in the FCGS-associated microbiome. Corroborating that functional shifts accompany taxonomic changes, the AMR and virulence factor expression similarly changed between the sampling points. Together, these taxonomic and functional shifts indicate that AP and FCGS are potentially linked and may be marked by changes in the oral microbiome, which supports the development of microbial-based clinical diagnostics and therapeutics.},
}
@article {pmid40137232,
year = {2025},
author = {Krivonos, DV and Fedorov, DE and Klimina, KM and Veselovsky, VA and Kovalchuk, SN and Pavlenko, AV and Yanushevich, OO and Andreev, DN and Sokolov, FS and Fomenko, AK and Devkota, MK and Andreev, NG and Zaborovsky, AV and Tsaregorodtsev, SV and Evdokimov, VV and Krikheli, NI and Bely, PA and Levchenko, OV and Maev, IV and Govorun, VM and Ilina, EN},
title = {Gut Mycobiome Changes During COVID-19 Disease.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {40137232},
issn = {2309-608X},
support = {&#x2116; 122030900064-9//The government task/ ; &#x2116;056-00108-22-01//The government task/ ; },
abstract = {The majority of metagenomic studies are based on the study of bacterial biota. At the same time, the COVID-19 pandemic has prompted interest in the study of both individual fungal pathogens and fungal communities (i.e., the mycobiome) as a whole. Here, in this work, we investigated the human gut mycobiome during COVID-19. Stool samples were collected from patients at two time points: at the time of admission to the hospital (the first time point) and at the time of discharge from the hospital (the second time point). The results of this study revealed that Geotrichum sp. is more represented in a group of patients with COVID-19. Therefore, Geotrichum sp. is elevated in patients at the time of admission to the hospital and underestimated at the time of discharge. Additionally, the influence of factors associated with the diversity of fungal gut microbiota was separately studied, including disease severity and age factors.},
}
@article {pmid40136572,
year = {2025},
author = {Malik, Y and Ali, I and Sajjad, A and Jing, L and Iqbal, I and Rehman, AU and Azam, T and Chen, X},
title = {Bacterial Diversity at Himalayan Pink Salt Extraction Site.},
journal = {Biology},
volume = {14},
number = {3},
pages = {},
pmid = {40136572},
issn = {2079-7737},
abstract = {Table salt, or sodium chloride, is extensively utilized in the culinary business as a flavoring agent, texture garnishing [...].},
}
@article {pmid40136549,
year = {2025},
author = {Pizzi, S and Conti, A and Di Canito, A and Casagrande Pierantoni, D and Foschino, R and Setati, ME and Vigentini, I},
title = {Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.},
journal = {Biology},
volume = {14},
number = {3},
pages = {},
pmid = {40136549},
issn = {2079-7737},
support = {150549//Italy/South Africa Joint Research Programme (ISARP) 2023-2025/ ; },
abstract = {This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.},
}
@article {pmid40136543,
year = {2025},
author = {Claros, MG and Bullones, A and Castro, AJ and Lima-Cabello, E and Viruel, M&#xc1; and Suárez, MF and Romero-Aranda, R and Fernández-Pozo, N and Veredas, FJ and Belver, A and Alché, JD},
title = {Multi-Omic Advances in Olive Tree (Olea europaea subsp. europaea L.) Under Salinity: Stepping Towards 'Smart Oliviculture'.},
journal = {Biology},
volume = {14},
number = {3},
pages = {},
pmid = {40136543},
issn = {2079-7737},
support = {TED2021-130015B-C21//Agencia Estatal de Investigaci&#xf3;n/ ; TED2021-130015B-C22//Agencia Estatal de Investigaci&#xf3;n/ ; PID2020-113324GB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2020-115853RR-C33//Agencia Estatal de Investigaci&#xf3;n/ ; PID2021-125805OA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; RED2022-134072-T//Agencia Estatal de Investigaci&#xf3;n/ ; RYC2020-030219-I//Agencia Estatal de Investigaci&#xf3;n/ ; EMERGIA20_00286//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ERDF-UE/ ; UMA20-FEDERJA-029//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ERDF-UE/ ; PYC20 RE 009 CSIC EEZ//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ERDF-UE/ ; },
abstract = {Soil salinisation is threatening crop sustainability worldwide, mainly due to anthropogenic climate change. Molecular mechanisms developed to counteract salinity have been intensely studied in model plants. Nevertheless, the economically relevant olive tree (Olea europaea subsp. europaea L.), being highly exposed to soil salinisation, deserves a specific review to extract the recent genomic advances that support the known morphological and biochemical mechanisms that make it a relative salt-tolerant crop. A comprehensive list of 98 olive cultivars classified by salt tolerance is provided, together with the list of available olive tree genomes and genes known to be involved in salt response. Na[+] and Cl[-] exclusion in leaves and retention in roots seem to be the most prominent adaptations, but cell wall thickening and antioxidant changes are also required for a tolerant response. Several post-translational modifications of proteins are emerging as key factors, together with microbiota amendments, making treatments with biostimulants and chemical compounds a promising approach to enable cultivation in already salinised soils. Low and high-throughput transcriptomics and metagenomics results obtained from salt-sensitive and -tolerant cultivars, and the future advantages of engineering specific metacaspases involved in programmed cell death and autophagy pathways to rapidly raise salt-tolerant cultivars or rootstocks are also discussed. The overview of bioinformatic tools focused on olive tree, combined with machine learning approaches for studying plant stress from a multi-omics perspective, indicates that the development of salt-tolerant cultivars or rootstocks adapted to soil salinisation is progressing. This could pave the way for 'smart oliviculture', promoting more productive and sustainable practices under salt stress.},
}
@article {pmid40134914,
year = {2025},
author = {Xu, J and Zeng, H and Li, H and Lin, X and Lin, T},
title = {Severe pneumonia caused by Chlamydia abortus complicated by hemophagocytic syndrome: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1547766},
pmid = {40134914},
issn = {2296-858X},
abstract = {BACKGROUND: Pneumonia caused by Chlamydia abortus (C. abortus) is uncommon, particularly when complicated by severe acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MODS). Hemophagocytic lymphohistiocytosis (HLH) is a rare and potentially fatal disease characterized by the uncontrolled activation and non-malignant expansion of macrophages and T lymphocytes. This report describes a case of severe pneumonia complicated by hemophagocytic lymphohistiocytosis, caused by Chlamydia abortus.<br><br>CASE INTRODUCTION: A 42-year-old female with no history of underlying medical conditions, no known exposure to poultry or avian animals, and no consumption of undercooked sheep or ewes contaminated with infected placenta, presented to the respiratory medicine department with a 3-day history of fever, cough, and sputum production. Initially diagnosed with community-acquired pneumonia, she was treated with piperacillin-tazobactam for 5 days. However, despite 12 h of high-flow oxygen therapy, her oxygenation did not improve, and she was transferred to the ICU, where she received additional treatments, including moxifloxacin and methylprednisolone. Her condition worsened further, prompting the initiation of veno-venous extracorporeal membrane oxygenation (VV-ECMO) and bronchoalveolar lavage for metagenomic next-generation sequencing (mNGS) analysis. The mNGS results identified Chlamydia abortus with a count of 180,791, leading to the cessation of moxifloxacin and the addition of omadacycline to her regimen. After 13 days of ECMO therapy, her condition improved, and the ECMO was discontinued. The endotracheal tube was successfully removed 15 days after intubation. However, 3 days later, the patient developed recurrent fever, pancytopenia, elevated ferritin, blood lipids, soluble CD25, and decreased natural killer cell activity, leading to a diagnosis of hemophagocytic lymphohistiocytosis (HLH). She was treated with ruxolitinib, etoposide, and other supportive medications. Despite treatment, her condition continued to deteriorate. Three days later, the family opted to discontinue therapy due to financial constraints. She passed away 12 h later.<br><br>CONCLUSION: Chlamydia abortus infection can result in severe acute respiratory distress syndrome (ARDS), necessitating prompt diagnosis and active clinical intervention. This case is unique due to the rare occurrence of HLH following Chlamydia abortus infection, a pathogen not commonly associated with this condition. Metagenomic next-generation sequencing (mNGS) offers a distinct advantage in rapidly and accurately identifying rare pathogen infections, while extracorporeal membrane oxygenation (ECMO) can be an effective treatment for severe pneumonia caused by Chlamydia abortus. It highlights the importance of early recognition and management of HLH in patients with severe, unexplained infections, particularly in those with unusual pathogens. Additionally, Chlamydia abortus infection may be complicated by HLH. Clinicians should remain vigilant for patients presenting with unexplained high fever, hepatosplenomegaly, and pancytopenia, and HLH screening should be initiated promptly. Early intervention can significantly improve patient survival rates.},
}
@article {pmid40134637,
year = {2025},
author = {Armstrong, E and Kulikova, M and Yee, N and Rishu, A and Muscedere, J and Sibley, S and Maslove, D and Boyd, JG and Evans, G and Detsky, M and Marshall, J and Taggart, LR and Friedrich, JO and Tsang, JLY and Duan, E and Ali Firdous, K and McCullagh, D and Findlater, A and Fowler, R and Daneman, N and Coburn, B},
title = {Impact of Antibiotic Duration on Gut Microbiome Composition and Antimicrobial Resistance: A Substudy of the BALANCE Randomized Controlled Trial.},
journal = {Open forum infectious diseases},
volume = {12},
number = {3},
pages = {ofaf137},
pmid = {40134637},
issn = {2328-8957},
abstract = {BACKGROUND: Maintaining a diverse gut microbiome and minimizing antimicrobial resistance gene (ARG) carriage through reduced antibiotic utilization may decrease antimicrobial resistance. We compared gut microbiome disruption and ARG carriage following 7 or 14 days of antibiotics for treatment of bacteremia in a substudy of the BALANCE randomized controlled trial.<br><br>METHODS: The BALANCE randomized controlled trial enrolled 3631 participants with bacteremia, who were randomized 1:1 to receive 7 or 14 days of antibiotics. Rectal swabs were collected from 131 participants and analyzed with metagenomic sequencing to characterize the gut microbiome and ARGs. The primary outcome was change in gut microbiome diversity at day 7 vs 14.<br><br>RESULTS: Forty-one participants (n = 28 in the 14-day group, n = 13 in the 7-day group) had samples available for the primary analysis, with an imbalance in piperacillin-tazobactam exposure between groups. Change in gut microbiome diversity at day 7 vs 14 was comparable between the 14-day group (median, 0.07; IQR, -0.46 to +0.51) and 7-day group (median, 0.19; IQR, -0.77 to +0.22; P = .49). Change in ARG abundance at day 7 vs 14 did not differ by treatment duration, nor did the abundance of individual ARGs. We did not observe any change in gut microbiome diversity or ARG carriage at enrollment vs day 7.<br><br>CONCLUSIONS: In this subset of patients from the BALANCE randomized controlled trial, we did not detect greater gut microbiome disruption or ARG carriage among participants who received 14 vs 7 days of antibiotics, but we were limited by small sample size and imbalances between groups.},
}
@article {pmid40134271,
year = {2025},
author = {Orme, W and Grimm, SL and Vella, DSN and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Coarfa, C and Madan, A},
title = {Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients.},
journal = {The Journal of neuropsychiatry and clinical neurosciences},
volume = {},
number = {},
pages = {appineuropsych20240126},
doi = {10.1176/appi.neuropsych.20240126},
pmid = {40134271},
issn = {1545-7222},
abstract = {OBJECTIVE: Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.<br><br>METHODS: In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.<br><br>RESULTS: Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R[2]>0.20), perceptual disturbance (maximum AUROC=0.763, R[2]=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.<br><br>CONCLUSIONS: Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.},
}
@article {pmid40133835,
year = {2025},
author = {Gao, N and Feng, S and Yu, X and Zhao, J and Wan, Y and Yao, Z and Li, D},
title = {Diagnostic value of metagenomic next-generation sequencing combined by medical thoracoscopy surgery among infectious pleural effusion patients.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {407},
pmid = {40133835},
issn = {1471-2334},
support = {ZR2014HQ050//Natural Science Foundation of Shandong province/ ; },
mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; *Pleural Effusion/microbiology/diagnosis ; Aged ; *Thoracoscopy/methods ; Adult ; Bacteria/isolation &amp; purification/genetics/classification ; Aged, 80 and over ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel method for identifying pathogens in infectious diseases. This study aimed to explored the application value of mNGS in diagnosing pulmonary infections with pleural effusion, confirmed by medical thoracoscopy.<br><br>METHODS: We retrospectively reviewed 25 patients with pulmonary infections and pleural effusion between July 2020 and December 2021. All patients had their diagnosis confirmed by medical thoracoscopy to obtain tissue samples for both traditional testing and mNGS. Samples included pleural effusion, successive sputum, and tissue obtained through medical thoracoscopy. We wanted to assess how effective mNGS was in accurately diagnosing these infections.<br><br>RESULTS: This study found that the positive predictive value of mNGS (76% (19/25)) was significantly higher than that of traditional testing (32% (8/25)). The most commonly identified pathogens were Mycobacterium tuberculosis (n&#x2009;=&#x2009;5), followed by Fusobacterium nucleatum (n&#x2009;=&#x2009;4), Torque teno virus (n&#x2009;=&#x2009;4), Streptococcus intermedius (n&#x2009;=&#x2009;3), Peptostreptococcus stomatis (n&#x2009;=&#x2009;2), Porphyromonas endodontalis (n&#x2009;=&#x2009;2), and Campylobacter rectus (n&#x2009;=&#x2009;2). The percentage of mNGS-positive cases was significantly higher than that from traditional testing for bacteria, but the superiority of mNGS for tuberculosis detection was insignificant. Ten cases were identified with mixed infections by mNGS, while no mixed infections were found by traditional testing.<br><br>CONCLUSIONS: Our study showed that using mNGS in combination with biopsy samples obtained through medical thoracoscopy resulted in higher positive rates compared to traditional tests and provided more evidence of pathogens for patients with infectious pleural effusion.},
}
@article {pmid40133828,
year = {2025},
author = {Lei, H and Liao, J and Lin, Y and Liu, T and Lei, W and Gao, W},
title = {Application of metagenomic next-generation sequencing in treatment guidance for deep neck space abscess.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {166},
pmid = {40133828},
issn = {1471-2180},
support = {82000950, 81972528, 82273053, 82203783//National Natural Science Foundation of China/ ; 82000950, 81972528, 82273053, 82203783//National Natural Science Foundation of China/ ; 2020YFC1316903//National Key Research and Development Program of China/ ; 2017004//Sun Yat-sen University/ ; 202201011050//Guangzhou Science, Technology and Innovation Commission/ ; 24QNPY345//Young Teacher Foundation of Sun Yat-sen University/ ; },
mesh = {Humans ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Neck/microbiology ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Abscess/microbiology/drug therapy ; Adult ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Aged ; Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Treatment Outcome ; },
abstract = {BACKGROUND: Infectious etiologies of deep neck space abscess (DNSA) by conventional culture tests can be challenging, which also leads to frequent irrational antibiotic usage. Metagenomic next-generation sequencing (mNGS), as a novel method for analyzing the complex microbial ecosystem from clinical samples, has been utilized in clinical research and practice of various infectious diseases but deep neck space abscess. We here aimed to explore the clinical value of mNGS for pathogen detection and treatment guidance in DNSA patients compared with conventional culture tests.<br><br>METHODS: One hundred six patients diagnosed with DNSA were retrospectively enrolled and allocated into mNGS group and culture group according to whether mNGS was conducted. The pathogen detection effectiveness was of mNGS was compared with conventional culture. Effectiveness of mNGS-modified antimicrobial therapy was evaluated by comparing the treatment outcomes between two groups.<br><br>RESULTS: mNGS showed a significantly higher detection rate than conventional culture (p&#x2009;<&#x2009;0.05) with faster result acquisition. Treatment success rate of patients in the mNGS group was significantly higher than in the culture group (RR: 1.22, 95%CI: 1.07-1.82, p&#x2009;=&#x2009;0.033). Besides, patients in the mNGS group had shorter duration of irrational antimicrobial therapy, shorter hospital stay and less medical costs (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: mNGS is an effective technology for facilitating pathogen detection and improving treatment outcomes of DNSA patients.},
}
@article {pmid40133298,
year = {2025},
author = {Bhanu, P and Buchke, S and Hemandhar-Kumar, N and Varsha, P and Kiran, SKR and Vikneswaran, G and Alva, A and Basavaraj, GS and Kumar, J},
title = {Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10303},
pmid = {40133298},
issn = {2045-2322},
support = {20210001//Bangalore Bioinnovation Centre/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology ; *Mouth/microbiology/virology ; *Microbiota/genetics ; *Metagenomics/methods ; *SARS-CoV-2/genetics/isolation &amp; purification ; Male ; Female ; Adult ; Middle Aged ; Metagenome ; Aged ; },
abstract = {COVID-19, caused by SARS-CoV-2, affects multiple body systems, including the oral cavity, where it may disrupt the oral microbiome in ways that contribute to disease pathology. Understanding the long-term interaction between SARS-CoV-2 and the oral microbiome is crucial, as it may reveal microbial markers valuable for diagnosing or monitoring persistent health issues in COVID-19 survivors. Metagenomic sequencing revealed significant microbial shifts in the oral microbiome of COVID-19 patients, showing reduced microbial diversity and increased prevalence of opportunistic pathogens compared to healthy individuals. Alpha diversity measures indicated lower microbial diversity and evenness, while beta diversity analyses demonstrated distinct microbial community compositions. Core microbiome analysis identified unique taxa in COVID-19 patients that may contribute to disease pathology, while differential abundance analysis highlighted specific taxa shifts, including an increase in potential pathogens. Our findings advance the understanding of microbial changes in the oral microbiome associated with COVID-19 and suggest potential targets for microbiome-based interventions. While these results indicate associations with possible health impacts, further research is needed to determine causative links and long-term implications for COVID-19 survivors. This foundational research highlights the potential for microbiome science to inform diagnostic tools, such as microbial markers for disease progression, and therapeutic approaches, including targeted probiotics, which could ultimately support better patient outcomes and public health strategies.},
}
@article {pmid40132505,
year = {2025},
author = {Wang, L and Zhang, W and Yao, J and Qi, Z and Liu, Y and Li, Z and Qu, J and Ma, Y and Zhang, Y},
title = {Effect of freeze-thaw cycle aging on biochar application in DEHP contaminated Mollisols: Insights from soil properties and microbial community.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118082},
doi = {10.1016/j.ecoenv.2025.118082},
pmid = {40132505},
issn = {1090-2414},
abstract = {Biochar holds significant promise for remediation of organic pollutants. However, the impact of biochar on di-(2-ethylhexyl) phthalate (DEHP)-contaminated Mollisols after freeze-thaw cycles is largely unknown, according to the seasonal traits observed at high latitudes. In this study, fresh biochar (BC) was produced from corn straw, and freeze-thaw aging biochar (FBC) was prepared by simulating winter temperatures in the Mollisol region of Northeast China using BC as a precursor. Pot experiments were conducted to evaluate the effects of freeze-thaw aging on the detoxification efficiency of biochar, the improvement of soil physical and chemical properties, and the regulation of soil microbial community structure and functional genes. The results indicated that biochar after freeze-thaw cycling significantly improved the physical and chemical properties of Mollisols compared with the control, reducing DEHP content by 99.08 % after 28 days. Metagenomic sequencing further revealed the presence of microorganisms and genetic elements potentially involved in DEHP degradation in the soil. The treatment group with freeze-thaw aging biochar exhibited higher microbial diversity and abundance, particularly in Proteobacteria, Bacteroides, and Firmicutes. Analysis of the DEHP degradation pathway via benzoic acid route revealed an increase in the abundance of degraded functional genes/enzymes (benC-xylZ, pacL, catB, pcaG, mhpE, and mhpF). The up-regulation of nitrogen fixation genes and nitrification genes (amoB, hao, narG, nifD, and vnfH) along with a 49.19 % increase in soil microbial biomass nitrogen suggested that freeze-thaw aging biochar benefited nitrogen cycling. Furthermore, the feasibility of applying biochar to high-latitude agricultural settings was validated using pakchoi (Brassica rapa L. ssp. chinensis) as a test crop. These findings suggest that the freeze-thaw aging process enhances the effectiveness of biochar in remediating DEHP-contaminated Mollisols. This study offers a novel perspective on the restoration and improvement of Mollisol productivity in high-latitude regions through biochar application.},
}
@article {pmid40132340,
year = {2025},
author = {Roselli, WR and de Oliveira Miraglia, FF and de Mello Malta, F and Fernandes, GBP and Ribas, GC and de Oliveira Godeiro Júnior, C and Amgarten, DE and Nunes, FCG and Trindade, M and de Almeida Junior, JN and Martino, MDV and Santana, RAF and Pinho, JRR and Doi, AM},
title = {Diagnosis of Cladophialophora bantiana cerebral infection by clinical metagenomics.},
journal = {Diagnostic microbiology and infectious disease},
volume = {112},
number = {3},
pages = {116822},
doi = {10.1016/j.diagmicrobio.2025.116822},
pmid = {40132340},
issn = {1879-0070},
abstract = {PURPOSE: Cladophialophora bantiana is a rare cause of severe central nervous system phaeohyphomycosis.<br><br>RESULTS: A 44-year-old woman from Northeastern Brazil with a history of scotomas, mental confusion, and impaired coordination presented Magnetic Resonance Imaging with vasogenic edema and nodular enhancement in the left occipital lobe. Brain biopsy showed neutrophilic exudate with eosinophils, macrophages, giant multinucleated cells, and septate hyphae with a brown-colored birefringent wall and acute angle branching. Metagenomic analysis of the biopsy's total RNA revealed the presence of RNA sequences highly similari to C. bantiana. Culture confirmed the presence of olivaceous-gray suede-like to floccose colonies, with septate dematiaceous hyphae and long conidia chains from undifferentiated conidiophores, consistent with C. bantiana.<br><br>CONCLUSIONS: This case highlights the potential of metagenomic testing as a tool for early diagnosis of infections caused by uncommon fungal pathogens. To our knowledge, this is the first report of C. bantiana central nervous system infection in Brazil.},
}
@article {pmid40135889,
year = {2025},
author = {Nielsen, ME and Søgaard, KK and Karst, SM and Krarup, AL and Albertsen, M and Nielsen, HL},
title = {Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0329524},
doi = {10.1128/spectrum.03295-24},
pmid = {40135889},
issn = {2165-0497},
abstract = {Bloodstream infections are a major cause of mortality, often leading to sepsis or septic shock. Rapid initiation of effective antimicrobial therapy is essential for survival; however, the current gold standard for identifying pathogens in bloodstream infections, blood culturing, has limitations with long turnaround time and poor sensitivity. This delay in refining empirical broad-spectrum antimicrobial treatments contributes to increased mortality and the development of antimicrobial resistance. In this study, we developed a metagenomic next-generation sequencing assay utilizing the Oxford Nanopore Technologies platform to sequence microbial cell-free DNA from blood plasma. We demonstrated proof of concept in a prospective observational clinical study including patients (n = 40) admitted to the emergency ward on suspicion of bloodstream infection. Study samples were drawn from the same venipuncture as a blood culture sample from the included patients. Nanopore metagenomic sequencing confirmed all microbiological findings in patients with positive blood cultures (n = 11) and identified pathogens relevant to the acute infection in an additional 11 patients with negative blood cultures. This proof-of-concept study demonstrates that culture-independent Nanopore metagenomic sequencing directly on blood plasma could be a feasible supplementary test for infection diagnostics in patients admitted with severe infections or sepsis. These findings support further studies on Nanopore metagenomic sequencing for sepsis diagnostics in larger cohorts to validate and expand the results from this study.IMPORTANCEThis study demonstrates the potential of Nanopore metagenomic sequencing as a rapid, culture-independent diagnostic tool for bloodstream infections, identifying pathogens missed by conventional blood cultures. The study highlights the method's promise in improving pathogen detection and warrants further validation in larger clinical studies.},
}
@article {pmid40135776,
year = {2025},
author = {Wang, J and Liu, Q and Jin, S and Yang, B and Wang, C and Tan, Y and Feng, W and Tao, J and Wang, H and Wang, Y and Yang, S and Cui, L},
title = {Characterization of bile microbiota in patients with obstructive jaundice associated with biliary tract diseases.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000841},
pmid = {40135776},
issn = {2155-384X},
abstract = {BACKGROUND: Cholangiocarcinoma (CHOL), a malignant tumor of the biliary system, is particularly concerning due to its high malignancy and poor prognosis, often leading to obstructive jaundice. The advent of metagenomic sequencing(mNGS) technology has expanded diagnostic capabilities, including the identification of microbes within tumors and their potential role in cancer progression.<br><br>OBJECTIVE: This study aims to explore the bacterial composition in bile from patients with obstructive jaundice of different etiologies and to investigate the association between bile microbiota and biochemical analytes, as well as their potential as biomarkers for diagnosis of obstructive jaundice diseases.<br><br>METHODS: Bile samples from patients with obstructive jaundice admitted to Beijing Friendship Hospital were collected and subjected to 16S rRNA and metagenomic sequencing. The study included patients diagnosed with benign biliary stricture, gallstone, and cholangiocarcinoma. Clinical data and bile chemical components were analyzed. The potential functional roles of the identified microbiota were predicted using bioinformatics tools.<br><br>RESULTS: The study enrolled 13 patients with benign biliary stricture, 19 with gallstones, and 10 with cholangiocarcinoma. Significant differences in bile chemical components and microbial diversity were observed among the groups. The bile microbiota was dominated by distinct phyla and genera across the groups, with Proteobacteria and Fusobacteriota enriched in benign biliary stricture, Firmicutes and Desulfobacterota in cholangiocarcinoma, and Synergistota in gallstone patients. Functional analysis revealed differences in gene functions related to metabolism and other biological processes. A correlation between bile microbiota and biochemical markers was established, and the combination of differential microbiota showed potential as a diagnostic marker for obstructive jaundice of different etiologies.<br><br>CONCLUSION: Bile microbiota varies significantly among patients with obstructive jaundice of different etiologies. The identified microbial signatures and their functional roles could serve as novel diagnostic markers and provide insights into the pathogenesis of biliary diseases.},
}
@article {pmid40135668,
year = {2025},
author = {Nassar, R and Nassar, M and Mohamed, L and Senok, A and Williams, D},
title = {Characterization and ex vivo modelling of endodontic infections from the Arabian Gulf region.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14227},
pmid = {40135668},
issn = {1365-2591},
support = {MBRU-CMRG2020-11//Mohammed Bin Rashid University of Medicine and Health Sciences/ ; 2201100262//University of Sharjah/ ; },
abstract = {AIM: The microbiota of endodontic infections in patients from the Arabian Gulf region (AGR) is largely unexplored. While research in different global regions has investigated the microbial composition of such infections, studies using shotgun metagenomic sequencing (SMS) alongside culture-dependent techniques (CDT) are limited. There are also few in vitro biofilm models that reflect the microbial profiles of endodontic infections. Therefore, by employing SMS and CDT, this research aimed to explore compositional and functional microbial profiles of endodontic infections from the AGR. The research also sought to develop ex vivo biofilms directly from endodontic infection samples.<br><br>METHODOLOGY: SMS and CDT were used to analyze 32 root canal samples from necrotic pulp. Patients' samples were categorized into two cohorts: symptomatic (n&#x2009;=&#x2009;19) and asymptomatic (n&#x2009;=&#x2009;13). Samples underwent sequencing followed by bioinformatic analysis to investigate microbial composition, resistome, virulome, and functional differences. Two representative samples (8R, 15R) were selected to develop ex vivo biofilms on hydroxyapatite coupons. Similarity between inoculum and developed biofilms was assessed using SMS and CDT. The reproducibility of developed biofilms was assessed based on microbial composition and relative abundance at the species level using correlation coefficient analysis.<br><br>RESULTS: Endodontic samples had high bacterial diversity, with a total of 366 bacterial species detected across the two cohorts. Several antibiotic resistance (n&#x2009;=&#x2009;59) and virulence (n&#x2009;=&#x2009;82) genes were identified, with no significant differences between the cohorts. CDT identified 28 bacterial species, with 71.4% of the isolated bacteria having phenotypic resistance to clinically relevant antibiotics. SMS showed that the ex vivo biofilms were polymicrobial. Biofilm derived from sample 15R had 9 species and was dominated by Enterococcus faecalis, while sample 8R had 12 species and was dominated by Streptococcus mutans. Pearson correlation analysis demonstrated a significant positive correlation between biological biofilm replicates, confirming the reproducibility of biofilm formation.<br><br>CONCLUSIONS: There was high bacterial diversity in root canal samples from necrotic pulp. Samples were shown to contain antibiotic resistance and virulence genes, with no differences evident between symptomatic and asymptomatic infections. A high number of isolated bacteria were resistant to clinically used antibiotics. Ex vivo biofilm models from clinical samples were successfully developed and reproducibly reflected a polymicrobial composition.},
}
@article {pmid40135504,
year = {2025},
author = {Pelto, J and Auranen, K and Kujala, JV and Lahti, L},
title = {Elementary methods provide more replicable results in microbial differential abundance analysis.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf130},
pmid = {40135504},
issn = {1477-4054},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Humans ; Reproducibility of Results ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.},
}
@article {pmid40132013,
year = {2025},
author = {Halo, BA and Aljabri, YAS and Yaish, MW},
title = {Drought-induced microbial dynamics in cowpea rhizosphere: Exploring bacterial diversity and bioinoculant prospects.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0320197},
doi = {10.1371/journal.pone.0320197},
pmid = {40132013},
issn = {1932-6203},
mesh = {*Rhizosphere ; *Vigna/microbiology/genetics ; *Droughts ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Biodiversity ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Microbiota ; Plant Roots/microbiology ; },
abstract = {Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.},
}
@article {pmid40131885,
year = {2025},
author = {Elsakhawy, OK and Roozitalab, A and Abouelkhair, MA},
title = {Genome sequence of a Tetraparvovirus ungulate 1 strain from a cow in Tennessee, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129124},
doi = {10.1128/mra.01291-24},
pmid = {40131885},
issn = {2576-098X},
abstract = {We report the genome sequence of a strain belonging to the species Tetraparvovirus ungulate 1 (hereafter referred to as UTPV1-1882), identified in a 4-month-old cow with respiratory disease in Tennessee, USA. The sequence data will improve the existing genomic database, which currently lacks information on these viruses in the United States.},
}
@article {pmid40131631,
year = {2025},
author = {Pavan, E and Pavón, JAR and Nunes, MRT and Carrasco, MM and Dos Santos, MAM and Slhessarenko, RD},
title = {Anellovirus species in the serum of acute febrile patients from Mato Grosso, central Western Brazil, 2019.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40131631},
issn = {1678-4405},
support = {FAPEMAT.0290384/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Mato Grosso/ ; 88887.838336/2023-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 309750/2020-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304781/2019-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 144451/2023-9 (PIBIC)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {The Anelloviridae family is one of the most diverse group of viruses within human virome, comprising 155 species distributed across 30 genera, four of which infect humans. Using a metagenomic approach to examine the frequency and diversity of viruses in the serum of patients with acute febrile illness in Mato Grosso during 2019, we identified and characterized two complete, three nearly complete and nine partial anellovirus genomes, including eleven putatively new species. Alphatorquevirus was the most prevalent genus (50%; n = 7), followed by Gammatorquevirus (35.7%; n = 5) and Betatorquevirus (14.3%; n = 2), consistent with global reports showing its dominance within Anelloviridae. Additionally, 65% of genomes were recovered from children, supporting higher anellovirus diversity and load in younger individuals.},
}
@article {pmid40131463,
year = {2025},
author = {Liu, H and Gan, Y and He, B and Liu, H and Zhuo, H and Tang, J and Xie, B and Shen, G and Ren, H and Jiang, X},
title = {mNGS technique was used to analyze the microbiome structure of intervertebral disc tissue in 99 patients with degenerative disc disease.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {40131463},
issn = {1432-0932},
abstract = {OBJECTIVE: Whether bacterial hypotoxic infection in the intervertebral disc is the cause of disc degenerative disease (DDD) is controversial. The mNGS technique can provide valuable insights by obtaining more comprehensive evidence of the presence of bacteria in the intervertebral disc. This study was designed to analyze the characteristics of intervertebral microbiome structure in patients with lumbar disc degenerative disease and its correlation with clinical indicators.<br><br>METHODS: A total of 104 patients with lumbar&#xa0;disc degenerative diseases were included in this study. The surgically removed lumbar intervertebral disc tissues were collected for clinical culture and metagenomic second-generation sequencing (mNGS), and the consistency of the two microbial detection methods was compared.According to the collected clinical information, patients were grouped according to the modified Pfirrmann grading, Modic typing and age, and the differences of microbial communities detected by mNGS among different groups were compared, including &#x3b1; diversity analysis, &#x3b2; diversity analysis, species abundance difference analysis, etc. Spearman correlation between clinical features and generic relative abundance was calculated.<br><br>RESULTS: The effective culture results of 104 intervertebral disc tissue samples were only 19 cases positive, with a positive rate of 18.3% (19/104), and the mNGS detection results were positive in 99 cases, with a positive rate of 95.2% (99/104). According to the 19 samples with positive culture, nearly half 47.4% (9/19) of staphylococcus species were positive, and all the positive species were basically epidermal common colonization species or environmental common bacteria. At the same time, we conducted two times of mNGS sequencing for these 19 samples, and the consistency rate between the two sequencing results and the culture results was 84.2% (16/19). According to the results of mNGS detection, 250 species from 110 genera were detected in 99 positive samples. The results of group analysis showed that patients with lower degree of disc degeneration (modified Pfirrmann&#x2009;&#x2264;&#x2009;4) and young patients (age&#x2009;<&#x2009;45&#xa0;years) had more abundant microbial communities in disc tissue (P&#x2009;<&#x2009;0.05).&#xa0;Correlation analysis showed that there was a positive correlation between Arcobacter skirrowii and improved Pfirrmann classification at the species level (P&#x2009;<&#x2009;0.01). There was a negative correlation between pseudomonas&#xa0;thermotolerans and modified Pfirrmann classification (P&#x2009;<&#x2009;0.05). There was a positive correlation between Staphylococcus hominis and Modic typing scores (P&#x2009;<&#x2009;0.05). Staphylococcus&#xa0;arlettae was negatively correlated with age (P&#x2009;<&#x2009;0.05). At the genus level, Arcobacter had a significant positive correlation with the modified Pfirrmann grade and Modic classification (P&#x2009;<&#x2009;0.05), Corynebacterium had a significant negative correlation with the modified Pfirrmann grade (P&#x2009;<&#x2009;0.05), and Pseudomonas had a significant negative correlation with age (P&#x2009;<&#x2009;0.05). After our follow-up of six months to one year, two of the patients included in this study eventually developed severe lumbar disc infection, and the rest did not develop infection.<br><br>CONCLUSIONS: This study proves that hypotoxic infection may be involved in the degeneration of intervertebral disc, and the bacterial species that cause this occult infection may be more abundant than previously thought. In addition, there was a significant correlation between the biome structure of these bacteria and clinical indicators. The hypothesis of the cause of this insidious infection has the potential to change the way the disease is treated.},
}
@article {pmid40131352,
year = {2025},
author = {Lu, W and Ji, R and Li, W},
title = {Invasive pulmonary and central nervous system aspergillosis: A case report and literature review.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02528},
pmid = {40131352},
issn = {1588-2640},
abstract = {Invasive aspergillosis primarily affects individuals with compromised immune systems. This study endeavors to suggest the importance of early diagnosis and treatment related to central nervous system (CNS) aspergillosis. Recognizing the typical and atypical imaging characteristics of CNS aspergillosis enables the early and aggressive treatment of an otherwise rapidly fatal infection. We reported a case of an elderly patient with a history of non-Hodgkin lymphoma and prostate cancer who underwent repeated chemotherapy and subsequently experienced a sudden disturbance of consciousness. The diagnosis was affirmed through metagenomic next-generation sequencing (mNGS) of sputum and cerebrospinal fluid. The treatment encompassed systemic antifungal agents and intrathecal injection of amphotericin B. Metagenomic sequencing of sputum and cerebrospinal fluid detected Aspergillus fumigatus and Aspergillus flavus, leading to a diagnosis of invasive pulmonary and CNS aspergillosis. Although the patient actively received combined systemic antifungal drugs (voriconazole and amphoteric B liposome) and intrathecal injection of amphotericin B, he ultimately succumbed to the infection. A review of similar cases from PubMed and Medline from 2014 to 2024, encompassing 64 patients, showed that while early diagnosis and combination therapy have improved survival rates, outcomes remain suboptimal. Invasive aspergillosis has a high mortality rate and requires early diagnosis and treatment. Metagenomic sequencing of pathogenic microorganisms constitutes a convenient approach to facilitate the early diagnosis of aspergillosis. Voriconazole is the preferred treatment for invasive aspergillosis. When CNS aspergillosis emerges, it might be necessary to combine other systemic antifungal agents with intrathecal injection of amphotericin B.},
}
@article {pmid40131312,
year = {2025},
author = {Herazo-Álvarez, J and Mora, M and Cuadros-Orellana, S and Vilches-Ponce, K and Hernández-García, R},
title = {A review of neural networks for metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf065},
pmid = {40131312},
issn = {1477-4054},
support = {2022-21221825//National Agency for Research and Development/ ; EQM210185//Fondequip/ ; },
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; Humans ; Machine Learning ; Metagenome ; Deep Learning ; },
abstract = {One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.},
}
@article {pmid40130931,
year = {2025},
author = {Xia, T and Yang, J and Chen, S and Li, H and Xu, S and Guo, K and Hou, S},
title = {Recovery of 26 metagenome-assembled genomes from the phycosphere of the marine diatom Skeletonema tropicum.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0101324},
doi = {10.1128/mra.01013-24},
pmid = {40130931},
issn = {2576-098X},
abstract = {Metagenome-assembled genomes (MAGs) were recovered from the phycosphere of marine diatom Skeletonema tropicum, which has been long-term maintained in artificial seawater. Most MAGs were found to be highly complete (>90%) with minimum contaminations (<5%), which could serve as reference genomes to investigate the interactions between Skeletonema and their phycosphere microbiota.},
}
@article {pmid40130924,
year = {2025},
author = {Fuchsman, CA and Cram, JA and Huntemann, M and Riley, R and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, T and Daum, C and Copeland, A and Chen, I-MA and Ivanova, NN and Kyrpides, NC and Graham, D and Eloe-Fadrosh, EA and Malkin, SY},
title = {Size-fractionated metagenomic depth profiles from two sulfidic stations in the Chesapeake Bay.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0008425},
doi = {10.1128/mra.00084-25},
pmid = {40130924},
issn = {2576-098X},
abstract = {We present 45 size-fractionated metagenomes collected from two stratified Chesapeake Bay mainstem stations during bottom water sulfidic conditions. This data set enables investigations into shifts in community structure and genomic potential across redox gradients and particle associations (free-living [0.2-3 µm], small [3-30 µm], medium [30-180 µm], and large [>180 µm] fractions).},
}
@article {pmid40130858,
year = {2025},
author = {Vaccaro, M and Pilat, AM and Gusmano, L and Pham, MTN and Barich, D and Gibson, A and Epalle, M and Frost, DJ and Volin, E and Slimak, ZC and Menke, CC and Fennessy, MS and Slonczewski, JL},
title = {Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303424},
doi = {10.1128/spectrum.03034-24},
pmid = {40130858},
issn = {2165-0497},
abstract = {UNLABELLED: Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.<br><br>IMPORTANCE: Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.},
}
@article {pmid40130853,
year = {2025},
author = {Lisha, W and Jiao, Q and Mengyuan, C and Jiajia, Q and Tianbin, T and Yilan, W and Linjie, H and Sufei, Y},
title = {Clinical evaluation of negative mNGS reports in sterile body fluids and tissues.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0201324},
doi = {10.1128/spectrum.02013-24},
pmid = {40130853},
issn = {2165-0497},
abstract = {Regarding metagenomics next-generation sequencing (mNGS) negative literature, there have been much discussions about methodology; thus, we collected clinical and laboratory information for retrospective evidence-based research. We retrospectively analyzed 150 negative mNGS results of patients suspected of having aseptic body fluid infections and divided them into a plasma group, cerebrospinal fluid (CSF) group, and others group according to the sample types. Based on the final laboratory and clinical diagnoses, the diagnostic accuracy of excluding infections in the plasma, CSF, and others groups of negative mNGS results were 72.0%, 40.4%, and 30.2%, respectively. The false-negative rates of the CSF and others group were relatively high. The positive impact rates of clinical application in the plasma, CSF, and others groups were 68.0%, 40.4%, and 25.6%, respectively. Three factors, including patient department distribution, admission symptoms, and doctors' judgment of patient infection were used to analyze the reasons for uncertain negative or false-negative results in mNGS. The clinical information analysis of false-negative patients' aims were to reduce the false-negative rate and improve the diagnostic accuracy of mNGS. On the selection of sampling timing in mNGS, within half a month after a patient develops suspected symptoms of infection, the earlier the mNGS test, the higher the true-negative rate.IMPORTANCEThere has been little research carried out on the diagnostic value of negative metagenomics next-generation sequencing (mNGS) results in clinical practice, especially for sterile body fluids. In the present study, plasma negative mNGS results showed the highest diagnostic accuracy for excluding infection. However, the cerebrospinal fluid and other mNGS false-negative rates were 59.6% and 69.8%, respectively. Our findings emphasized the role of negative mNGS results in practical clinical applications and clarified that patients, mNGS sampling time, and doctor's decision making were the key factors for the diagnosis of clinical infections. More attention should be paid to the diagnostic role of mNGS true negatives, the analysis of clinical patterns of false negatives, and improving the diagnostic accuracy of mNGS.},
}
@article {pmid40130725,
year = {2025},
author = {Filis, G and Bezantakou, D and Rigkos, K and Noti, D and Saridis, P and Zarafeta, D and Skretas, G},
title = {ProteoSeeker: A Feature-Rich Metagenomic Analysis Tool for Accessible and Comprehensive Metagenomic Exploration.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2414877},
doi = {10.1002/advs.202414877},
pmid = {40130725},
issn = {2198-3844},
support = {T2EDK-02899//Operational Program Competitiveness, Entrepreneurship, and Innovation of the NSRF 2014-2020/ ; ATTP4-0340328//Operational Program "Attica 2014-2020" of the NSRF 2014-2020/ ; 101&#xa0;079&#xa0;363//Horizon Europe Programme/ ; 101&#xa0;087&#xa0;471//Horizon Europe Programme/ ; 101087471//HORIZON EUROPE Widening participation and spreading excellence/ ; },
abstract = {The vast majority of microbial diversity remains unculturable, limiting access to novel biotechnological resources. Advances in metagenomics have expanded the understanding of microbial communities, yet targeted protein discovery remains challenging. This study introduces ProteoSeeker, a command-line tool for streamlined metagenomic protein identification and annotation. ProteoSeeker operates in two primary modes: i) Seek mode, which screens the proteins according to user-defined protein families, and ii) Taxonomy mode, which uncovers the taxonomy of the host organisms. By automating key steps, ProteoSeeker reduces computational complexity, enabling time-efficient and comprehensive metagenomic analysis for both specialized and nonspecialized users. The efficiency of ProteoSeeker to achieve targeted enzyme discovery is demonstrated by identifying extremophilic enzymes with desired biochemical features, such as amylases for starch hydrolysis and carbonic anhydrases for CO2 capture applications. By democratizing functional metagenomics, ProteoSeeker is anticipated to accelerate biotechnology, synthetic biology, and biomedical research and innovation.},
}
@article {pmid40130207,
year = {2025},
author = {Lewin, S and Wehrhan, M and Wende, S and Sommer, M and Kolb, S},
title = {Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf020},
doi = {10.1093/ismeco/ycaf020},
pmid = {40130207},
issn = {2730-6151},
abstract = {Tillage erosion poses threats to crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosystem services provided by plant microbiomes. However, targeting microbiomes at the agroecosystem scale necessitates bridging the gap to microscale structures of microbiomes. We hypothesized that differences of microbial nitrogen (N) cycle guilds in the rhizosphere of rye align with a soil catena that has been formed by tillage erosion. The rhizosphere was sampled at four sites, which captured a complete tillage erosion gradient from extremely eroded to depositional soils. The gene abundances characteristic of microbial N cycle guilds were assessed via metagenomics. The eroded sites showed the lowest plant productivity and soil mineral N availability, which was associated with an enrichment of glnA in the rhizosphere. Genes associated with dissimilatory nitrate-to-ammonium reducers and diazotrophy prevailed in the eroded soil profiles. The strongest correlations of the biomasses of rye plants along the catena with N cycle functions were observed for norBC. Thus, tillage erosion as a legacy of agricultural management aligns with substantial differences in rhizosphere microbiome functionality in N cycling. These microbiome differences were linked to plant shoot properties. Thus, the dynamics of the microbiome can be indirectly assessed by remote sensing.},
}
@article {pmid40130011,
year = {2025},
author = {Keenum, I and Jackson, SA and Eloe-Fadrosh, E and Schriml, LM},
title = {A standards perspective on genomic data reusability and reproducibility.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1572937},
doi = {10.3389/fbinf.2025.1572937},
pmid = {40130011},
issn = {2673-7647},
abstract = {Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi'Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series "A Year of Data Reuse" in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.},
}
@article {pmid40129931,
year = {2025},
author = {Lee, G and Rosa, BA and Fernandez-Baca, MV and Martin, J and Ore, RA and Ortiz, P and Cabada, MM and Mitreva, M},
title = {Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1555171},
doi = {10.3389/fcimb.2025.1555171},
pmid = {40129931},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Peru ; Animals ; *Fasciola hepatica/drug effects/genetics ; *Fascioliasis/drug therapy/microbiology ; *Triclabendazole/therapeutic use ; Treatment Outcome ; *Anthelmintics/pharmacology/therapeutic use ; Female ; Male ; Adult ; Middle Aged ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Metagenomics ; Young Adult ; Feces/microbiology/parasitology ; },
abstract = {BACKGROUND: Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.<br><br>METHODS: In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.<br><br>RESULTS AND DISCUSSION: Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.<br><br>CONCLUSIONS: Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.},
}
@article {pmid40129370,
year = {2025},
author = {Lázaro, &#xc1; and Gómez-Ramírez, P and Vila-Donat, P and Cimbalo, A and Manyes, L},
title = {Effects of pumpkin and fermented whey on fecal microbiota profile against AFB1 and OTA exposure in Wistar rats.},
journal = {Toxicology mechanisms and methods},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/15376516.2025.2484636},
pmid = {40129370},
issn = {1537-6524},
abstract = {Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28 day-exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA and AFB1 + OTA), while there was an increase - although not in all groups - when adding the functional ingredients. The main difference between the sexes was found in FW + AFB1 + OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.},
}
@article {pmid40129261,
year = {2025},
author = {Boden, JS and Som, SM and Brazelton, WJ and Anderson, RE and Stüeken, EE},
title = {Evaluating Serpentinization as a Source of Phosphite to Microbial Communities in Hydrothermal Vents.},
journal = {Geobiology},
volume = {23},
number = {2},
pages = {e70016},
doi = {10.1111/gbi.70016},
pmid = {40129261},
issn = {1472-4669},
support = {NE/V010824/1//Natural Environment Research Council/ ; 80NSSC19K1427//NASA Planetary Science Division ISFM Program/ ; OCE-1536405//National Science Foundation/ ; 80NSSC18K0829//NASA Astrobiology Program/ ; 80NSSC19K1427//NASA Astrobiology Program/ ; },
mesh = {*Hydrothermal Vents/microbiology ; *Phosphites/chemistry/metabolism ; Microbiota ; Bacteria/genetics/metabolism/classification ; Phosphorus/metabolism/analysis ; },
abstract = {Previous studies have documented the presence of phosphite, a reduced and highly soluble form of phosphorus, in serpentinites, which has led to the hypothesis that serpentinizing hydrothermal vents could have been an important source of bioavailable phosphorus for early microbial communities in the Archean. Here, we test this hypothesis by evaluating the genomic hallmarks of phosphorus usage in microbial communities living in modern hydrothermal vents with and without influence from serpentinization. These genomic analyses are combined with results from a geochemical model that calculates phosphorus speciation during serpentinization as a function of temperature, water:rock ratio, and lithology at thermodynamic equilibrium. We find little to no genomic evidence of phosphite use in serpentinizing environments at the Voltri Massif or the Von Damm hydrothermal field at the Mid Cayman Rise, but relatively more in the Lost City hydrothermal field, Coast Range Ophiolite Microbial Observatory, The Cedars, and chimney samples from Old City hydrothermal field and Prony Bay hydrothermal field, as well as in the non-serpentinizing hydrothermal vents at Axial Seamount. Geochemical modeling shows that phosphite production is favored at ca 275°C-325°C and low water:rock ratios, which may explain previous observations of phosphite in serpentinite rocks; however, most of the initial phosphate is trapped in apatite during serpentinization, suppressing the absolute phosphite yield. As a result, phosphite from serpentinizing vents could have supported microbial growth around olivine minerals in chimney walls and suspended aggregates, but it is unlikely to have fueled substantial primary productivity in diffusely venting fluids during life's origin and evolution in the Archean unless substrates equivalent to dunites (composed of > 90 wt% olivine) were more common.},
}
@article {pmid40128855,
year = {2025},
author = {DeVeaux, AL and Hall-Moore, C and Shaikh, N and Wallace, M and Burnham, CD and Schnadower, D and Kuppermann, N and Mahajan, P and Ramilo, O and Tarr, PI and Dantas, G and Schwartz, DJ},
title = {Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {82},
pmid = {40128855},
issn = {2049-2618},
support = {R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; T32GM139774/GM/NIGMS NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Male ; *Metagenomics/methods ; Infant, Newborn ; *Fever/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Urinary Tract Infections/microbiology ; Case-Control Studies ; Bacterial Infections/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.<br><br>RESULTS: We studied a cohort of febrile term infants&#x2009;<&#x2009;60&#xa0;days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (>&#x2009;99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.<br><br>CONCLUSIONS: The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.},
}
@article {pmid40128848,
year = {2025},
author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC},
title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {81},
pmid = {40128848},
issn = {2049-2618},
support = {T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; R01-OD028099-01//NIH Transformative Award/ ; R01-OD028099-01//NIH Transformative Award/ ; P30-ES002109//NIEHS Core Center Grant/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Feces/microbiology ; *Bacteria/genetics/classification/metabolism ; Mice ; Animals ; Epigenesis, Genetic ; Epigenome ; Female ; Male ; Phosphates/metabolism ; },
abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.<br><br>RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.},
}
@article {pmid40128686,
year = {2025},
author = {Sun, N and Zhang, J and Guo, W and Cao, J and Chen, Y and Gao, D and Xia, X},
title = {Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {165},
pmid = {40128686},
issn = {1471-2180},
support = {SY202214//Suqian Sci&amp;Tech Program/ ; SY202214//Suqian Sci&amp;Tech Program/ ; 81601857//National Natural Science Foundation of China/ ; YKK18216//Health Technology Development Special Foundation of Nanjing City/ ; YKK18216//Health Technology Development Special Foundation of Nanjing City/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Body Fluids/microbiology/virology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Male ; Middle Aged ; Female ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Adolescent ; Cell-Free Nucleic Acids/genetics ; DNA, Bacterial/genetics ; Child ; Aged, 80 and over ; Child, Preschool ; },
abstract = {OBJECTIVES: This study aims to evaluate and compare the effectiveness of metagenomic next-generation sequencing (mNGS) in identifying pathogens from clinical body fluid samples, with a specific focus on the application of microbial cell-free DNA (cfDNA) mNGS.<br><br>METHODS: A total of 125 clinical body fluid samples were collected. All samples underwent mNGS targeting whole-cell DNA (wcDNA), with 30 samples also analyzed for cfDNA mNGS and 41 subjected to 16S rRNA NGS for comparative analysis. Patient clinical data, including culture results, were obtained from electronic medical records.<br><br>RESULTS: In comparison to cfDNA mNGS, the mean proportion of host DNA in wcDNA mNGS was 84%, significantly lower than the 95% observed in cfDNA mNGS (p&#x2009;<&#x2009;0.05). Using culture results as a reference, concordance rates were 63.33% (19/30) for wcDNA mNGS and 46.67% (14/30) for cfDNA mNGS. Additionally, wcDNA mNGS showed greater consistency in bacterial detection with culture results, achieving a rate of 70.7% (29/41) compared to 58.54% (24/41) for 16S rRNA NGS. The sensitivity and specificity of wcDNA mNGS for pathogen detection in body fluid samples were 74.07% and 56.34%, respectively, when compared to culture results.<br><br>CONCLUSION: Whole-cell DNA mNGS demonstrates significantly higher sensitivity for pathogen detection and identification compared to both cfDNA mNGS and 16S rRNA NGS in clinical body fluid samples, particularly those associated with abdominal infections. However, the compromised specificity of wcDNA mNGS highlights the necessity for careful interpretation in clinical practice.},
}
@article {pmid40128614,
year = {2025},
author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM},
title = {Author Correction: Metagenomic estimation of dietary intake from human stool.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42255-025-01284-z},
pmid = {40128614},
issn = {2522-5812},
}
@article {pmid40128575,
year = {2025},
author = {Yun, H and Seo, JH and Kim, YG and Yang, J},
title = {Impact of scented candle use on indoor air quality and airborne microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10181},
pmid = {40128575},
issn = {2045-2322},
support = {RS-2023-00244833//National Research Foundation of Korea/ ; },
mesh = {*Air Pollution, Indoor/analysis ; *Microbiota ; *Particulate Matter/analysis ; *Air Microbiology ; Humans ; Bacteria/classification/isolation &amp; purification ; Environmental Monitoring/methods ; Extracellular Vesicles ; },
abstract = {Indoor air quality has become a growing concern worldwide due to its significant impact on human health, particularly in residential environments where people spend most of their time. Many studies have examined particulate matter (PM) in indoor air and indoor bioaerosols. However, there is a significant lack of research on airborne micro-sized bacteria (m-AB) and nano-sized bacterial extracellular vesicles (n-ABE), particularly those produced by common household activities, such as burning scented candles. This study investigates changes in PM concentrations and indoor microbiome composition resulting from candle use. Air samples were collected from three locations in residential homes: at the candle-lit spot (CL), 3 m away (3m_CL), and 6 m away (6m_CL). PM10 concentrations peaked at 1.52 times the baseline at the source after 5 min of burning, while PM2.5 and PM1 remained elevated at 3m_CL and 6m_CL over time. Before burning, dominant m-AB genera included Phyllobacterium and Pseudomonas, while post-burning, Phyllobacterium myrsinacearum in n-ABE significantly increased, marking its first detection in indoor air. This suggests that existing airborne bacteria may undergo growth or apoptosis due to combustion byproducts. These findings highlight the importance of improving ventilation in indoor spaces to minimize health risks from prolonged exposure to airborne particles and bacterial vesicles.},
}
@article {pmid40128554,
year = {2025},
author = {Toma, R and Hu, L and Banavar, G and Vuyisich, M},
title = {Preparation of robust synthetic control samples and their use in a metatranscriptomic clinical test.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10101},
pmid = {40128554},
issn = {2045-2322},
mesh = {Humans ; Reproducibility of Results ; *Transcriptome ; Metagenomics/methods ; Gene Expression Profiling/methods ; },
abstract = {Metatranscriptomics (MT) has the potential to revolutionize the field of molecular diagnostics. Due to the complexity of MT diagnostic models, positive and negative control materials for specific disease indications can be difficult to obtain. Controls must often be sourced directly from patients. This introduces logistical burdens, assay variability, and limits high throughput clinical laboratory operations. To overcome this limitation, we developed a method for generating Synthetic Control (SC) samples, which duplicate the nucleic acid signature of complex clinical specimens and produce the desired test outcome. SCs can be easily and cost-effectively produced in large quantities (> 100,000 SCs per amplification cycle), enabling high throughput diagnostic testing. Here, we report the generation of Synthetic Positive Control (SPC) samples. SPCs were validated and implemented in a clinical laboratory. The SPCs produced robust positive signals (average OC risk score of 0.996) and high levels of reproducibility (%CV of 0.29%) in a high throughput automated CLIA laboratory. SCs are a novel and useful method for the generation of high quality controls for MT-based diagnostic tests, and their adoption could herald the widespread use of MT tests in molecular diagnostics.},
}
@article {pmid40128535,
year = {2025},
author = {Han, H and Wang, Z and Zhu, S},
title = {Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2865},
pmid = {40128535},
issn = {2041-1723},
support = {62272105//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; *Benchmarking ; *Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; },
abstract = {Metagenomic binning is a culture-free approach that facilitates the recovery of metagenome-assembled genomes by grouping genomic fragments. However, there remains a lack of a comprehensive benchmark to evaluate the performance of metagenomic binning tools across various combinations of data types and binning modes. In this study, we benchmark 13 metagenomic binning tools using short-read, long-read, and hybrid data under co-assembly, single-sample, and multi-sample binning, respectively. The benchmark results demonstrate that multi-sample binning exhibits optimal performance across short-read, long-read, and hybrid data. Moreover, multi-sample binning outperforms other binning modes in identifying potential antibiotic resistance gene hosts and near-complete strains containing potential biosynthetic gene clusters across diverse data types. This study also recommends three efficient binners across all data-binning combinations, as well as high-performance binners for each combination.},
}
@article {pmid40128181,
year = {2025},
author = {Yan, W and Shi, X and Zhao, Y and Liu, X and Jia, X and Gao, L and Yuan, J and Liao, A and Yasui, H and Wang, X and Wang, X and Zhang, R and Wang, H},
title = {Microbiota-reprogrammed phosphatidylcholine inactivates cytotoxic CD8 T cells through UFMylation via exosomal SerpinB9 in multiple myeloma.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2863},
pmid = {40128181},
issn = {2041-1723},
support = {2022-YGJC-61;2022-MS-219//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Female ; Animals ; Mice ; Humans ; Cell Line ; *T-Lymphocytes, Cytotoxic/immunology ; *Gastrointestinal Microbiome ; *Phosphatidylcholines/immunology/metabolism ; *Multiple Myeloma/genetics/immunology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Exosomes/immunology/metabolism ; *Serpins/genetics/immunology/metabolism ; *Membrane Proteins/genetics/immunology/metabolism ; },
abstract = {Gut microbiome influences tumorigenesis and tumor progression through regulating the tumor microenvironment (TME) and modifying blood metabolites. However, the mechanisms by which gut microbiome and blood metabolites regulate the TME in multiple myeloma (MM) remain unclear. By employing16S rRNA gene sequencing coupled with metagenomics and ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, we find that Lachnospiraceae are high and phosphatidylcholine (PC) are low in MM patients. We further show that Lachnospiraceae inhibits PC production from MM cells and enhances cytotoxic CD8 T cell function. Mechanistically, PC promotes Sb9 mRNA maturation in MM cells by LIN28A/B via lysophosphatidic acid, thus enhances exosamal Sb9 production. Exosamal Sb9 then reduces GZMB expression by suppressing tumor protein p53 (TP53) UFMylation via the competitive binding of TP53 with the ubiquitin-fold modifier conjugating enzyme 1 in CD8 T cells. We thus show that Lachnospiraceae and PC may be potential therapeutic targets for MM treatment.},
}
@article {pmid40128138,
year = {2025},
author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J},
title = {Corrigendum to "The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen" [J. Ethnopharmacol. (2025) 337(Pt 1) 118816].},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119657},
doi = {10.1016/j.jep.2025.119657},
pmid = {40128138},
issn = {1872-7573},
}
@article {pmid40127879,
year = {2025},
author = {Mirsalami, SM and Mirsalami, M},
title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {130},
number = {},
pages = {105738},
doi = {10.1016/j.meegid.2025.105738},
pmid = {40127879},
issn = {1567-7257},
abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.},
}
@article {pmid40127846,
year = {2025},
author = {Brito, J and Frade-González, C and Almenglo, F and González-Cortés, JJ and Valle, A and Durán-Ruiz, MC and Ramírez, M},
title = {Anoxic desulfurization of biogas rich in hydrogen sulfide through feedback control using biotrickling filters: Operational limits and multi-omics analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132439},
doi = {10.1016/j.biortech.2025.132439},
pmid = {40127846},
issn = {1873-2976},
abstract = {Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m[-3] h[-1] with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.},
}
@article {pmid40127751,
year = {2025},
author = {Lim, TW and Huang, S and Burrow, MF and McGrath, C},
title = {A randomised crossover clinical trial of the efficacy of an ultrasonic cleaner combined with a denture cleanser on the microbiome on removable dentures among community-dwelling older adults.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105709},
doi = {10.1016/j.jdent.2025.105709},
pmid = {40127751},
issn = {1879-176X},
abstract = {OBJECTIVE: To evaluate and characterise the microbial compositional changes of removable dentures after interventions by comparing the efficacy of the test arm (a portable self-operated ultrasonic cleaner combined with an enzymatic peroxide-based denture cleanser solution) to the control arm (immersion of the denture in the same cleanser solution followed by conventional brushing).<br><br>MATERIALS AND METHODS: A prospective, single-blind, block-randomised, two-period crossover, controlled clinical trial was conducted, involving 56 community-dwelling older adults wearing removable acrylic dentures. They were block-randomized into the test/control or control/test denture cleaning sequence. Type IIB Restriction-site Associated DNA for Microbiome metagenomic sequencing was adopted to characterize the species-resolved microbial composition for denture biofilm.<br><br>RESULTS: For the intervention effect, the overall microbial richness in both arms was not significantly different based on the Chao 1 index (P=0.343). However, Beta diversity analysis (Jaccard qualitative distance matrix) demonstrated significant differences in the microbial community structures between the Test and Control arms after interventions, confirmed by the Permanova test (R[2]=0.01118, P=0.034). Among the opportunistic pathogenic bacteria, Pseudomonas aeruginosa was detected as one of the top 30 species by relative abundance at the end of the clinical trial, and Enterobacter kobei was significantly enriched in the control arm, as determined by LEfSe analysis.<br><br>CONCLUSIONS: The microbial community of denture biofilm samples after both interventions were significantly 'shifted' and had limited numbers of opportunistic pathogens, suggesting the interventions equally effective in mitigating the overall number of pathogenic bacteria.<br><br>CLINICAL SIGNIFICANCE: Denture cleaning intervention using ultrasonic cleaner combined with immersion in denture cleanser solution appears to be effective in shifting the denture microbiome with reduced pathogenic bacteria among community-dwelling denture wearers.},
}
@article {pmid40127491,
year = {2025},
author = {Penner, M and Klein, OJ and Gantz, M and Nintzel, FEH and Prowald, AC and Boss, S and Barker, P and Dupree, P and Hollfelder, F},
title = {Fluorogenic, Subsingle-Turnover Monitoring of Enzymatic Reactions Involving NAD(P)H Provides a Generalized Platform for Directed Ultrahigh-Throughput Evolution of Biocatalysts in Microdroplets.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.4c11804},
pmid = {40127491},
issn = {1520-5126},
abstract = {Enzyme engineering and discovery are crucial for a sustainable future bioeconomy. Harvesting new biocatalysts from large libraries through directed evolution or functional metagenomics requires accessible, rapid assays. Ultrahigh-throughput screening formats often require optical readouts, leading to the use of model substrates that may misreport target activity and necessitate bespoke synthesis. This is a particular challenge when screening glycosyl hydrolases, which leverage molecular recognition beyond the target glycosidic bond, so that complex chemical synthesis would have to be deployed to build a fluoro- or chromogenic substrate. In contrast, coupled assays represent a modular "plug-and-play" system: any enzyme-substrate pairing can be investigated, provided the reaction can produce a common intermediate which links the catalytic reaction to a detection cascade readout. Here, we establish a detection cascade producing a fluorescent readout in response to NAD(P)H via glutathione reductase and a subsequent thiol-mediated uncaging reaction, with a low nanomolar detection limit in plates. Further scaling down to microfluidic droplet screening is possible: the fluorophore is leakage-free and we report 3 orders of magnitude-improved sensitivity compared to absorbance-based systems, with a resolution of 361,000 product molecules per droplet. Our approach enables the use of nonfluorogenic substrates in droplet-based enrichments, with applicability in screening for glycosyl hydrolases and imine reductases (IREDs). To demonstrate the assay's readiness for combinatorial experiments, one round of directed evolution was performed to select a glycosidase processing a natural substrate, beechwood xylan, with improved kinetic parameters from a pool of >10[6] mutagenized sequences.},
}
@article {pmid40127066,
year = {2025},
author = {Pankovics, P and Takáts, K and Urbán, P and Mátics, R and Reuter, G and Boros, &#xc1;},
title = {Identification of a potential interspecies reassortant rotavirus G and avastrovirus 2 co-infection from black-headed gull (Chroicocephalus ridibundus) in Hungary.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0317400},
doi = {10.1371/journal.pone.0317400},
pmid = {40127066},
issn = {1932-6203},
mesh = {*Rotavirus/genetics/isolation &amp; purification ; Animals ; Hungary ; *Reassortant Viruses/genetics/isolation &amp; purification ; *Charadriiformes/virology ; *Phylogeny ; *Genome, Viral ; Avastrovirus/genetics/isolation &amp; purification/classification ; Coinfection/virology ; Rotavirus Infections/virology/veterinary ; Bird Diseases/virology/epidemiology ; Feces/virology ; Astroviridae Infections/virology/veterinary ; },
abstract = {The black-headed gull is the most common nesting gull species in Hungary. Based on the lifestyle and feeding habits of the black-headed gull, which is highly adapted to the human environment, they can be carriers and spreaders of potential human and other animal pathogens. Between 2014 and 2018 within the framework of the "Life Bird Ringing program" a total of 7 faecal samples were collected from gulls and one sample (MR04) was randomly selected for viral metagenomics and mass sequencing. 95.4% and 4% of the reads were classified into family Seadornaviridae and Astroviridae, respectively, and then were verified by RT-PCR method. In this study, the complete genome of a potential interspecies reassortant rotavirus (RV) strain gull/MR04_RV/HUN/2014 (PP239049-PP239059) and the partial ORF1ab, complete ORF2 of a novel avian nephritis virus strain gull/MR04_AAstV/HUN/2014 (PP239060) was discussed. The strain gull/MR04_RV/HUN/2014 was closely related to rotavirus G (RVG) viruses based on the proteins VP1-VP3, VP6, NSP2, NSP3, and NSP5, but it was more related to the human rotavirus B (RVB) strain Bang373 based on the NSP1, NSP4 and VP7, VP4 proteins, which is assumed to be the result of reassortment between different RVG-RVB rotavirus species. The strain gull/MR04_AAstV/HUN/2014 belonged to the genus Avastrovirus species avastrovirus 2 (AAstV-2) and is related to members of group 6 of avian nephritis viruses (ANVs), but based on the genetic distances it may be the first representative of a separate group. Additional gull samples were found to be negative by RT-PCR. Gulls, which are well adapted to the human environment, could potentially spread enterically transmitted viral pathogens like interspecies reassortant rotaviruses (RVG/RVB), but further molecular surveillance is needed to explore more deeply the viral communities of gulls or other related species adapted to human environments.},
}
@article {pmid40127030,
year = {2025},
author = {Abraham, A and Green, A and Ferrolino, J and Flerlage, T and Gowen, A and Allison, KJ and Suliman, AY and Bhakta, N and McArthur, J and Srinivasan, S and Hayden, RT and Hijano, DR},
title = {Utility and Safety of Bronchoalveolar Lavage for Diagnosis and Management of Respiratory Illnesses in Immunocompromised Children.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {14},
number = {3},
pages = {},
doi = {10.1093/jpids/piaf015},
pmid = {40127030},
issn = {2048-7207},
support = {//American Lebanese Syrian Associated Charities/ ; },
mesh = {Humans ; *Immunocompromised Host ; Retrospective Studies ; *Bronchoalveolar Lavage ; Child ; Child, Preschool ; Female ; Male ; *Respiratory Tract Infections/diagnosis/drug therapy ; Infant ; Adolescent ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Acute respiratory illnesses (ARIs) in immunocompromised children have diverse causes, which can obscure accurate diagnosis and lead to unnecessary antimicrobial use. The risk-benefit ratio of bronchoalveolar lavage (BAL) in these patients is debated. This study aimed to evaluate the safety, yield, and utility of BAL in managing ARIs in immunocompromised children.<br><br>METHODS: This retrospective review examined BALs performed on immunocompromised children with ARI at St. Jude Children's Research Hospital between 2016 and 2021. Microbiological and molecular test results were reviewed from BAL, respiratory tract, and blood within 7 days of the BAL. The final ARI diagnosis was determined by the primary team, changes in antimicrobial management and adverse events were assessed.<br><br>RESULTS: BAL identified a potential pathogen in 84/137 (61.3%) of ARI episodes. BAL results contributed to changes in antimicrobial management in 120 (87.6%) cases and contributed to the ARI diagnosis in 106 (77.3%) cases. In 81 (59.1%) cases, ARI diagnosis was established solely from BAL results (infectious [33.3%], noninfectious [63%], multifactorial [3.7%]). BAL results usually agreed with the ARI diagnosis, but 31/137 (22.6%) were not concordant. Post-BAL, only 5 (3.6%) had increased supplemental oxygen&#x2005;>&#x2005;24 hours, and 3 (3.4%) required new, persistent intubation. Consolidative or nodular pulmonary lesions and post-hematopoietic cell transplant had the highest BAL yields, with no significant differences based on the diffuseness of lesions.<br><br>CONCLUSIONS: BAL is a safe, high-yield diagnostic procedure in immunocompromised children, with results leading to changes in clinical management of ARI. Prospective studies are needed to generate BAL guidelines for ARI in this population.},
}
@article {pmid40126889,
year = {2025},
author = {Cheng, GB and Bongcam-Rudloff, E and Schnürer, A},
title = {Metagenomic Exploration Uncovers Several Novel 'Candidatus' Species Involved in Acetate Metabolism in High-Ammonia Thermophilic Biogas Processes.},
journal = {Microbial biotechnology},
volume = {18},
number = {3},
pages = {e70133},
doi = {10.1111/1751-7915.70133},
pmid = {40126889},
issn = {1751-7915},
support = {2018-01341//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {*Ammonia/metabolism ; *Biofuels ; *Acetates/metabolism ; *Bioreactors/microbiology ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics ; Archaea/metabolism/genetics/classification ; Anaerobiosis ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; Metagenome ; Methane/metabolism ; },
abstract = {Biogas reactors operating at elevated ammonia levels are commonly susceptible to process disturbances, further augmented at thermophilic temperatures. The major cause is assumed to be linked to inhibition followed by an imbalance between different functional microbial groups, centred around the last two steps of the anaerobic digestion, involving acetogens, syntrophic acetate oxidisers (SAOB) and methanogens. Acetogens are key contributors to reactor efficiency, acting as the crucial link between the hydrolysis and fermentation steps and the final methanogenesis step. Their major product is acetate, at high ammonia levels further converted by SAOB and hydrogenotrophic methanogens to biogas. Even though these functionally different processes are well recognised, less is known about the responsible organism at elevated temperature and ammonia conditions. The main aim of this study was to garner insights into the penultimate stages in three thermophilic reactors (52°C) operated under high ammonia levels (FAN 0.7-1.0 g/L; TAN 3.6-4.4 g/L). The primary objective was to identify potential acetogens and SAOBs. Metagenomic data from the three reactors were analysed for the reductive acetyl-CoA pathway (Wood-Ljungdahl Pathway) and glycine synthase reductase pathway. The results revealed a lack of true acetogens but uncovered three potential SAOB candidates that harbour the WLP, 'Candidatus Thermodarwinisyntropha acetovorans', 'Candidatus Thermosyntrophaceticus schinkii', 'Candidatus Thermotepidanaerobacter aceticum', and a potential lipid-degrader 'Candidatus Thermosyntrophomonas ammoiaca'.},
}
@article {pmid40126871,
year = {2025},
author = {Yang, S},
title = {The Economics of Cell-Free DNA Metagenomic Next-Generation Sequencing for Pathogen Detection.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf027},
pmid = {40126871},
issn = {1530-8561},
}
@article {pmid40126624,
year = {2025},
author = {Orellana, E and Zampieri, G and De Bernardini, N and Guerrero, LD and Erijman, L and Campanaro, S and Treu, L},
title = {Sustainable Food Waste Management in Anaerobic Digesters: Prediction of the Organic Load Impact by Metagenome-Scale Metabolic Modeling.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11180},
pmid = {40126624},
issn = {1520-5851},
abstract = {The increasing urbanization has led to rising waste and energy demands, necessitating innovative solutions. A sustainable food waste management approach involves anaerobic codigestion with sewage sludge, enhancing biogas production while managing waste. Although this technology has been successfully tested, the biological mechanisms determining its efficiency are still poorly understood. This study leverages genome-scale metabolic modeling of 138 metagenome-assembled genomes to explore species interactions in lab-scale anaerobic reactors fed with sewage sludge to increasing proportions of food waste. The models showed positive correlations with experimental biogas production (CH4: r = 0.54, CO2: r = 0.66), validating their reliability. The dominant methanogen, Methanothrix sp., adapted its metabolism based on feedstock, affecting methane yields, which ranged from 2.5 to 3 mmol/g of volatile solids·h with sewage sludge to 10-14 mmol/g of VS·h with high food waste. The integration of extracellular enzymes into the models highlighted the role in methane production of pectin degradation, protein hydrolysis, and lipid metabolism, mediated by Proteiniphilum sp., Kiritimatiellae sp., and Olb16 sp. The study identified 475 mutualistic interactions involving amino acid, hydrogen, acetate, and phosphate exchange and 44 competitive interactions in hydrolytic and fermentative processes. These insights can help optimize anaerobic digestion and sustainable waste management in urban settings.},
}
@article {pmid40126388,
year = {2025},
author = {Zhang, Q and Su, T and Pan, Y and Wang, X and Zhang, C and Qin, H and Li, M and Li, Q and Li, X and Guo, J and Wu, L and Qin, L and Liu, T},
title = {Malus hupehensis leaves: a functional beverage for alleviating hepatic inflammation and modulating gut microbiota in diabetic mice.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo05325g},
pmid = {40126388},
issn = {2042-650X},
abstract = {Malus hupehensis leaves (MHL), consumed as a daily beverage in Chinese folk tradition and recently recognized as a new food material, are abundant in polyphenols and bioactive compounds that demonstrate hypoglycemic, lipid-lowering, and anti-inflammatory effects. However, the antidiabetic mechanisms have not been fully elucidated. This study aimed to investigate the protective mechanisms of Malus hupehensis leaves' extract (MHLE) against type 2 diabetes mellitus (T2DM). The results showed that MHLE effectively ameliorated glucose and lipid metabolic abnormalities in db/db mice, and attenuated hepatic macrophage activation. Transcriptomic analysis of the liver revealed that MHLE primarily affects genes involved in inflammatory responses and inhibited the TLR4/MAPK pathway to reduce hepatic inflammation. Metagenomic sequencing identified changes in gut microbiota composition and showed that MHLE restored the abundance of Lachnospiraceae bacterium, Oscillospiraceae bacterium, and Clostridia bacterium while reducing the abundance of Escherichia coli, thereby ameliorating gut dysbiosis. The integrated regulation of metabolism, immune response, and the microbial environment by MHLE significantly alleviated symptoms of T2DM. This study offers strong scientific evidence for the potential use of MHL as a functional food.},
}
@article {pmid40125310,
year = {2025},
author = {Xiao, Y and Jing, D and Xiao, H and Mao, M and Kuang, Y and Shen, M and Lv, C and Jian, X and Peng, C and Chen, X},
title = {Metagenomics Analysis of Altered Gut Microbiome in Psoriasis and the Mediation Analysis: A Case-Control Study.},
journal = {Psoriasis (Auckland, N.Z.)},
volume = {15},
number = {},
pages = {45-54},
doi = {10.2147/PTT.S505283},
pmid = {40125310},
issn = {2230-326X},
abstract = {PURPOSE: Psoriasis is an inflammatory disease linked to gut microbiome dysbiosis. However, the mechanisms underlying gut microbiome changes caused by dietary habits in psoriasis remain unclear.<br><br>PATIENTS AND METHODS: We performed a case-control study including 64 psoriasis patients and 64 age-, sex-, and body mass index (BMI)-matched controls. Stool samples were collected for metagenomics sequencing. The differential abundance analysis was performed to identify differentially abundant taxa between psoriasis and control groups. The dietary intake frequency information of each included subject was obtained through face-to-face interviews. Mediation analysis was used to identify potential mediators of the gut microbiome alterations in psoriasis.<br><br>RESULTS: The gut microbiome of psoriasis patients was significantly alterated when compared to controls. Anaerostipes Hadrus, Blautia Wexlerae, and the other six species may be beneficial to psoriasis. However, Prevotella Copri and Eggerthellaceae could be pathogenic bacteria. The study also identified correlations between specific dietary habits and psoriasis, with the largest correlation observed between poultry consumption and psoriasis (OR=0.735, P=0.001), followed by red meat (OR=0.784, P=0.007) and fresh vegetables (OR=0.794, P=0.028). Mediation analysis revealed that Anaerostipes hadrus, Dorea longicatena, and Eggerthella lenta mediated the association between poultry and psoriasis.<br><br>CONCLUSION: The characteristics of intestinal flora in psoriasis patients were significantly different from controls. Intestinal flora mediated the association between diet and psoriasis to some extent. This study provides new insights for adjuvant treatments of psoriasis through dietary and intestinal microbiota interventions.},
}
@article {pmid40125276,
year = {2025},
author = {Zhu, X and Angelidaki, I and Zhang, T and Ju, F},
title = {Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions.},
journal = {ACS environmental Au},
volume = {5},
number = {2},
pages = {183-196},
doi = {10.1021/acsenvironau.4c00071},
pmid = {40125276},
issn = {2694-2518},
abstract = {Anaerobic digestion (AD) systems are vital for converting organic waste to green bioenergy but also serve as a non-negligible environmental reservoir for antibiotic-resistance genes (ARGs) and resistant bacteria of environmental and human health concerns. This study profiles the antibiotic resistome of 90 full-scale biogas reactors and reveals that AD microbiomes harbor at least 30 types and 1257 subtypes of ARGs, of which 16% are located on plasmids showing potential mobility. The total abundance of AD-ARGs ranges widely from 0.13 to 7.81 copies per cell and is distributed into 42-739 subtypes, significantly influenced (P < 0.05) by operational conditions like digestion temperature and substrate types. Compared with the ambient and mesophilic digesters, the thermophilic digesters harbor a significantly lower abundance and diversity as well as greatly reduced mobility and host pathogenicity levels (all P < 0.05) of ARGs, revealing that a higher digestion temperature mitigates the overall resistome risks. The comprehensive analysis of basic traits and key traits of the AD resistome is demonstrated to provide crucial quantitative and qualitative insights into the diversity, distribution pattern, and health risks of ARGs in full-scale AD systems. The revealed knowledge offers new guidance for improving environmental resistome management and developing oriented mitigation strategies to minimize the unwanted spread of clinically important antimicrobial resistance from AD systems.},
}
@article {pmid40124740,
year = {2025},
author = {Brucato, N and Lisant, V and Kinipi, C and Kik, A and Besnard, G and Leavesley, M and Ricaut, FX},
title = {Influence of betel nut chewing on oral microbiome in Papua New Guinea.},
journal = {Evolution, medicine, and public health},
volume = {13},
number = {1},
pages = {36-44},
doi = {10.1093/emph/eoae030},
pmid = {40124740},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: For thousands of years, betel nut has been used as a psychoactive agent in Asian and Oceanian populations. Betel nut chewing was associated with the alteration of human oral microbiome and with diseases such as oral cancer and periodontitis, but only in populations of Asian cultural background. We studied the influence of betel nut chewing on the oral microbiome in Papua New Guinea, where half of the population uses betel nut and the prevalence of these diseases is one of the highest in the world.<br><br>METHODOLOGY: We characterized the oral microbiomes of 100 Papua New Guineans. We defined two cohorts of betel chewers (n&#x2005;=&#x2005;50) and non-chewers (n&#x2005;=&#x2005;50) based on a genetic approach to identify the presence of betel nut in saliva. We statistically compared the alpha and beta microbial diversities between the two cohorts. We performed linear discriminant analyses to identify bacterial species more prevalent in each cohort.<br><br>RESULTS: We found that oral microbial diversity is significantly different between betel chewers and non-chewers. The dysbiosis observed in betel chewers, led to an increase of pathogenic bacterial species including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, known to be in the aetiology of periodontal diseases.<br><br>CONCLUSIONS AND IMPLICATIONS: Our study strongly supports the alteration of human oral microbiome by betel nut use, potentially leading to periodontal diseases. It also shows the need to consider local specificities (e.g. different habits, betel nut types, and oral microbial diversities) to better characterize the impact of betel nut chewing on health.},
}
@article {pmid40124696,
year = {2025},
author = {Li, S and Zhang, S and Zhou, T and Ge, Z and Li, Y and Zhang, J and Zhu, Y and Li, S},
title = {The second generation metagenomic sequencing of cerebrospinal fluid for diagnosis of non-eschar scrub typhus.},
journal = {Oxford medical case reports},
volume = {2025},
number = {3},
pages = {omae198},
doi = {10.1093/omcr/omae198},
pmid = {40124696},
issn = {2053-8855},
abstract = {Tsutsugamushi disease, is an infectious disease transmitted by ticks and caused by the rickettsiella. It is characterized by eschar, fever, rash, and flu-like symptoms. However, diagnosing atypical cases without an eschar and with negative Weil-Felix test results poses a significant diagnostic challenge. This study presents a noteworthy case of non-eschar typhus which was effectively diagnosed using advanced next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) samples.},
}
@article {pmid40124394,
year = {2025},
author = {Ma, CM and Zhang, FS and Zhao, XH and Yang, Y and Wang, B and Wang, Y and Liu, XF and Bian, X and Xu, ZX and Zhang, G and Qu, LZ and Zhang, N},
title = {Genistein improves depression-like behavior in rats by regulating intestinal flora and altering glutamate gene expression.},
journal = {Current research in food science},
volume = {10},
number = {},
pages = {101020},
doi = {10.1016/j.crfs.2025.101020},
pmid = {40124394},
issn = {2665-9271},
abstract = {Depression is a mental disorder, and genistein is known to have antidepressant effects, but its mechanism of action is still unclear. Here, the mechanism of genistein improving depression based on gut microbiota was explored using classic behavioral indicators of depression combined with genomic technology. The behavioral evaluation showed that rats gavaged with 20-40 mg/kg genistein showed an increase in body weight, glucose preference, absenteeism score, body temperature, and 5-hydroxytryptamine (5-HT) content, while a decrease in adrenocorticotropic hormone (ACTH) and corticosterone (CORT) content compared to the depression rat model group, but there was no significant difference compared to the positive control (fluoxetine). The results of high-throughput sequencing showed that genistein increased the relative abundance of Firmicutes and Actinobacteriota and decreased the relative abundance of Bacteroidota at the phylum level. At the genus level, the abundance of Bifidobacterium, a short-chain fatty acid producing bacterium, was increased. Furthermore, metagenome results revealed that the antidepressant effect of genistein can be achieved by promoting glutamate metabolism, increasing glutamic acid decarboxylase (GAD) expression levels, promoting γ-aminobutyric acid (GABA) synthesis, and indirectly increasing 5-HT levels.},
}
@article {pmid40124227,
year = {2025},
author = {Sun, C and Dong, Q and An, H and Liu, Y and Lv, W and Liu, W and Ji, H and Yang, X},
title = {Responses of Soil Microbial Communities and Functions in an Alpine Grassland of the Qinghai Lake Basin With Grazing Disturbance.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e71082},
doi = {10.1002/ece3.71082},
pmid = {40124227},
issn = {2045-7758},
abstract = {Soil ecosystems host diverse microbial communities, which are influenced by various environmental factors, soil properties, vegetation characteristics, and anthropogenic activities, such as livestock grazing. Grazing serves as a critical management practice in the alpine grasslands of the Qinghai-Tibet Plateau, affecting soil microbial communities and their functions through processes such as forage consumption, trampling, and the deposition of feces and urine. In this study, we utilized the scientific and technological platform "Alpine Grassland-Livestock Adaptive Management Technology Platform" in Qinghai Province to examine the effects of grazing intensity on soil microbial communities and functions. Experimental treatments included different grazing intensities (light grazing, moderate grazing, and heavy grazing), along with a no-grazing control. Metagenomic sequencing technology was employed to investigate the impact of these grazing intensities on the microbial community composition and functional attributes in alpine grasslands. The results indicated that: (1) Actinobacteria, Proteobacteria, and Chloroflexi were the dominant bacterial communities in the soil, while Ascomycota, Mucoromycota, and Basidiomycota represented the primary fungal communities. (2) Grazing had a greater impact on soil fungal communities than on bacterial communities, altering the Shannon diversity index and Simpson index of soil fungal communities. (3) Soil pH and soil moisture were important factors influencing changes in soil microbial communities. (4) Functional analysis focusing on the "nitrogen metabolism" pathway indicated that under light grazing conditions, the relative abundance of multiple functional genes, particularly those involved in denitrification, decreased.},
}
@article {pmid40123920,
year = {2025},
author = {Jimenez, K and Kong, Y and Zhang, Y and Ferketic, D and Nagori, SK and Yang, J and Yulo, AA and Kramer, B and Prado, OG and Cason, T and Chowdhry, R and Kemsley, A and Espinosa, LM and Steele, JA and Griffith, J and Jay, JA},
title = {Evaluation of a modified IDEXX method for antimicrobial resistance monitoring of extended Beta-lactamases-producing Escherichia coli in impacted waters near the U.S.-Mexico border.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {100997},
pmid = {40123920},
issn = {2352-7714},
abstract = {As part of a One Health approach, the World Health Organization (WHO) has deemed extended beta-lactamases-producing Escherichia coli (ESBL-Ec) as an appropriate proxy for antimicrobial resistance (AMR) in human, animal, and environmental samples. Traditional methods for ESBL-Ec quantification involve a labor-intensive process of membrane filtration, culturing in the presence and absence of antibiotics, and colony confirmation. The emerging modified IDEXX method utilizes IDEXX Colilert-18 test kits, recognized by the USEPA for the enumeration of total coliforms and E. coli in water samples, modified with cefotaxime for measurement of ESBL-Ec in environmental samples. However, this method has yet to be validated for ocean or sewage-contaminated water and has not been compared against the plate-based method with mTEC for surface water. In this study, ESBL-Ec in ocean and river waters of the Tijuana River Estuary were analyzed by three methods: membrane filtration using mTEC plates (as outlined in USEPA Method 1603), membrane filtration using TBX plates (as outlined in the WHO Tricycle Protocol), and Colilert-18 spiked with cefotaxime (Hornsby et al., 2023). Levels of ESBL-Ec were elevated in the Tijuana River Estuary and nearby ocean samples, as high as 2.2 × 10[6] CFU/100 mL. The modified IDEXX method correlated with membrane filtration methods using selective mTEC (r = 0.967, p < 0.001, n = 14) and TBX (r = 0.95, p < 0.001, n = 14) agars. These results indicate that the modified IDEXX method can be used as a more accessible alternative to the traditional culturing methods as a screening tool for antibiotic resistance in urban aquatic environments. Advantages of the IDEXX-based method including portability, lower Biosafety Level requirements, fewer dilutions to stay within the dynamic range, greater ease of maintaining sterility during analysis, and less required staff training are discussed. Future studies into the validity of the modified IDEXX method compared to qPCR and metagenomic sequencing are needed.},
}
@article {pmid40123796,
year = {2025},
author = {Kim, SH and Kwak, MJ and Hwang, JK and Keum, J and Jin, HY and Lee, CY and Tanpure, RS and Kim, YJ and Hoh, JK and Park, JY and Chung, W and Jeon, BH and Park, HK},
title = {Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {937-945},
pmid = {40123796},
issn = {2001-0370},
abstract = {BACKGROUND: High-risk infants are usually treated with empirical antibiotics after birth, regardless of the evidence of infection; however, their gut microbiome and metabolome have seldom been studied. This study investigated the influence of antibiotic exposure on the gut microbiome and associated metabolic pathways in term and preterm infants.<br><br>METHODS: Thirty-six infants within 10 days of birth who were admitted to a neonatal intensive care unit/newborn nursery unit were divided into four groups based on maturity (gestational age) and use of empirical antibiotics. Genomic DNA was extracted from the fecal samples and underwent high-throughput 16S rRNA amplicon sequencing using the Illumina platforms. Taxonomic classification, diversity analysis, and metagenomic function prediction were performed.<br><br>RESULTS: Preterm infants with empirical antibiotics showed a significantly decreased population of Firmicutes (p&#x202f;=&#x202f;0.003) and an increased population of Proteobacteria (p&#x202f;<&#x202f;0.001) compared to other groups. At the genus level, the populations of Raoultella (p&#x202f;=&#x202f;0.065) and Escherichia (p&#x202f;=&#x202f;0.052) showed an increased trend. The change in microbial composition was correlated with increased heme biosynthesis and decreased hemoglobin levels.<br><br>CONCLUSION: Collectively, our finding suggested that empirical antibiotic exposure in preterm infants alters the gut microbiome, potentially leading to adverse health outcomes. This dysbiosis may affect heme metabolism, increasing the risk of anemia in these vulnerable infants. Therefore, antibiotic use should be carefully tailored to minimize potential harm.},
}
@article {pmid40123706,
year = {2025},
author = {Min, S and Lu, Q and Zhang, Y},
title = {A Case of Severe Community-Acquired Pneumonia Caused by Coinfection of Five Pathogens.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1515-1519},
pmid = {40123706},
issn = {1178-6973},
abstract = {INTRODUCTION: Severe pneumonia is a serious pulmonary infection, and its high morbidity and mortality are associated with underlying diseases, treatment-induced immunodeficiency, co-infection of multiple pathogens, and increase of multi-resistant pathogens; For severe community-acquired pneumonia (SCAP) in immunocompromised patients, most of which are infected with rare atypical pathogens, mNGS as an unbiased and hypothesis-free approach to rapidly detect potential infectious agents in pulmonary mixed infections. The cases of simultaneous co-infection of five non-respiratory core pathogens represented by Nocardia farcinica have not been reported.<br><br>CASE PRESENTATION: This article will elaborate on a case of immunocompromised patient with nephrotic syndrome after corticosteroid treatment, who was diagnosed as SCAP after hospital admission and relevant laboratory examination. Bronchoalveolar lavage fluid (BALF) metagenome next-generation sequencing (mNGS) method identified as Nocardia farcinica, Aspergillus fumigatus, Pneumocystis jirovecii, cytomegalovirus and human coronavirus OC43 five pathogens co-infection, the patient improved and he was discharged after receiving the combination treatment of imipenem, ganciclovir, compound sulfamethoxazole, and fluconazole.<br><br>CONCLUSION: For SCAP patients with immunocompromised, there may be possible co-infection of multiple rare pathogens, low positive rate of conventional laboratory tests, mNGS can quickly and accurately identify pathogens, which can be used for targeted drug treatment, promote the early recovery of patients and reduce the abuse of broad-spectrum antibiotics.},
}
@article {pmid40122890,
year = {2025},
author = {Nori, SRC and Walsh, CJ and McAuliffe, FM and Moore, RL and Van Sinderen, D and Feehily, C and Cotter, PD},
title = {Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {49},
pmid = {40122890},
issn = {2055-5008},
support = {H2020-MSCA-COFUND-2019-945385//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; },
mesh = {Female ; *Vagina/microbiology ; Humans ; *Lactobacillus/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; *Lactobacillus crispatus/genetics/isolation &amp; purification ; Pregnancy ; Microbiota ; Ireland ; Host Microbial Interactions ; Metagenome ; Genome, Bacterial ; Gardnerella vaginalis/genetics/isolation &amp; purification/classification ; },
abstract = {The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.},
}
@article {pmid40122843,
year = {2025},
author = {Ashraf, S and Jerome, H and Bugembe, DL and Ssemwanga, D and Byaruhanga, T and Kayiwa, JT and Downing, R and Salazar-Gonzalez, JF and Salazar, MG and Shepherd, JG and Wilkie, C and Davis, C and Logan, N and Vattipally, SB and Wilkie, GS and da Silva Filipe, A and Ssekagiri, A and Namuwulya, P and Bukenya, H and Kigozi, BK and McConnell, WW and Willett, BJ and Balinandi, S and Lutwama, J and Kaleebu, P and Bwogi, J and Thomson, EC},
title = {Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2844},
pmid = {40122843},
issn = {2041-1723},
support = {MC_UU_00034/6//RCUK | Medical Research Council (MRC)/ ; MC_PC_ MR/Y002814/1//RCUK | Medical Research Council (MRC)/ ; 102789/Z/13/A//Wellcome Trust (Wellcome)/ ; },
mesh = {Humans ; Uganda/epidemiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Adolescent ; Middle Aged ; Child ; Young Adult ; Child, Preschool ; Fever/virology/diagnosis ; Prospective Studies ; Viruses/genetics/isolation &amp; purification/classification ; Virus Diseases/epidemiology/virology/diagnosis ; Disease Outbreaks ; Aged ; Acute Disease ; Yellow Fever/epidemiology/virology/diagnosis ; Dengue/epidemiology/virology/diagnosis ; Infant ; Rift Valley Fever/epidemiology/diagnosis/virology ; Hemorrhagic Fever, Crimean/epidemiology/diagnosis/virology ; },
abstract = {Viruses associated with acute febrile illness in Africa cause a spectrum of clinical disease from mild to life-threatening. Routine diagnostic methods are insufficient to identify all viral pathogens in this region. In this study, 1281 febrile Ugandan patients were prospectively recruited as part of the CDC-UVRI Acute Febrile Illness Study and pre-screened for common pathogens. 210/1281 undiagnosed samples, and 20 additional samples from viral outbreaks were subjected to metagenomic sequencing. Viral pathogens were identified in 44/230 (19%), including respiratory, hepatitis, blood-borne, gastrointestinal and vector-borne viruses. Importantly, one case of Crimean-Congo haemorrhagic fever and two cases each of Rift Valley fever, dengue and yellow fever were detected in 7/230 (3%) of cases. Le Dantec virus, last reported in 1969, was also identified in one patient. The presence of high-consequence and (re-)emerging viruses of public health concern highlights the need for enhanced population-based diagnostic surveillance in the African region.},
}
@article {pmid40122128,
year = {2025},
author = {Zhang, D and Wang, Q and Li, D and Chen, S and Chen, J and Zhu, X and Bai, F},
title = {Gut microbiome composition and metabolic activity in metabolic associated fatty liver disease.},
journal = {Virulence},
volume = {},
number = {},
pages = {2482158},
doi = {10.1080/21505594.2025.2482158},
pmid = {40122128},
issn = {2150-5608},
abstract = {OBJECTIVE: Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. The objective of our study was to elucidate the characteristics of the gut microbiome and alterations in plasma metabolites among MAFLD patients.<br><br>METHODS: Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS.<br><br>RESULTS: LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to be increased by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis&#xff08;HS&#xff09;respectively. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC&#x2009;=&#x2009;0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC&#x2009;=&#x2009;0.94) in the prediction of the MAFLD HS progress. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with &#x3b2;-Alanine, Uric acid and L-Valine. Pseudoruminococcus massiliensis have a strong positive correlation with &#x3b2;-Alanine.<br><br>CONCLUSION: Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predicts HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis, and ultimately cause MAFLD. The observed association between Ruminococcaceae bacteria and &#x3b2;-Alanine or Uric acid in these patients could offer fresh insights into the disease mechanism.},
}
@article {pmid40122011,
year = {2025},
author = {Yin, M and Li, P and Chen, C and Jia, R and Xia, B and Liu, Y and Liu, A and Liu, L and Li, ZH},
title = {Bioremediation potential of sulfadiazine-degrading bacteria: Impacts on ryegrass growth and soil functionality.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {138012},
doi = {10.1016/j.jhazmat.2025.138012},
pmid = {40122011},
issn = {1873-3336},
abstract = {The extensive use of antibiotics, particularly sulfadiazine (SDZ), has led to significant environmental contamination and the proliferation of antibiotic resistance genes (ARGs). This study investigates the bioremediation potential of two SDZ-degrading bacterial strains, Acinetobacter sp. M9 and Enterobacter sp. H1, and their impact on ryegrass (Lolium perenne) growth and the inter-root microenvironment in SDZ-contaminated soils. A pot experiment combined with amplicon and metagenomic sequencing revealed that inoculation with M9 and H1 significantly enhanced ryegrass growth by alleviating oxidative stress, increasing chlorophyll content, and improving soil nutrient availability. The strains also promoted SDZ degradation efficiency and improved carbon and nitrogen cycling through the upregulation of key functional genes. Furthermore, microbial community analysis demonstrated increased alpha diversity, shifts in dominant taxa, and functional enrichment in pollutant degradation pathways. The dynamics of ARGs revealed a decrease in aminoglycoside, rifamycin, and streptomycin resistance genes, while sulfonamide resistance genes increased due to the residual SDZ stress. These findings highlight the potential of M9 and H1 as sustainable bioremediation agents to mitigate antibiotic contamination, improve soil health, and support plant growth in polluted environments.},
}
@article {pmid40121909,
year = {2025},
author = {Thomson, R and Le, C and Wang, L and Batstone, DJ and Zhou, Y and Oehmen, A},
title = {Higher order volatile fatty acid metabolism and atypical polyhydroxyalkanoate production in fermentation-enhanced biological phosphorus removal.},
journal = {Water research},
volume = {280},
number = {},
pages = {123503},
doi = {10.1016/j.watres.2025.123503},
pmid = {40121909},
issn = {1879-2448},
abstract = {Enhanced biological phosphorus removal (EBPR) is an established wastewater treatment process, but its wider implementation has been limited by factors like high temperature and low carbon availability. Fermentation-enhanced EBPR (F-EBPR) processes have shown promise in addressing these limitations, but the underlying mechanisms are not fully understood. This study investigates the metabolism of higher order (C4-5) volatile fatty acids (VFAs) in F-EBPR systems using a combination of carbon isotope labelling and shotgun metagenomic sequencing analyses. Results show that butyrate (HBu) uptake leads to the formation of both typical (C4-5) and atypical (C6+) polyhydroxyalkanoates (PHAs) through a combination ofβ-oxidation and standard condensation pathways, while the putative role of HBu oxidisers were identified relative to substrate composition in F-EBPR processes. Metagenomic analysis reveals the presence of genes required for higher order VFA metabolism in both polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). This study also highlights the limitations of current models in describing F-EBPR processes and emphasises the need for improved models that account for higher order VFA metabolism and microbial community dynamics.},
}
@article {pmid40121477,
year = {2025},
author = {Zhang, Q and Feng, Y and Xia, Y and Shao, Q and Zhao, M and Xu, P and Tang, T and Liu, J and Jin, B and Liu, S and Jiang, C},
title = {Clinical efficacy of metagenomic next-generation sequencing for the detection of pathogens in peritoneal dialysis-related peritonitis: a prospective cohort study.},
journal = {European journal of medical research},
volume = {30},
number = {1},
pages = {198},
pmid = {40121477},
issn = {2047-783X},
support = {2021- LCYJ- PY- 12//Fundings for Clinical Trials from the Affiliated Drum Tower Hospital, Medical School of Nanjing University/ ; YKK21090//Nanjing Healthcare Science and Technology Development Special Fund Project/ ; },
mesh = {Humans ; *Peritonitis/microbiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been reported to improve pathogen identification in infectious diseases. This prospective cohort study aimed to explore the etiological diagnostic value of mNGS in peritoneal dialysis (PD)-related peritonitis.<br><br>METHODS: Patients with PD-related peritonitis were consecutively recruited at the Nephrology Department of Nanjing Drum Tower Hospital. PD effluent samples for mNGS and culture were collected simultaneously. The positive rate, detection time, and consistency of mNGS and culture were compared.<br><br>RESULTS: From August 1, 2021 to August 31, 2022, 38 patients with 41 episodes of PD-related peritonitis were enrolled. The positive rate of mNGS was higher than that of culture, although not statistically significant (92.7% vs 78.0%, P&#x2009;=&#x2009;0.109). The average reporting time of mNGS was significantly shorter than that of culture (30.4&#x2009;&#xb1;&#x2009;10.5 vs 86.9&#x2009;&#xb1;&#x2009;22.2&#xa0;h, P&#x2009;<&#x2009;0.001). mNGS identified more co-pathogens and unusual pathogens than culture, with multiple pathogens being detected in nearly half of the samples. Among the 30 samples that tested positive by both methods, 27 (90%) showed completely (13 cases) or partly (14 cases) matched results between mNGS and culture. Fourteen patients (with 14 episodes of peritonitis) had used antibiotics within 2&#xa0;weeks before specimen collection. Antibiotic usage led to a significant decrease in the culture-positive rate (57.1% vs 88.9%, P&#x2009;=&#x2009;0.042), while the mNGS-positive rate remained unaffected (92.9% vs 92.6%, P&#x2009;=&#x2009;1.000).<br><br>CONCLUSIONS: This study revealed that mNGS exhibited higher sensitivity and shorter reporting time compared to culture in detecting pathogens in PD-related peritonitis. For samples that yielded positive results by both methods, the consistency between mNGS and culture was substantial. mNGS may offer a novel approach for the etiological diagnosis of PD-associated peritonitis, particularly in cases involving prior antibiotic use and unusual pathogens.},
}
@article {pmid40121075,
year = {2025},
author = {Omura, SN and Nureki, O},
title = {General and robust sample preparation strategies for cryo-EM studies of CRISPR-Cas9 and Cas12 enzymes.},
journal = {Methods in enzymology},
volume = {712},
number = {},
pages = {23-39},
doi = {10.1016/bs.mie.2025.01.052},
pmid = {40121075},
issn = {1557-7988},
mesh = {*Cryoelectron Microscopy/methods ; *CRISPR-Cas Systems ; *CRISPR-Associated Proteins/genetics/chemistry/metabolism ; Gene Editing/methods ; CRISPR-Associated Protein 9/genetics/chemistry/metabolism ; Bacterial Proteins/genetics/chemistry/metabolism ; Endodeoxyribonucleases ; },
abstract = {Cas9 and Cas12 are RNA-guided DNA endonucleases derived from prokaryotic CRISPR-Cas adaptive immune systems that have been repurposed as versatile genome-engineering tools. Computational mining of genomes and metagenomes has expanded the diversity of Cas9 and Cas12 enzymes that can be used to develop versatile, orthogonal molecular toolboxes. Structural information is pivotal to uncovering the precise molecular mechanisms of newly discovered Cas enzymes and providing a foundation for their application in genome editing. In this chapter, we describe detailed protocols for the preparation of Cas9 and Cas12 enzymes for cryo-electron microscopy. These methods will enable fast and robust structural determination of newly discovered Cas9 and Cas12 enzymes, which will enhance the understanding of diverse CRISPR-Cas effectors and provide a molecular framework for expanding CRISPR-based genome-editing technologies.},
}
@article {pmid40121033,
year = {2025},
author = {Wong, MK and Boukhaled, GM and Armstrong, E and Liu, R and Heirali, AA and Yee, NR and Tsang, J and Spiliopoulou, P and Schneeberger, PHH and Wang, BX and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {3},
pages = {},
doi = {10.1136/jitc-2024-010681},
pmid = {40121033},
issn = {2051-1426},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/drug therapy/therapy ; *Immunoglobulin G/blood/immunology ; Male ; Female ; Middle Aged ; Aged ; },
abstract = {BACKGROUND: Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.<br><br>METHODS: Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.<br><br>RESULTS: Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3[+] CD4[+] T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14[+] and CD16[+] monocyte populations were decreased in these individuals.<br><br>CONCLUSION: These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.},
}
@article {pmid40120232,
year = {2025},
author = {Ebmeyer, S and Kristiansson, E and Larsson, DGJ},
title = {Unraveling the origins of mobile antibiotic resistance genes using random forest classification of large-scale genomic data.},
journal = {Environment international},
volume = {198},
number = {},
pages = {109374},
doi = {10.1016/j.envint.2025.109374},
pmid = {40120232},
issn = {1873-6750},
abstract = {Understanding in which environments and under what conditions chromosomal antibiotic resistance genes (ARGs) acquire increased mobility is crucial to effectively mitigate their emergence in and dissemination among pathogens. In order to identify the conditions and environments facilitating these processes, it is valuable to know from which bacterial species mobile ARGs were mobilized initially, before their dissemination to other species. In this study, we used data generated from > 1.5 million publicly available bacterial genome assemblies to train a random forest classifier to identify the origins of mobile genes. Analysis of the models' predictions revealed the previously unknown origins of 12 mobile ARG groups, which confer resistance to 4 different classes of antibiotics. This included ARGs conferring resistance to tetracyclines, an antibiotic class for which, to the best of our knowledge, no recent origins of ARGs have previously been convincingly demonstrated. All identified origin species in this study are known opportunistic pathogens, and some are the origin of multiple mobile ARGs. An analysis of public metagenomes from different sources indicates that most of the origin species are particularly abundant in municipal wastewaters, a few were highly abundant in animal feces and three were most common in environments polluted with waste from antibiotic manufacturing. This study highlights environments where these origin species thrive and where there is a need for limiting antibiotic selection pressures.},
}
@article {pmid40120189,
year = {2025},
author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y},
title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.},
journal = {Water research},
volume = {279},
number = {},
pages = {123497},
doi = {10.1016/j.watres.2025.123497},
pmid = {40120189},
issn = {1879-2448},
abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.},
}
@article {pmid40119849,
year = {2025},
author = {Riva, A and Sahin, E and Volpedo, G and Catania, NT and Venara, I and Biagioli, V and Balagura, G and Amadori, E and De Caro, C and Cerulli Irelli, E and Di Bonaventura, C and Zara, F and Sezerman, OU and Russo, E and Striano, P},
title = {Medication-resistant epilepsy is associated with a unique gut microbiota signature.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18367},
pmid = {40119849},
issn = {1528-1167},
support = {MDBR-23-004-STXBP1//Fingerprinting a multiomics biomarker profile in patients with STXBP1-RD/ ; PNRR-MUR-M4C2 PE0000006//MNESYS/ ; },
abstract = {OBJECTIVE: Dysfunction of the microbiota-gut-brain axis is emerging as a new pathogenic mechanism in epilepsy, potentially impacting on medication response and disease outcome. We investigated the composition of the gut microbiota in a cohort of medication-resistant (MR) and medication-sensitive (MS) pediatric patients with epilepsy.<br><br>METHODS: Children with epilepsy of genetic and presumed genetic etiologies were evaluated clinically and subgrouped into MR and MS. Age-matched healthy controls (HCs) were also recruited. A food diary was used to evaluate nutritional habits, and the Rome IV questionnaire was used to record gastrointestinal symptoms. The microbiota composition was assessed in stool samples through 16S rRNA. &#x3b1;-Diversity (AD) and &#x3b2;-diversity (BD) were calculated, and differential abundance analysis was performed using linear multivariable models (significance: p.adj&#x2009;<&#x2009;.05).<br><br>RESULTS: Forty-one patients (MR:MS&#x2009;=&#x2009;20:21) with a mean age of 7.2&#x2009;years (&#xb1;4.6 SD) and 27 age-matched HCs were recruited. No significant differences in AD were found when comparing patients and HCs. Significant positive correlation was found between AD and age (Chao1 p.adj&#x2009;=&#x2009;.0004, Shannon p.adj&#x2009;=&#x2009;.0004, Simpson p.adj&#x2009;=&#x2009;.0028). BD depicted a different bacterial profile in the epilepsy groups compared to HCs (MS vs. HC: Bray-Curtis F&#x2009;=&#x2009;1.783, p&#x2009;=&#x2009;.001; Jaccard F&#x2009;=&#x2009;1.24, p&#x2009;=&#x2009;.001; MR vs. HC: Bray-Curtis F&#x2009;=&#x2009;2.24, p&#x2009;=&#x2009;.001; Jaccard F&#x2009;=&#x2009;1.364, p&#x2009;=&#x2009;.001). At the genus level, the epilepsy groups were characterized by a significant increase in Hungatella (MS vs. HC: +4.95 log2 change; MR vs. HC: +6.72 log2 change); the [Eubacterium] siraeum group changed between the MR and MS subgroups.<br><br>SIGNIFICANCE: Epileptic patients display unique gut metagenomic signatures compared to HCs. Moreover, a different ratio of the butyrate-producing [Eubacterium] siraeum group suggests dissimilarities between patients based on the response to antiseizure medications.},
}
@article {pmid40119394,
year = {2025},
author = {Guo, R and Chang, Y and Wang, D and Sun, H and Gu, T and Zong, Y and Zhou, S and Huang, Z and Chen, L and Tian, Y and Xu, W and Lu, L and Zeng, T},
title = {Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {30},
pmid = {40119394},
issn = {2524-4671},
support = {CARS-42//China Agriculture Research System of MOF and MARA/ ; 2021C02068//Zhejiang Province Agricultural New Breeding Major Science and Technology Special Project/ ; LZ23C170001//Zhejiang Provincial Natural Science Foundation of China/ ; 32472892//National Natural Science Foundation of China/ ; 2022YFD1300100//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The gut microbiota exerts a critical influence on energy metabolism homeostasis and productive performance in avian species. Given the diminishing availability of arable land and intensifying competition for finite resources between livestock production and human populations, the agricultural sector faces dual imperatives to enhance productive efficiency while mitigating ecological footprints. Within this paradigm, optimizing nutrient assimilation efficiency in commercial waterfowl operations emerges as a strategic priority. This investigation employs an integrated multi-omics approach framework (metagenomic, metabolomic, and transcriptomic analyses) to elucidate the mechanistic relationships between cecal microbial consortia and feed conversion ratios in Shan Partridge ducks.<br><br>RESULTS: Based on the analysis of metagenome data, a total of 34 phyla, 1033 genera and 3262 species of bacteria were identified by metagenomic sequencing analysis. At the phylum level, 31 phylums had higher mean abundance in the low residual feed intake (LRFI) group than in the high residual feed intake (HRFI) group. Among them, the expression of microbiome Elusimicrobiota was significantly higher in the LRFI group than in the HRFI group (P&#x2009;<&#x2009;0.05). And we also found a significant differences in secondary metabolites biosynthesis, transport, and catabolism pathways between the two groups in microbial function (P&#x2009;<&#x2009;0.05). Based on metabolomic analysis, 17 different metabolites were found. Among them, Lipids and lipid molecules accounted for the highest proportion. Whereas the liver is very closely related to lipid metabolism, we are close to understanding whether an individual's energy utilization efficiency is related to gene expression in the liver. We selected six ducks from each group of six ducks each for liver transcriptome analysis. A total of 322 differential genes were identified in the transcriptome analysis results, and 319 genes were significantly down-regulated. Among them, we found that prostaglandin endoperoxide synthase 2 (PTGS2) might be a key hub gene regulating RFI by co-occurrence network analysis. Interestingly, the differential gene PTGS2 was enriched in the arachidonic acid pathway at the same time as the differential metabolite 15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2). In addition, the results of the association analysis of differential metabolites with microorganisms also revealed a significant negative correlation between 15d-PGJ2 and Elusimicrobiota.<br><br>CONCLUSION: Based on comprehensive analysis of the research results, we speculate that the Elusimicrobiota may affect the feed utilization efficiency in ducks by regulating the expression of the PTGS2 gene.},
}
@article {pmid40119266,
year = {2025},
author = {Zhou, Y and Ren, D and Li, Y and Gui, S},
title = {A case of septic shock caused by drug-resistant Edwardsiella tarda and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {393},
pmid = {40119266},
issn = {1471-2334},
support = {SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; },
mesh = {Humans ; *Shock, Septic/microbiology/drug therapy ; *Edwardsiella tarda/drug effects/isolation &amp; purification/genetics ; Female ; Adult ; *Enterobacteriaceae Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Piperacillin, Tazobactam Drug Combination/therapeutic use ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: Edwardsiella tarda (E. tarda) causes highly mortality, which is rare in septic patients. We herein reported a case of septic shock caused by drug-resistant E. tarda.<br><br>CASE PRESENTATION: We herein describe a 32-year-old female with septic shock who had the medical history of abortion 1 month ago and "systemic lupus erythematosus and rheumatoid arthritis" presented abdominal pain, diarrhea, and dyspnea as the primary symptoms and rapidly deteriorated to MODS following breakfast (undercooked fish porridge) in the ICU. Sepsis surviving bundle was initiated by collecting pathogen culture (sputum, urine and blood samples), empirically broad-spectrum antibiotics administration (Meropenem), along with fluid resuscitation, vasopressor use. E. tarda was confirmed both in blood culture and mNGS (metagenomics next generation sequencing). Thus, the antibiotics were switched to piperacillin-tazobactam according to the susceptibility test that was susceptible to piperacillin-tazobactam and resistant to ampicillin, quinolones and gentamicin. The patient finally recovered and discharged after 18 days of ICU treatment.<br><br>CONCLUSIONS: Empiric antibiotics should be selected with piperacillin-tazobactam and amikacin, and avoid ampicillin, quinolones and gentamicin for suspecting E. tarda infection in southern China. Bacteremia complicated with septic shock caused by E. tarda requires intensive care to improve survival rates.},
}
@article {pmid40119088,
year = {2025},
author = {Santos, CA and Morais, MAB and Mandelli, F and Lima, EA and Miyamoto, RY and Higasi, PMR and Araujo, EA and Paixão, DAA and Junior, JM and Motta, ML and Streit, RSA and Morão, LG and Silva, CBC and Wolf, LD and Terrasan, CRF and Bulka, NR and Diogo, JA and Fuzita, FJ and Colombari, FM and Santos, CR and Rodrigues, PT and Silva, DB and Grisel, S and Bernardes, JS and Terrapon, N and Lombard, V and Filho, AJC and Henrissat, B and Bissaro, B and Berrin, JG and Persinoti, GF and Murakami, MT},
title = {Publisher Correction: A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-025-08872-9},
pmid = {40119088},
issn = {1476-4687},
}
@article {pmid40118380,
year = {2025},
author = {Guo, D and Fan, J and Zhang, X and Chen, S and Du, X},
title = {Next-generation Sequencing assistance in the diagnosis of Active Tuberculosis following Allogeneic Hematopoietic Stem Cell Transplantation: A Case Series.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102683},
doi = {10.1016/j.jiac.2025.102683},
pmid = {40118380},
issn = {1437-7780},
abstract = {Tuberculosis poses a rare but life-threatening complication for patients undergoing hematopoietic stem cell transplantation. In a case series spanning January 2020 to January 2024, we evaluated the application of metagenomic Next-Generation Sequencing in the early diagnosis of tuberculosis in patients following allogeneic hematopoietic stem cell transplantation. We identified 9 cases of post-transplant tuberculosis, predominantly pulmonary, with 1 case of disseminated disease. In early fluid samples from patients with post-transplant active tuberculosis, metagenomic next-generation sequencing detected Mycobacterium tuberculosis complex earlier than conventional tests, enabling rapid diagnosis. In this study, metagenomic next-generation sequencing showed a sensitivity of 66.6% and specificity of 100%, higher than TB-DNA and Xpert (55.6%). Concurrently, among mNGS-positive samples, 4 (44.4%) were from peripheral blood and 3 (33.3%) from bronchoalveolar lavage fluid. The combination of metagenomic Next-Generation sequencing and Xpert may enhance the capacity for detecting Mycobacterium tuberculosis complex in extrapulmonary specimens from post-transplant patients. The time from symptom onset to Next-Generation Sequencing positivity was 2 to 76 days, and from transplantation to TB diagnosis was 30 to 485 days. Despite some fatalities, the majority of patients completed extended anti-tuberculosis treatment and are under regular follow-up, highlighting the value of Next-Generation Sequencing in diagnosing tuberculosis in this high-risk population.},
}
@article {pmid40118224,
year = {2025},
author = {Bai, M and Wang, B and Zhao, W and Qiu, H and Su, S and Wang, Y and Qin, Y and Wang, C and Zhao, Z and Gao, Z and Yang, C},
title = {Novel anammox-enhanced A-B wastewater treatment process based on carbon capture concept.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132431},
doi = {10.1016/j.biortech.2025.132431},
pmid = {40118224},
issn = {1873-2976},
abstract = {The high energy consumption and high carbon footprint of sewage treatment are technical shortcomings of the conventional activated sludge process. To address the emergency issue, this research demonstrated the viability of a pre-anammox enhanced A-B process to treat municipal wastewater while achieving an energy-efficient operation. In the proposed A-B process, an anaerobic moving bed biofilm reactor (A-MBBR) functions as the A-stage for COD capture, while a nitrification MBBR functions as the B-stage. The results show that during the 210-days of operation, 83.3 % of the influent COD was converted in the A-stage, and 93.1 % NH4[+]-N removal was achieved, resulting in an effluent NH4[+]-N concentration of 0.9 mg/L. The metagenomic sequencing results show that, in the B-stage MBBR, Nitrosomonas was the main ammonia-oxidizing bacterium (4.9 % relative abundance) and Nitrospira was the main nitrite-oxidizing bacterium (18.0 % relative abundance). In the A-stage MBBR, Thauera was the dominant denitrification bacterium (9.2 % relative abundance) and Candidatus Brocadia was the dominant anammox bacterium. Finally, hdh and hzs were key anammox genes detected in this system. This study clearly demonstrates a novel pre-anammox enhanced A-B process with an energy-efficient operation.},
}
@article {pmid40118220,
year = {2025},
author = {Rozera, T and Pasolli, E and Segata, N and Ianiro, G},
title = {Machine learning and artificial intelligence in the multi-omics approach to gut microbiota.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.02.035},
pmid = {40118220},
issn = {1528-0012},
abstract = {The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depicting the complexity of the gut microbial ecosystem. However, these tools generate a large data stream, which integration is needed to produce clinically useful readouts but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools show potential for clinical implementation, including the discovery of microbial biomarkers for disease classification or prediction, the prediction of response to specific treatments, the fine-tuning of microbiome-modulating therapies. Here we discuss the state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome.},
}
@article {pmid40118219,
year = {2025},
author = {Yan, R and Zhang, L and Chen, Y and Zheng, Y and Xu, P and Xu, Z},
title = {Therapeutic potential of gut microbiota modulation in epilepsy: A focus on short-chain fatty acids.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {106880},
doi = {10.1016/j.nbd.2025.106880},
pmid = {40118219},
issn = {1095-953X},
abstract = {According to the criteria established by the International League Against Epilepsy (ILAE), epilepsy is defined as a disorder characterized by at least two unprovoked seizures occurring more than 24 h apart. Its pathogenesis is closely related to various physiological and pathological factors. Advances in high-throughput metagenomic sequencing have increasingly highlighted the role of gut microbiota dysbiosis in epilepsy. Short-chain fatty acids (SCFAs), the major metabolites of the gut microbiota and key regulators of the gut-brain axis, support physiological homeostasis through multiple mechanisms. Recent studies have indicated that SCFAs not only regulate seizures by maintaining intestinal barrier integrity and modulating intestinal immune responses, but also affect the structure and function of the blood-brain barrier (BBB) and regulate neuroinflammation. This review, based on current literatures, explores the relationship between SCFAs and epilepsy, emphasizing how SCFAs affect epilepsy by modulating the intestinal barrier and BBB. In-depth studies on SCFAs may reveal their therapeutic potential and inform the development of gut microbiota-targeted epilepsy treatments.},
}
@article {pmid40117915,
year = {2025},
author = {Ghemrawi, M and Ramírez Torres, A and Netherland, M and Wang, Y and Hasan, NA and El-Fahmawi, B and Duncan, G and McCord, B},
title = {Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse.},
journal = {Forensic science international. Genetics},
volume = {78},
number = {},
pages = {103266},
doi = {10.1016/j.fsigen.2025.103266},
pmid = {40117915},
issn = {1878-0326},
abstract = {The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.},
}
@article {pmid40117911,
year = {2025},
author = {Wang, J and Feng, Y and Cheng, H and Qian, K and Wan, B and Liu, S and Liu, Y and Hu, J},
title = {Management strategies and outcomes for fracture-related infection of patellar fractures.},
journal = {Injury},
volume = {56},
number = {4},
pages = {112272},
doi = {10.1016/j.injury.2025.112272},
pmid = {40117911},
issn = {1879-0267},
abstract = {INTRODUCTION: Fracture-related infection (FRI) poses a substantial challenge in orthopaedic trauma surgery, potentially leading to permanent functional impairment or necessitating amputation in patients who are expected to recover fully. Data on the incidence, pathogen detection rates, outcomes, and optimal management strategies for patellar FRI are limited. Therefore, this study aimed to identify the most common pathogens associated with patellar fixation-related infections, evaluate the functional outcome associated with FRI of the patella, and develop a management algorithm for addressing these severe complications.<br><br>METHODS: This retrospective review analyzed a prospectively maintained database to identify all patients with FRI of the patella treated at our institution between January 2015 and August 2023. Data on demographics, fracture characteristics, surgical details, and outcomes were collected. Descriptive statistical analyses were performed using SPSS software.<br><br>RESULTS: Over the 9-year period, 32 cases of patellar fractures complicated by infection following surgical treatment were identified, with complete follow-up data available (mean age, 56.5 &#xb1; 15.8 years). Infection occurred in 13 patients within 2 weeks of fixation and in 19 patients between 2 and 10 weeks postoperatively. Following debridement, nine patients retained their original fixation, eight underwent hardware removal, and 15 underwent hardware replacement. Seven patients developed septic arthritis and were managed with arthroscopic knee lavage. Metagenomic next-generation sequencing demonstrated a sensitivity of 93.8 % (30/32), which was significantly higher than that of traditional microbiological culture (53.1 %; P < 0.01). All surgical incisions achieved primary healing within 2 weeks post-closure with no recurrence of infection, skin necrosis, osteomyelitis, or nonunion. At the final follow-up, all fractures had united, with the B&#xf6;stman patellar fracture functional scores ranging from 24 to 29, resulting in a 100 % excellent/good rate.<br><br>CONCLUSIONS: Comprehensive and multidisciplinary management approaches can achieve successful bone union and favourable long-term outcomes in patients with patellar FRI. However, further validation through large-scale studies is necessary to confirm these findings.},
}
@article {pmid40117769,
year = {2025},
author = {Jiang, Z and Fang, W and Jiang, Y and Hu, Y and Dong, Y and Li, P and Shi, L},
title = {Arsenic mobilization by Bathyarchaeia in subsurface sediments at the Jianghan Plain, China.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {138002},
doi = {10.1016/j.jhazmat.2025.138002},
pmid = {40117769},
issn = {1873-3336},
abstract = {As one of the most abundant microorganisms on Earth, Bathyarchaeia with diverse abilities to degrade complex organic carbon play a vital role in the global carbon cycle. However, the role of Bathyarchaeia in arsenic (As) metabolism and their contribution to As mobilization in aquifers remain unclear. In this study, we recovered 15 Bathyarchaeota metagenome-assembled genomes (MAGs) from metagenomes of borehole sediments in the Jianghan Plain (JHP), China. Together with 374 representative Bathyarchaeia MAGs from public databases, six As metabolism genes i.e. arrA, arsR, arsA, arsB, arsC (Trx) and arsM were identified, accounting for 4.4, 47.6, 20.3, 38.3, 37.5 and 49.4 % of total Bathyarchaeia MAGs, respectively. Heterologous expression of multiple arsC and arsM genes of Bathyarchaeia MAGs obtained from JHP sediments validated their abilities for As(V) reduction and As(III) methylation at environmentally relevant As concentration. These results indicate that in addition to providing bioavailable carbon sources for other microbial functional populations, Bathyarchaeia directly participate in As mobilization in the JHP aquifer via As(V) reduction and As(III) methylation. The diversified distribution of arsC and arsM in the class Bathyarchaeia suggests that Bathyarchaeia may contribute to As cycling in other As-rich environments, such as hot spring, saline lakes, marine hydrothermal sediments and soils.},
}
@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf015},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.<br><br>FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.<br><br>CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}
@article {pmid40116459,
year = {2025},
author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M},
title = {Dietary protein source alters gut microbiota composition and function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf048},
pmid = {40116459},
issn = {1751-7370},
support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; },
abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.},
}
@article {pmid40116405,
year = {2025},
author = {Shekhawat, N},
title = {Precision Medicine for Diagnosis of Microbial Keratitis.},
journal = {International ophthalmology clinics},
volume = {65},
number = {2},
pages = {20-25},
doi = {10.1097/IIO.0000000000000562},
pmid = {40116405},
issn = {1536-9617},
mesh = {Humans ; *Precision Medicine/methods ; *Eye Infections, Bacterial/diagnosis/microbiology ; *Keratitis/diagnosis/microbiology ; Eye Infections, Fungal/diagnosis/microbiology ; Cornea/microbiology ; Bacteria/genetics/isolation &amp; purification ; Proteomics/methods ; },
abstract = {Microbial keratitis (MK) is the leading cause of corneal blindness and can be caused by several species of bacteria, fungi, or parasites. Accurate and timely identification of the causative microbe is critical for initiating targeted antimicrobial and anti-inflammatory treatment and preventing vision loss. MK diagnosis currently relies on corneal culture or microscopy, which have suboptimal yield and can produce inconclusive results. MK requires immediate treatment with empiric antimicrobials, followed by targeted treatment after the microbe is identified. The clinical utility of anti-inflammatory therapy in MK remains controversial and likely differs due to host- and microbe-specific factors. Newer diagnostic techniques such as whole genome sequencing, metagenomic deep sequencing, transcriptomics, and proteomics have the potential to greatly improve timeliness, accuracy, and precision when diagnosing and treating MK. Metagenomic deep sequencing can identify pathogenic microbes with comparable or superior accuracy to traditional microbiology techniques, enabling faster and more accurate diagnosis and initiation of appropriate treatment. Whole genome sequencing of corneal culture isolates has the potential to provide patient-specific insights about microbial phylogenetics, antimicrobial resistance genes, and virulence factors to enable more targeted antimicrobial therapy. Characterization of the host immune response using RNA sequencing or tear proteomics could help inform the use of tailored anti-inflammatory therapies to prevent corneal damage. Although most of these precision medicine approaches are in the research phase, they show the potential to customize MK treatment based on host and microbial factors and improve clinical outcomes.},
}
@article {pmid40115744,
year = {2025},
author = {Kimmel, M and Tong, B and Devall, AE and Björvang, RD and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Skalkidou, A and Hugerth, LW},
title = {Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.},
journal = {Biological psychiatry global open science},
volume = {5},
number = {3},
pages = {100453},
pmid = {40115744},
issn = {2667-1743},
abstract = {BACKGROUND: In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relation to mental distress.<br><br>METHODS: During the second and third trimester, individuals from the United States and Sweden completed the Edinburgh Postnatal Depression Scale and provided fecal samples for whole-genome metagenomics. A total of 832 and 161 samples were sequenced and analyzed from the Swedish cohort and the U.S. cohort, respectively. Multiple characterizations of the microbial community were analyzed in relation to distress measured using the Edinburgh Postnatal Depression Scale. Principal coordinate analysis and distance-based redundancy analysis assessed variation in functional gut-brain modules. For the U.S. cohort, the Trier Social Stress Test was administered 8 weeks postpartum while collecting salivary cortisol.<br><br>RESULTS: Principal coordinate analysis identified 4 sample clusters based on the gut-brain modules distinguished by functions such as short-chain fatty acid synthesis and cortisol degradation. While with distance-based redundancy analysis, mental distress subtypes did not significantly contribute to variation in gut-brain modules (p&#xa0;= .085 for Sweden, p&#xa0;= .23 for the U.S.), a U.S. sample cluster distinguished by lower cortisol degradation from another cluster with higher gut microbial cortisol degradation abundance had significantly higher odds of being associated with depression (p&#xa0;= .024). The U.S. sample cluster with lower gut microbial cortisol degradation abundance also had significantly higher cortisol levels after a postpartum social stressor.<br><br>CONCLUSIONS: Further studies are warranted to investigate the potential for the gut microbiome to serve as biomarkers of gut-brain axis health during pregnancy across disparate populations.},
}
@article {pmid40115680,
year = {2025},
author = {Patankar, C and Kulsum, U and Mahajan, S and Kumar, S and Kale, D and Sharma, VK and Nema, S and Biswas, D},
title = {Mapping Viral Landscapes: Genomic Surveillance of Aedes Mosquitoes From Central India.},
journal = {Cureus},
volume = {17},
number = {2},
pages = {e79206},
pmid = {40115680},
issn = {2168-8184},
abstract = {BACKGROUND: Mosquito-borne viral diseases pose a significant impact on human health, with the potential to cause widespread outbreaks of diseases. Monitoring viral genomes in mosquito populations can lead to informed risk assessment and promote early diagnosis. However, a standardized methodology is lacking to decipher circulating viral sequences in mosquito populations collected from human habitats. Our study aims to establish and evaluate a system of viral metagenomic analysis in the Aedes mosquito population.<br><br>METHODS: Mosquitoes were collected using CDC-approved BG-Sentinel version 2 traps (Biogents AG, Regensburg, Germany) and battery-operated vacuum aspirators from different locations in the Bhopal region, India. They were sorted based on genus, gender, location, and collection date. The RNA was extracted from the homogenized mosquito pools and reverse transcribed. Complementary DNA (cDNA) was amplified using sequence-independent, single-prime amplification (SISPA). Further, polymerase chain reaction (PCR) products were sequenced using the Illumina NovaSeq 6000 platform (Illumina, Inc., San Diego, CA). Bioinformatic analysis of the reads was performed using Trimmomatic (Bolger&#xa0;AM, Lohse M, Usadel B (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data (Bioinformatics, btu170) for trimming low-quality raw reads. Later, Kraken2 and Bracken (Johns Hopkins University, Baltimore, MD)&#xa0;were used for the identification of viral sequences.<br><br>RESULTS: The study examined virus diversity and seasonal distribution in mosquito populations collected from 13 sites in Bhopal, India, over 15 months. A total of 31 mosquito pools of female Aedes mosquitoes were analyzed. Metagenomic analysis revealed viruses encompassing plant, animal, insect, fungal, and bacteriophage hosts. The highest mosquito catch was during the post-monsoon period, while virus diversity peaked during the monsoon. Seasonal variations showed a higher frequency and diversity of viruses during the monsoon than during pre- and post-monsoon periods. The findings highlight the importance of temporal and ecological factors in viral surveillance and mosquito-borne disease management.<br><br>CONCLUSIONS: Our findings demonstrate the potential of combining entomological and genomic surveillance for monitoring virus circulation in mosquito populations, which may be implemented as a routine surveillance tool for the timely detection of spikes in viruses with human pathogenic potential and thus inform targeted vector control measures to avert potential outbreaks in the future.},
}
@article {pmid40115125,
year = {2025},
author = {Pavloudi, C and Santi, I and Azua, I and Baña, Z and Bastianini, M and Belser, C and Bilbao, J and Bitz-Thorsen, J and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Daguin, C and Díaz de Cerio, O and Exter, K and Fauvelot, C and Frada, MJ and Galand, PE and Garczarek, L and González Fernández, J and Guillou, L and Hablützel, PI and Heynderickx, H and Houbin, C and Kervella, AE and Krystallas, A and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhaes, C and Maidanou, M and Margiotta, F and Montresor, M and Not, F and Paredes, E and Percopo, I and Péru, E and Poulain, J and Præbel, K and Rigaut-Jalabert, F and Romac, S and Stavroulaki, M and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Trano, AC and Wincker, P and Pade, N},
title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e143585},
pmid = {40115125},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.},
}
@article {pmid40115072,
year = {2025},
author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X},
title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1433131},
pmid = {40115072},
issn = {2235-2988},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.<br><br>RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.<br><br>CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.},
}
@article {pmid40114670,
year = {2025},
author = {Hu, W and Teng, Y and Wang, X and Xu, Y and Sun, Y and Wang, H and Li, Y and Dai, S and Zhong, M and Luo, Y},
title = {Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae160},
pmid = {40114670},
issn = {2730-6151},
abstract = {Biological nitrogen fixation by diazotrophs is a crucial biogeochemical process in global terrestrial ecosystems, especially in nitrogen-limited, organic-contaminated soils. The metabolic activities of diazotrophs and their ability to supply fixed nitrogen may facilitate the transformation of organic pollutants. However, the active diazotrophic communities in organic-contaminated soils and their potential metabolic functions have received little attention. In the current study, the relationship between biological nitrogen fixation and polychlorinated biphenyl (PCB) metabolism was analyzed in situ in paddy soil contaminated with a representative tetrachlorobiphenyl (PCB52). [15]N-DNA stable isotope probing was combined with high-throughput sequencing to identify active diazotrophs, which were distributed in 14 phyla, predominantly Cyanobacteria (23.40%). Subsequent metagenome binning and functional gene mining revealed that some mixotrophic cyanobacteria (e.g. FACHB-36 and Cylindrospermum) contain essential genes for nitrogen fixation, PCB metabolism, and photosynthesis. The bifunctionality of Cylindrospermum sp. in nitrogen fixation and PCB metabolism was further confirmed by metabolite analyses of Cylindrospermum sp. from a culture collection as a representative species, which showed that Cylindrospermum sp. metabolized PCB and produced 2-chlorobiphenyl and 2,5-dihydroxybenzonic acid. Collectively, these findings indicate that active diazotrophs, particularly mixotrophic cyanobacteria, have important ecological remediation functions and are a promising nature-based in situ remediation solution for organic-contaminated environments.},
}
@article {pmid40114290,
year = {2025},
author = {Demina, T and Marttila, H and Pessi, IS and Männistö, MK and Dutilh, BE and Roux, S and Hultman, J},
title = {Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {79},
pmid = {40114290},
issn = {2049-2618},
mesh = {*Soil Microbiology ; *Genome, Viral ; *Virome ; *Tundra ; *Phylogeny ; *Metagenome ; Arctic Regions ; Finland ; Bacteriophages/genetics/classification/isolation &amp; purification ; Acidobacteria/genetics/classification/isolation &amp; purification ; Soil ; DNA, Viral/genetics ; },
abstract = {BACKGROUND: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.<br><br>RESULTS: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisj&#xe4;rvi, Finland (69&#xb0;N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98&#xa0;kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisj&#xe4;rvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisj&#xe4;rvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisj&#xe4;rvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.<br><br>CONCLUSIONS: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.},
}
@article {pmid40114168,
year = {2025},
author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S},
title = {Multiple primary malignancies and gut microbiome.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {516},
pmid = {40114168},
issn = {1471-2407},
support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Enterovirus/isolation &amp; purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; },
abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.<br><br>OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.<br><br>METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.<br><br>RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.<br><br>CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.},
}
@article {pmid40113957,
year = {2025},
author = {Lai, Y and Chen, B and Chen, S and Shen, Y},
title = {Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9579},
pmid = {40113957},
issn = {2045-2322},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Aged ; Middle Aged ; Retrospective Studies ; Adult ; Aged, 80 and over ; Respiratory Tract Infections/microbiology/diagnosis/drug therapy ; Bacteria/genetics/isolation &amp; purification/classification ; Metagenome ; },
abstract = {Pulmonary infections remain a leading cause of infectious disease-related hospitalizations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool for identifying pathogens responsible for pulmonary infections. However, implementing mNGS in clinical practice presents several challenges. We conducted a retrospective analysis of 97 patients with suspected pulmonary infections who were admitted to our hospital and underwent mNGS alongside conventional microbiologic tests (CMT) over the past three years. We compared the diagnostic efficacy of mNGS versus CMT and assessed the clinical applications and challenges associated with mNGS in managing pulmonary infections. mNGS detected pathogens in 63.9% of cases, outperforming CMT (27.8%) and showing notable improvements in identifying Mycobacterium, fungal species, and rare pathogens. Antibiotic regimens were adjusted for 77.4% of patients with positive mNGS results, with clinical improvement observed in 93.5%. Of the 138 microbial strains initially identified by mNGS as possible pathogens, 65 (47.1%) were reclassified as colonizing organisms upon further clinical evaluation, including bacteria and fungi commonly associated with pulmonary infections. Notably, one patient was diagnosed with aspiration pneumonia due to oral anaerobes, which mNGS had categorized as normal microbial flora. In conclusion, mNGS serves as a valuable diagnostic approach for pulmonary infections, enhancing etiologic precision and informing patient management. Nevertheless, a comprehensive clinical interpretation of mNGS-identified microorganisms is essential to achieve accurate diagnosis.},
}
@article {pmid40113286,
year = {2025},
author = {Li, F and Qiu, CS and Wang, CC and Xu, F and Wang, D and Liu, NN and Chen, X and Wang, SP},
title = {[Distribution Characteristics and Influencing Factors of Antibiotic Resistance Genes in Surface Sediments of Regulating Pond in South-to-North Water Transfer Pumping Station].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {3},
pages = {1435-1442},
doi = {10.13227/j.hjkx.202312226},
pmid = {40113286},
issn = {0250-3301},
mesh = {*Geologic Sediments/microbiology ; China ; *Drug Resistance, Microbial/genetics ; Ponds/microbiology ; Genes, Bacterial ; Environmental Monitoring ; Water Supply ; Bacteria/genetics/classification ; Rivers/microbiology ; Water Microbiology ; },
abstract = {As an important facility to ensure the safety of the water supply, the regulating pond of a raw water pumping station in the Tianjin Section of the middle route of the South-to-North Water Transfer Project linked the raw water from the Hanjiang River with the urban water plants. Surface sediment samples from different regions of the regulator pond were collected in summer, autumn, and winter of 2022 and spring of 2023, respectively. Metagenomic sequencing technology was used to analyze the distribution characteristics and influencing factors of antibiotic resistance genes （ARGs）, and the correlation between sediment ARGs and physicochemical indices, microbial community structure, and mobile genetic elements （MGEs） was also analyzed. The results showed that 20 antibiotic resistance types and 921 ARGs subtypes were detected in the surface sediment samples of the regulator pond. The dominant ARGs in the samples at different sampling times and sampling points were multidrug resistance, MLS, tetracycline, and glycopeptides, and the main resistance mechanism was efflux pump. Correlation analysis showed that TN, NO3[-]-N, TP, and OM of sediments were significantly correlated （P<0.05） with various ARGs of the top 20 ARGs. Among the top 20 microbial genera, 19 species were significantly correlated （P<0.05） with ARGs. The MGEs types of conjugate transfer protein, recombinase, and transposase were significantly positively correlated （P<0.05） with the top 20 ARGs.},
}
@article {pmid40113151,
year = {2025},
author = {Zhang, W and Wen, L and Xin, Z and Wang, G and Lin, H and Wang, H and Wei, B and Yan, X and Wang, W and Guo, B},
title = {Research on the histopathology of Larimichthys crocea affected by white gill disease and analysis of its bacterial and viral community characteristics.},
journal = {Fish &amp; shellfish immunology},
volume = {},
number = {},
pages = {110287},
doi = {10.1016/j.fsi.2025.110287},
pmid = {40113151},
issn = {1095-9947},
abstract = {White gill disease (WGD) is one of the major diseases affecting Larimichthys crocea, although its etiology remains unclear. To investigate the causes of WGD, this study selected WGD-affected Larimichthys crocea (WG) and healthy Larimichthys crocea (NH) from multiple aquaculture regions for pathological analysis and analysis of bacterial and viral community characteristics. The results indicated severe tissue damage and significant inflammatory responses, as evidenced by clinical manifestations and electron microscopy. Two bacterial species, Photobacterium damselae and Vibrio campbellii, were isolated from all lesion tissues. Additionally, 16S full-length sequencing results showed that Photobacterium damselae and Vibrio campbellii dominated in the tissues of Larimichthys crocea, with a combined relative abundance of approximately 90%. There were no significant differences in α-diversity and β-diversity between the NH group and WG group from the three aquaculture regions, and no significant biomarkers were identified. The diversity of DNA and RNA viruses did not show significant differences between the NH and WG groups, although both types of viruses exhibited notable synergistic and antagonistic relationships. Analyses from 16S full-length sequencing, metagenomics, and metatranscriptomics revealed that the related functional genes were primarily enriched in various metabolic pathways, including glycine biosynthesis, membrane transport, and energy metabolism. The metatranscriptomic analysis indicated that the expression levels of genes related to antibiotic resistance, biosynthesis, transport, and degradation processes were significantly downregulated in the WG group. Finally, through PCR, qPCR, and metagenomic sequencing, we were unable to detect iridovirus in Larimichthys crocea, further suggesting that the causes of WGD may differ across aquaculture regions compared to previous reports. This study indicates that the etiology of WGD may involve complex ecological and metabolic mechanisms, rather than being merely the result of a single pathogen infection. This research provides a comprehensive analysis of the microbial communities in WGD-affected Larimichthys crocea from multiple aquaculture regions for the first time, providing a theoretical basis for further elucidating the causes of WGD and developing preventive measures.},
}
@article {pmid40113108,
year = {2025},
author = {Ruan, Z and Shi, H and Chang, L and Zhang, J and Fu, M and Li, R and Zeng, D and Yang, Y and Li, R and Ai, L and Wang, Y and Hai, B},
title = {The Diagnostic Efficacy of Metagenomic Next-Generation Sequencing (mNGS) in Pathogen Identification of Pediatric Pneumonia using Bronchoalveolar Lavage Fluid (BALF): A Systematic Review and Meta-Analysis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107492},
doi = {10.1016/j.micpath.2025.107492},
pmid = {40113108},
issn = {1096-1208},
abstract = {OBJECTIVE: This meta-analysis evaluates and compares the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) with conventional microbiological tests (CMTs) in diagnosing pediatric pneumonia using bronchoalveolar lavage fluid (BALF).<br><br>METHODS: Data were sourced from Embase, Medline (via PubMed), Web of Science, and the Cochrane Library. The pooled positive detection rate (PDR) of pathogens was estimated using fixed-effects or random-effects models. Subgroup analyses explored factors influencing mNGS diagnostic performance. Data analysis was conducted using Review Manager (RevMan) 5.4 and Stata version 16.0.<br><br>RESULTS: The pooled PDR of mNGS was 85.83%, which is higher than the pooled PDR of 49.97% for CMTs. A random-effects model indicated that, compared to CMTs, mNGS has a significantly higher PDR in pediatric pneumonia (OR=3.99, 95%CI: 2.12-7.50, P<0.0001, I[2]=81%). Subgroup analysis indicated that mNGS exhibited greater advantages in the group using the QIAamp kit (OR=5.55, 95% CI: 3.03-10.16, P<0.00001), the group using the Illumina Nextseq platform (OR=4.87, 95% CI: 2.97-7.99, P<0.00001), the DNA-only mNGS group (OR=4.54, 95% CI: 2.73-7.54, P<0.00001), and the non-severe pneumonia group (OR=4.76, 95% CI: 3.51-6.46, P<0.00001). However, when the subgroups were categorized as mixed infections or single-pathogen infections, no statistically significant differences were observed (Mixed: OR=1.77, 95% CI: 0.30-10.56, P=0.53; Single: OR=3.97, 95% CI: 0.42-37.87, P=0.23) CONCLUSION: mNGS demonstrates high diagnostic efficacy in detecting pathogens in BALF from pediatric patients with pneumonia. The diagnostic stability of mNGS is influenced by sample extraction, sequencing platforms, positive interpretation criteria, and disease status. Standardized procedures and technologies can enhance mNGS diagnostic performance.},
}
@article {pmid40112621,
year = {2025},
author = {Ma, C and Zhao, Y and Ma, B and Li, X and Li, X and Chen, X},
title = {Co-critical golden-flower fungus (Eurotium repens) contributed to characteristic flavor formation of two Yunnan jinhua teas through jinhua formation during the storage.},
journal = {Food chemistry},
volume = {479},
number = {},
pages = {143765},
doi = {10.1016/j.foodchem.2025.143765},
pmid = {40112621},
issn = {1873-7072},
abstract = {Jinhua formation during the storage (JFDS) was found in two Yunnan teas that were defined as jinhua ripened Pu-erh tea (JRIPT) and jinhua white tea (JWT), respectively. Integrated multi-omics of metagenomics, volatilomics and metabolomics was developed to elucidate JFDS mechanism. Overall, JFDS caused significant differences in characteristic flavor, microbial community structure and volatile organic compounds (VOCs) profile. Among 14 co-critical fungi, Eurotium repens was regarded as the golden-flower fungus for JFDS, and had higher relative abundance in Yunnan jinhua teas over 50 %. Based on 291 VOCs and 83 odor-active compounds, E. repens directly promoted glycoside hydrolysis and carotene degradation to formulate β-linalool, β-ionone and 3,4-dehydro-β-ionone for jinhua fungus aroma of JWT. With Arxula adeninivorans synergy, E. repens activity contributed to Chinese medicine-like smell of JRIPT through sesquiterpenes and methoxybenzenes accumulation. Additionally, E. repens activity in the JFDS accelerated catechins oxidative polymerization, and other flavonoids conversion to enhance mellow taste.},
}
@article {pmid40111891,
year = {2025},
author = {Díez-Madueño, K and Montero, I and Fernández-Gosende, M and Martínez-Álvarez, N and Hidalgo-Cantabrana, C and de la Cueva Dobao, P and Coto-Segura, P},
title = {Compositional and Functional Profile of Gut Microbiota in a Cohort of Adult Spanish Patients with Atopic Dermatitis Using Metagenomics: A Cross-Sectional Study.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {},
number = {},
pages = {},
doi = {10.1089/derm.2024.0536},
pmid = {40111891},
issn = {2162-5220},
abstract = {Background: The role of gut dysbiosis in the pathophysiology of atopic dermatitis (AD) through immune system (IS) imbalance is a novel line of investigation currently under discussion. This study aimed to characterize compare the composition and functional profile of the gut microbiota (GM) between adults with AD and healthy individuals. Methods: Observational cross-sectional study, where fecal samples from 70 adults (38 patients and 32 controls) were analyzed using metagenomics and bioinformatics. Results: Differences between the GM of patients with AD and healthy individuals were demonstrated. Reduced microbial diversity was found in subjects with AD. Bacterial species with lower abundance primarily belonged to the families Ruminococcaceae, Akkermansiaceae, and Methanobacteriaceae. Several microbial metabolic pathways were found to be decreased in patients with AD, including amino acid biosynthesis, vitamin biosynthesis, fatty acids and lipids biosynthesis, and energy metabolism. Conclusion: Adults with AD exhibited a distinct GM compared to healthy individuals. Changes were demonstrated both compositionally and functionally. Further investigation is mandatory to elucidate the potential link and causal relationship between gut dysbiosis and AD, which may be crucial for a deeper understanding of the disease's pathophysiology and the development of novel therapeutic approaches.},
}
@article {pmid40111684,
year = {2025},
author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA},
title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {31-51},
pmid = {40111684},
issn = {0065-2598},
mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; },
abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.},
}
@article {pmid40111141,
year = {2025},
author = {Yang, F and Zhang, Y and Qi, B and Chen, L and Lin, F and Wu, J and Gong, S and Cao, L and Zeng, M and Cheng, Q and Jiang, D and Tang, S and He, J and Xu, Z and Li, T and Ni, Z and Li, Y and Huang, X and Pan, C and Liu, R and Lan, Y},
title = {Clinical Manifestations and Prognosis of Patients With Mucormycosis in Intensive Care Units in Western China: A Multi-Center Retrospective Study.},
journal = {Mycoses},
volume = {68},
number = {3},
pages = {e70042},
doi = {10.1111/myc.70042},
pmid = {40111141},
issn = {1439-0507},
support = {2023QN02//Research Fund of Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital/ ; 2025ZNSFSC1542//Sichuan Science and Technology Program/ ; },
mesh = {Humans ; *Mucormycosis/mortality/diagnosis/drug therapy/epidemiology/microbiology ; Female ; Male ; Middle Aged ; Retrospective Studies ; *Intensive Care Units ; China/epidemiology ; Aged ; *Antifungal Agents/therapeutic use ; Adult ; Prognosis ; Critical Illness ; Amphotericin B/therapeutic use ; },
abstract = {BACKGROUND: Mucormycosis is a life-threatening fungal infection with high mortality in critically ill patients. Clinical manifestations and outcomes of mucormycosis in intensive care units (ICUs) remain poorly investigated.<br><br>METHODS: We conducted a multicenter retrospective study including 43 adult patients with confirmed mucormycosis admitted to 14 tertiary ICUs between January 2014 and May 2022. Clinical characteristics, diagnostic approaches, treatment strategies, and outcomes were analysed.<br><br>RESULTS: The mean age was 56.8&#x2009;&#xb1;&#x2009;16.2&#x2009;years, with 16/43 (37.2%) female patients. The 28-day survival rate was 46.5% (20/43). Lung involvement was predominant (29/43, 67.4%), and 29/43 (67.4%) patients received amphotericin B therapy. Survivors showed significantly better treatment response compared to non-survivors (16/20, 80% vs. 4/23, 17.4%, p&#x2009;<&#x2009;0.001). Non-survivors demonstrated significantly higher levels of aspartate aminotransferase, C-reactive protein, and white blood cells, along with lower albumin levels. Metagenomic next-generation sequencing (mNGS) was associated with a shorter time to diagnosis. Multivariate analysis identified age, respiratory failure, time from symptom onset to diagnosis, and antifungal treatment response as independent predictors of 28-day mortality (AUC&#x2009;=&#x2009;0.852).<br><br>CONCLUSION: In critically ill patients with mucormycosis, early diagnosis and prompt targeted therapy are crucial determinants of survival, with our newly developed prediction model providing a practical tool for risk stratification, while mNGS shows promise in expediting diagnosis.},
}
@article {pmid40111052,
year = {2025},
author = {Martí, JM and Kok, CR and Thissen, JB and Mulakken, NJ and Avila-Herrera, A and Jaing, CJ and Allen, JE and Be, NA},
title = {Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0123924},
doi = {10.1128/msystems.01239-24},
pmid = {40111052},
issn = {2379-5077},
abstract = {UNLABELLED: Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size-currently exceeding 10[12] nucleotides-and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.<br><br>IMPORTANCE: Accurately identifying the diverse microbes present in a sample, whether from the human gut, a soil sample, or a crime scene, is crucial for fields ranging from medicine to environmental science. Researchers rely on comprehensive DNA databases to match sequenced DNA fragments to known microbial species. However, the widely used NCBI nt database, while vast, poses significant challenges. Its massive size makes it difficult for many researchers to use effectively with taxonomic classifiers, and inconsistencies and contamination within the database can impact the accuracy of microbial identification. This work addresses these challenges by providing cleaned, updated, and validated nt-based databases specifically optimized for the widely used Centrifuge classification tool. This new resource demonstrably reduces errors and improves the reliability of microbial identification across diverse taxonomic groups. Moreover, by providing readily usable indexes, we overcome the size barrier, enabling researchers to leverage the full potential of the nt database for metagenomic analysis. Our findings underscore the need to treat reference databases as dynamic entities, emphasizing continuous quality control and versioning as essential practices for robust and reproducible metagenomics research.},
}
@article {pmid40111022,
year = {2025},
author = {Lim, SJ and Rogers, A and Rosario, K and Kerr, M and Garrett, M and Koester, J and Hubbard, K and Breitbart, M},
title = {Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0109024},
doi = {10.1128/msphere.01090-24},
pmid = {40111022},
issn = {2379-5042},
abstract = {Harmful algal blooms (HABs) caused by the dinoflagellate Karenia brevis frequently occur in the eastern Gulf of Mexico, where they negatively impact the environment, human health, and economy. Very little is known about viruses associated with K. brevis blooms, although viral infection of other HAB-forming phytoplankton species can play an important role in bloom dynamics. We used viral metagenomics to identify viruses in 11 pooled seawater samples collected from southwest Florida, USA, in 2021 during a severe, spatiotemporally dynamic K. brevis bloom. Assembled viral genomes were similar to published genomes from the order Picornavirales, family Marnaviridae, and genera Sogarnavirus, Bacillarnavirus, and Marnavirus. Several of the cultured viruses from these groups infect bloom-forming diatoms (Chaetoceros sp. and Rhizosolenia setigera) and the raphidophyte Heterosigma akashiwo. We also recovered unclassified Riboviria genomes related to a Symbiodinium positive-sense ssRNA virus sequenced from coral dinoflagellate symbionts. Reverse-transcriptase PCR assays were performed to monitor the occurrence of seven representative virus genomes in these samples from 2021 and 43 seawater samples collected during a subsequent, typical bloom between November 2022 and May 2023. Over half of the samples contained multiple viruses, and at least one viral genome was detected in 44 of the 54 samples collected across seasons and years, highlighting the ubiquity of these viruses in this region. Alpha diversity was highest in the summer months and positively correlated with K. brevis cell counts. Multiple regression revealed month and the presence of unclassified Riboviria sequences most similar to dinoflagellate viruses as significant predictors of K. brevis cellular abundance.IMPORTANCEHarmful algal blooms caused by the dinoflagellate Karenia brevis negatively impact the tourism, fisheries, and public health sectors. Anticipated impacts of climate change, nutrient pollution, and ocean acidification may sustain and/or exacerbate K. brevis blooms in the future, underscoring the need for proactive monitoring, communication, and mitigation strategies. This study represents a pioneering effort in monitoring viruses associated with K. brevis blooms. The findings lay the groundwork for studying the effects of environmental drivers on K. brevis blooms and their associated viruses, as well as for exploring the roles of viruses in bloom dynamics and potential applications of viruses as biocontrol agents for K. brevis blooms. Furthermore, the comparison of viral dynamics relative to local and regional bloom dynamics in this study helps inform future monitoring and modeling needs.},
}
@article {pmid40110701,
year = {2025},
author = {Liang, H and Li, T and Chen, Y and Wang, J and Aslam, M and Qin, H and Fan, W and Du, H and Kao, SJ and Lin, S},
title = {Urea Amidolyase as an Enzyme for Urea Utilisation in Phytoplankton: Functional Display in Chlamydomonas reinhardtii.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17734},
doi = {10.1111/mec.17734},
pmid = {40110701},
issn = {1365-294X},
support = {42206116//Natural Science Foundation of China/ ; 2024A1515011467&#xff1b;2025A1515010095//Natural Science Foundation of Guangdong Province, China/ ; 2021B1212050025//Science and Technology Plan Projects of Guangdong Province/ ; 2022KCXTD008//Program for University Innovation Team of Guangdong Province/ ; 2024-MRB-00-001//Research on Breeding Technology of Candidate Species for Guangdong Modern Marine Ranching/ ; },
abstract = {Urea is an important source of nitrogen for many phytoplankton with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but urea amidolyase (UAL), albeit known to exist, has hardly been studied. Here, the species distribution, expression patterns and functional roles of UAL are examined. We found a widespread occurrence of UAL across six major phytoplankton lineages, along with evidence of a potential URE-independent evolutionary trajectory and lineage-specific losses. Quantitative analyses based on marine planktonic metagenomes and metatranscriptomes revealed that UAL is as prevalent as URE, but exhibits higher expression levels in phytoplankton than in bacteria, suggesting that UAL plays a crucial role in nitrogen nutrition in marine phytoplankton. Furthermore, using the CRISPR/Cas9 genome editing method and Chlamydomonas reinhardtii as the algal model, we showed that DUR2 in UAL is essential for urea utilisation, as its knockout completely abolishes the ability of algae to grow under urea as the sole nitrogen source. This study unveils an unappreciated mechanism in algae for utilising urea as a nutrient, underscores the need to consider both URE and UAL enzyme systems to model urea utilisation by algae and provides a crucial gene (DUR2) as a potential genetic marker for detecting the contribution of UAL to urea utilisation in phytoplankton.},
}
@article {pmid40110433,
year = {2025},
author = {Cheng, C and Zheng, Y and Wang, X and Tao, J and Cheng, D},
title = {Research in etiology of Floppy Kid Syndrome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1557951},
pmid = {40110433},
issn = {2297-1769},
abstract = {Floppy Kid Syndrome (FKS) is a common and serious disease in goats, with incidence rates ranging from 10 to 50% and mortality rates between 20 and 60%. This study aimed to investigate the etiology of FKS through blood biochemical analysis and metagenomic sequencing. Blood biochemical analysis revealed metabolic disorders in FKS-affected goats, including acidosis and hypoglycemia. Metagenomic analysis showed marked gastric and gut dysbacteriosis, characterized by an increase in pathogenic bacteria such as Escherichia coli and Staphylococcus aureus, alongside a significant reduction in probiotic like Lactobacillus amylovorus. Furthermore, species diversity and richness were notably lower in FKS-affected goats compared to healthy goats. Based on these findings, we infer that FKS is a multifactorial disease caused by gastric and gut dysbacteriosis. The immaturity of the digestive system in newborn goats, combined with environmental stressors (such as sudden changes in weather), leads to gastric and gut dysbacteriosis, with a significant reduction in probiotic and an overgrowth of pathogenic bacteria. The dysbacteriosis, along with the inability to properly digest excessive milk intake, contributes to the accumulation of undigested milk in the digestive tract, creating an environment conducive to pathogenic bacteria growth. The fermentation of milk and the production of excessive lactic acid by pathogenic bacteria are absorbed into the bloodstream, causing acidosis and hypoglycemia. These metabolic disorders, in conjunction with the dysbacteriosis and systemic dysfunction, lead to the onset of FKS. These results underscore the critical role of gastric and gut dysbacteriosis in the pathogenesis of FKS, highlighting the need for targeted preventive and therapeutic strategies.},
}
@article {pmid40109965,
year = {2025},
author = {Zou, Z and Tang, F and Qiao, L and Wang, S and Zhang, H},
title = {Integrating sequencing methods with machine learning for antimicrobial susceptibility testing in pediatric infections: current advances and future insights.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1528696},
pmid = {40109965},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) presents a critical challenge in clinical settings, particularly among pediatric patients with life-threatening conditions such as sepsis, meningitis, and neonatal infections. The increasing prevalence of multi- and pan-resistant pathogens is strongly associated with adverse clinical outcomes. Recent technological advances in sequencing methods, including metagenomic next-generation sequencing (mNGS), Oxford Nanopore Technologies (ONT), and targeted sequencing (TS), have significantly enhanced the detection of both pathogens and their associated resistance genes. However, discrepancies between resistance gene detection and antimicrobial susceptibility testing (AST) often hinder the direct clinical application of sequencing results. These inconsistencies may arise from factors such as genetic mutations or variants in resistance genes, differences in the phenotypic expression of resistance, and the influence of environmental conditions on resistance levels, which can lead to variations in the observed resistance patterns. Machine learning (ML) provides a promising solution by integrating large-scale resistance data with sequencing outcomes, enabling more accurate predictions of pathogen drug susceptibility. This review explores the application of sequencing technologies and ML in the context of pediatric infections, with a focus on their potential to track the evolution of resistance genes and predict antibiotic susceptibility. The goal of this review is to promote the incorporation of ML-based predictions into clinical practice, thereby improving the management of AMR in pediatric populations.},
}
@article {pmid40109771,
year = {2025},
author = {Chen, HB and Liu, J and Zhang, Y and Huang, H and Wang, LN},
title = {Application of metagenomic next-generation sequencing in the diagnosis of pathogens in patients with diabetes complicated by community-acquired pneumonia.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20221048},
pmid = {40109771},
issn = {2391-5412},
abstract = {To explore the clinical utility and optimal timing of metagenomic next-generation sequencing (mNGS) in diagnosing pathogens in patients with diabetes complicated by community-acquired pneumonia (CAP). The study included 50 hospitalized patients diagnosed with diabetes complicated by CAP who underwent conventional microbiological testing (CMT) and mNGS using bronchoalveolar lavage fluid. Among the 50 cases, 16% presented no respiratory symptoms. There were significant increases in inflammatory markers such as C-reactive protein, erythrocyte sedimentation rate, and interleukin-6, with patchy imaging changes being the most prevalent. The positive rates for pathogen detection by mNGS and CMTs were 78 and 21% (P < 0.05). The mNGS was significantly better than the CMTs in the detection of rare pathogens such as Anaerobes, Chlamydia psittaci, Legionella pneumophila, Mycobacterium bovis, Aspergillus fumigatus, and Pneumocystis japonicus (P < 0.05). After clinical interpretation, 85% (22/26) of viruses, 24% (9/37) of bacteria, and 25% (2/8) of fungi were non-pathogen organisms by mNGS. There was a significant difference in the rates of adjustment in anti-infection treatment strategies based on the pathogen detection results from CMTs and mNGS, which were 2 and 46%, respectively (P < 0.05). We found that mNGS was superior to CMTs in terms of the positive rate of pathogen detection, detecting mixed infection incidence, rare pathogen detection rates, and the adjustment of treatment strategies. However, mNGS results need to be interpreted in the context of the clinic.},
}
@article {pmid40109467,
year = {2025},
author = {Han, Y and Shen, S and Fu, J and Ren, Q},
title = {[Mechanisms of Wandai Decoction in Improving Vaginal Flora of Vulvovaginal Candidiasis of the Spleen Deficiency and Excessive Dampness Type: A Study Based on Metagenomics and Metabolomics].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {1},
pages = {68-73},
pmid = {40109467},
issn = {1672-173X},
mesh = {Female ; Humans ; *Vagina/microbiology ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Metabolomics ; *Drugs, Chinese Herbal/therapeutic use/administration &amp; dosage ; *Fluconazole/pharmacology/therapeutic use ; Metagenomics ; Antifungal Agents/therapeutic use ; Adult ; Spleen/metabolism/microbiology ; },
abstract = {OBJECTIVE: To explore the mechanism by which Wandai Decoction prevents and treats vulvovaginal candidiasis (VVC) of the spleen deficiency and excessive dampness type and restores the vaginal flora structure, and to identify the potential metabolic pathways involved using metagenomics and metabolomics.<br><br>METHODS: Twenty VVC patients who met the inclusion criteria were randomly assigned to a Wandai Decoction group and a fluconazole group (n = 10 in each group). Subjects in the fluconazole group were given a single oral dose of 150 mg fluconazole, while those in the Wandai Decoction group took the Wandai Decoction orally for 14 days. The vulvovaginal signs and symptoms (VSS) scores of both patient groups were evaluated before and after treatment. Vaginal secretions were collected before and after treatment. The Illumina sequencing and the liquid chromatography with tandem mass spectrometry (LC-MS/MS) platform were used to conduct metagenomic and metabolomics analyses of the vaginal secretions, respectively.<br><br>RESULTS: The VSS score results showed that the VSS scores of both groups decreased after treatment compared with those before treatment (P < 0.01), and there was no statistically significant difference in the VSS scores between the two groups after treatment. Metagenomics results showed that, after treatment, the vaginal microbial communities in the Wandai Decoction group were of CST &#x2161; and &#x2164; types (predominated by Lactobacillus gasseri and Lactobacillus jensenii), while those in the fluconazole group were Lactobacillus_intestinalis and Streptococcus_sp._oral_ taxon_431. KEGG functional enrichment analysis results showed that, in terms of the cell cycle and meiosis functions of Candida albicans, statistically significant differences between the Wandai Decoction and fluconazole groups were observed (P < 0.05). Metabolomic analysis identified 120 differential metabolites between the two groups after treatment. The results of KEGG metabolic pathway enrichment analysis of differential metabolites showed that the Wandai Decoction might be significantly superior to fluconazole in improving local vaginal metabolic pathways of &#x3b1;-linolenic acid, glycerophospholipid metabolism, pentose and glucuronic acid interconversion, and arachidonic acid.<br><br>CONCLUSION: The Wandai Decoction can improve the vaginal flora of VVC patients. It may be superior to fluconazole in the signaling pathways of the cell cycle and meiosis. The improvement of the vaginal flora by the Wandai Decoction may be associated with its effect on metabolic pathways of glycerophospholipid metabolism, pentose and glucuronic acid interconversion, and others in the vagina.},
}
@article {pmid40109356,
year = {2025},
author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL},
title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.},
journal = {ACS ES&amp;T engineering},
volume = {5},
number = {3},
pages = {772-781},
pmid = {40109356},
issn = {2690-0645},
abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.},
}
@article {pmid40108525,
year = {2025},
author = {Liu, G and Chen, T and Tian, X and Ai, Y and Chen, Z and Liu, J and Sun, Z},
title = {Brain abscess due to clostridium celerecrescens: first report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {386},
pmid = {40108525},
issn = {1471-2334},
support = {82371407//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Brain Abscess/microbiology/diagnostic imaging/drug therapy ; Female ; *Clostridium Infections/microbiology/diagnosis/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Adolescent ; *Clostridium/isolation &amp; purification/genetics ; Foreign Bodies/complications/surgery ; Debridement ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Brain abscess caused by atypical pathogens presents significant diagnostic and therapeutic challenges. The unusual clinical presentations, coupled with incomplete or inaccurate patient histories, often result in misdiagnosis and inappropriate treatment.<br><br>CASE PRESENTATION: We report a case of a retained intracranial bamboo foreign body resulting in a brain abscess. A female adolescent presented with a newly developed mass on the eyelid. Medical imaging identified a foreign body that had penetrated the frontal lobes via the transorbital route, leading to the formation of a brain abscess. The foreign body was successfully removed through transnasal endoscopy. Inflamed tissue adherent to the foreign body was cultured and analyzed using metagenomic next-generation sequencing (mNGS), which identified Clostridium celerecrescens as the causative pathogen. The patient fully recovered after surgical debridement and two weeks of antibiotic therapy.<br><br>CONCLUSIONS: Infections caused by C. celerecrescens are exceedingly rare in clinical practice. This case highlights the bacterium's ability to adhere to a bamboo foreign body, leading to the formation of a rare brain abscess. mNGS proves to be a valuable diagnostic tool for identifying uncommon infectious agents.},
}
@article {pmid40108202,
year = {2025},
author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA},
title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {46},
pmid = {40108202},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; },
abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.},
}
@article {pmid40108151,
year = {2025},
author = {Krueger, ME and Boles, JS and Simon, ZD and Alvarez, SD and McFarland, NR and Okun, MS and Zimmermann, EM and Forsmark, CE and Tansey, MG},
title = {Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {50},
pmid = {40108151},
issn = {2373-8057},
support = {PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; },
abstract = {Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson's disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development.},
}
@article {pmid40107220,
year = {2025},
author = {Zhang, T and Zhou, S and Cheng, C and Yang, Y and Yang, D and Shi, D and Li, H and Yang, Z and Chen, T and Li, J and Jin, M},
title = {Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118063},
doi = {10.1016/j.ecoenv.2025.118063},
pmid = {40107220},
issn = {1090-2414},
abstract = {The microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profiling of potential pathogens, antibiotic-resistant pathogens (ARPs), and multidrug-resistant pathogens (MDRPs) in the Hai River, which runs through the central city of Tianjin, was conducted using metagenomic assembled genome (MAG) analysis. Of the 436 recovered MAGs assigned to 430 species, 110 MAGs were identified as potential pathogens due to the presence of virulence factors (VFs), whereas 19 MAGs containing both antibiotic resistance genes (ARGs) and VFs, were classified as potential ARPs, predominantly belonging to the genera Kluyvera, Enterobacter, and Klebsiella. Notably, nine species of MDRPs, including Enterobacter kobei, Klebsiella pneumoniae, Morganella morganii, Kluyvera intermedia, Aeromonas salmonicida, Rahnella aceris, Hafnia paralvei, the unidentified species Sep. D_bin46, and Vibrio cholerae, exhibited resistance to multidrug, beta-lactam, polymyxin, bacitracin, tetracycline, other peptide antibiotics, macrolide-lincosamide-streptogramin, aminoglycoside, and chloramphenicol. The unknown pathogen Sep. D_bin46, classified under Aeromonas, showed resistance to both carbapenems and polymyxins. The strong co-occurrence of ARGs, VFs, and mobile genetic elements suggests a significant risk of ARGs and VFs transfers among MDRPs with last-resort ARGs (r > 0.8; p < 0.05). Interestingly, the sampling location significantly influenced the presence of pathogens, ARPs, and MDRPs carrying last-resort ARGs in the water. Notably, their abundance was lower downstream of the Hai River compared to upstream. This observation suggests that urban environmental sanitation facilities may be more effective in reducing contaminants as the river flows from upstream to downstream. Nevertheless, the presence of pathogens, ARPs, and MDRPs with last-resort ARGs in the water underscores the ongoing microbiological risks associated with urban surface water.},
}
@article {pmid40107213,
year = {2025},
author = {Lu, W and Guo, X and Wu, Y and Sun, S and Wang, Q and Guo, J and Zhao, HP and Lai, CY},
title = {Particulate methane monooxygenase and cytochrome P450-induced reactive oxygen species facilitate 17β-estradiol biodegradation in a methane-fed biofilm.},
journal = {Water research},
volume = {280},
number = {},
pages = {123501},
doi = {10.1016/j.watres.2025.123501},
pmid = {40107213},
issn = {1879-2448},
abstract = {Methane-fed biosystems have shown great potential for degrading various organic micropollutants, yet underlying molecular degradation mechanisms remain largely unexplored. In this study, we uncover the critical role of biogenic reactive oxygen species (ROS) in driving the degradation of 17β-estradiol (E2) within a methane-fed biofilm reactor. Metagenomic analyses confirm that aerobic methanotrophs, specifically Methylococcus and Methylomonas, are responsible for the efficient degradation of E2, achieving a degradation rate of 367.7 ± 8.3 μg/L/d. ROS scavenging in conjunction with enzyme inhibition experiments indicate that particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) could generate hydroxyl radicals (•OH), which are the primary ROS involved in E2 degradation. Molecular dynamics simulations suggest that E2 can enter the active catalytic site of pMMO through electrostatic attraction. Four amino acid residues are found to form stable hydrogen bonds with E2, with a high binding free energy, indicating a high affinity for the substrate. Additionally, density functional theory calculations combined with transformation product analysis reveal that •OH targets carbon atoms on the benzene ring and the hydroxyl group attaches to the cyclopentane ring, primarily through hydrogen abstraction and hydroxylation reactions. This work provides critical insights into the mechanisms of E2 biodegradation in methane-fed systems and highlights the potential for optimizing microbial pathways to enhance the degradation of organic micropollutants from contaminated water.},
}
@article {pmid40107211,
year = {2025},
author = {Gong, Q and Zeng, W and Hao, X and Wang, Y and Peng, Y},
title = {DNA stable isotope probing and metagenomics reveal temperature responses of sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) system.},
journal = {Water research},
volume = {280},
number = {},
pages = {123494},
doi = {10.1016/j.watres.2025.123494},
pmid = {40107211},
issn = {1879-2448},
abstract = {The sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) process showed significant advantages in energy conservation and resource recovery in municipal wastewater treatment. However, its application in regions with seasonal temperature fluctuations and high latitudes is challenged by low temperatures. In this study, the feasibility of the SPDA process for treating low-strength municipal wastewater across a wide temperature range (30-10 °C) was systematically investigated. The results demonstrated that thiosulfate-driven autotrophic partial denitrification maintained an efficient nitrate removal rate of 7.82 mg NO3[-]-N/gVSS/h and a nitrate to nitrite transformation rate of 62.7 % even at temperatures as low as 10 °C. Molecular ecological network and DNA-SIP revealed that dominant sulfur-oxidizing bacteria (SOB) shifted from norank_f_Hydrogenophilaceae and Thiobacillus at higher temperatures (30-20 °C) to Thiobacillus and Sulfurimonas as temperature decreased, thus ensuring the performance of autotrophic partial denitrification and consistent nitrite supply for anammox. Metagenomic analysis showed that the abundance of functional genes related to sulfur conversion increased almost universally, ensuring a stable electron supply for nitrate reduction through sulfur oxidation at low temperatures. The functional genes responsible for nitrate reduction changed from nar genes at higher temperatures to nap genes at lower temperatures, while a decrease in the abundance of hzs and hdh genes corresponding to reduced anammox performance. This study highlights the stable performance of the sulfur-driven autotrophic denitrification at low temperatures and the reliability of coupling with anammox, extending the applicability of SPDA to a broader geographical range.},
}
@article {pmid40107206,
year = {2025},
author = {Tang, H and Chen, Y and Tang, X and Wei, M and Hu, J and Zhang, X and Xiang, D and Yang, Q and Han, D},
title = {Corrigendum to "Yield of clinical metagenomics: insights from real-world practice for tissue infections" [eBioMedicine 111(2025), 105536].},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105574},
doi = {10.1016/j.ebiom.2025.105574},
pmid = {40107206},
issn = {2352-3964},
}
@article {pmid40107015,
year = {2025},
author = {Xia, Z and Luo, G and Gou, LY and Zhang, W and Ji, EG and Li, S and Gao, T and Abi, KM and Yang, F},
title = {Metaviromic and metagenomic study of the pathogens in unexplained pneumonia cases in goats.},
journal = {Veterinary microbiology},
volume = {304},
number = {},
pages = {110469},
doi = {10.1016/j.vetmic.2025.110469},
pmid = {40107015},
issn = {1873-2542},
abstract = {Goats are an economically important livestock species in China. However, the high mortality rate due to pneumonia represents a significant challenge to the development of intensive goat farms. 10 goat lung tissue samples were collected in this study, and all samples exhibited pneumonia of different severity as determined by lung lesion scoring and histopathological examination. Subsequently, this study employed qRT-PCR to measure the relative expression level of pro-inflammatory cytokines in lung tissue, and conducted metaviromic and metagenomic analyses to elucidate the structure and composition of the pulmonary microbiota, the correlation between the abundance of specific microbes and inflammatory factors, and between microbial abundance and the expression of virulence genes. Metaviromic results indicated that Ungulate tetraparvovirus 4 (83.3 %) had the highest relative abundance in the viral composition. Metagenomic data showed that Mycoplasma (28.2 %) and Streptococcus (24.8 %) are the primary dominant genus in goat pneumonia. Notably, a total of 8 pathogens associated with pneumonia in humans or animals were identified across all samples, including Mycoplasma ovipneumoniae, Streptococcus agalactiae, Streptococcus pneumoniae, Escherichia coli, Bordetella hinzii, Bibersteinia trehalosi, Bordetella pertussis, and Pasteurella multocida, with mixed infections with multiple pathogens are very common in this study. Correlation analysis indicates a significant association between the degree of pathogen co-infection and the severity of pulmonary lesions. Furthermore, Pasteurella multocida showed a significant positive correlation with the expression of IL-6 (P< 0.01). The pneumonia samples also revealed a multitude of virulence factors associated with bacterial pathogenicity including those related to biofilm formation, endotoxin production, bacterial invasion and evasion of host immunity. In conclusion, the present study can provide a reference for clinical pathogen diagnosis of unexplained pneumonia in goats.},
}
@article {pmid40105325,
year = {2025},
author = {Zhang, H and Lu, T and Guo, S and He, T and Shin, M-K and Luo, C and Tong, J and Zhang, Y},
title = {Rumen microbes affect the somatic cell counts of dairy cows by modulating glutathione metabolism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0109324},
doi = {10.1128/msystems.01093-24},
pmid = {40105325},
issn = {2379-5077},
abstract = {Healthy mammary glands are essential for high-quality milk production in the dairy industry. The relationship between somatic cell counts (SCCs), rumen fermentation, and microbiota interactions remains unclear. This study integrated physiological indicators, high-throughput 16S rRNA gene sequencing, and metagenomics data analysis to investigate the mechanisms linking rumen microbes and mastitis and to evaluate the changes in milk production and serum cytokine levels in cows with low (L-SCC) and high (H-SCC) somatic cell counts. Compared with the L-SCC group, the H-SCC group exhibited significantly lower lactose and fat contents in milk, reduced rumen fermentation product levels, and increased abundances of Bacteroidetes, Firmicutes, Lachnospiraceae, Prevotella, and Rumiclostridium. Elevated serum levels of IgG2, IgM, IL-1β, IL-6, and TNF-ɑ in the H-SCC group indicated inflammation and rumen microbiota dysbiosis. Functional analysis of microbial communities revealed significant enrichment in pathways related to glutathione metabolism, thyroid hormone synthesis, hypertrophic cardiomyopathy (HCM), the phosphotransferase system (PTS), the P53 signaling pathway, and the Jak-STAT signaling pathway. Correlation network analysis showed that changes in bacterial families, such as Rikenellaceae, Muribaculaceae, and Prevotellaceae, were associated with cytokines, rumen fermentation, and milk quality. The study highlights the interaction between rumen microbiota homeostasis and mammary gland health, indicating that rumen fermentation status influences serum inflammation and milk quality. Modulating rumen fermentation to enhance mammary gland immune function presents a viable strategy for sustainable dairy industry development with long-lived, highly productive cows.IMPORTANCEHigh somatic cell counts (SCCs) are a key biomarker of mastitis and are associated with decreased milk production and significant economic losses in dairy farming. This study systematically examines the relationship between elevated SCCs, rumen microbial dysbiosis, and host inflammatory responses, shedding light on the intricate interplay between microbial ecosystems and host physiology. The findings highlight the potential for microbiota-targeted interventions to reduce inflammation, improve milk composition, and enhance dairy cow productivity. Rather than presuming a direct causative link between SCC-associated dysbiosis and inflammation, this research focuses on their interdependent dynamics, offering a nuanced understanding of the complex biological mechanisms involved. This work advances knowledge of host-microbiota interactions in livestock, providing practical insights for the development of innovative strategies to manage mastitis and improve overall herd health. By adhering to One Health principles, this study underscores the significance of sustainable agricultural practices that prioritize animal welfare, environmental stewardship, and food security. These findings establish a robust foundation for future research into microbiota-driven solutions aimed at enhancing the health and productivity of dairy cattle.},
}
@article {pmid40104686,
year = {2025},
author = {Lin, X and Zhang, R and Cui, FQ and Hong, W and Yang, S and Ju, F and Xi, C and Sun, X and Song, L},
title = {Natural-selected plastics biodegradation species and enzymes in landfills.},
journal = {PNAS nexus},
volume = {4},
number = {3},
pages = {pgaf066},
pmid = {40104686},
issn = {2752-6542},
abstract = {Biodegradation is a promising and environmentally friendly strategy for plastic pollution management. Landfills decompose municipal solid waste, including almost 50% of global plastic debris and even some of the oldest synthetic plastics, fostering naturally selected plastic biodegradation. Herein, we present a global collection of plastic biocatalytic enzymes from landfills using metagenomics and machine learning. Metagenomic analysis identified 117 plastic-degrading genes, with 39 incorporated in 22 prokaryotic metagenome-assembled genomes (MAGs). A machine-learning approach predicted 978,107 candidate plastic-degrading genes, 712 of which were encoded respectively by 150 MAGs. Our results highlight landfills as reservoirs of diverse, naturally selected plastic-degrading microbes and enzymes, serving as references and/or models for biocatalysis engineering and in situ bioremediation of plastic pollution.},
}
@article {pmid40104674,
year = {2025},
author = {Nawrocki, EP and Petrov, AI and Williams, KP},
title = {Expansion of the tmRNA sequence database and new tools for search and visualization.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqaf019},
pmid = {40104674},
issn = {2631-9268},
mesh = {*RNA, Bacterial/genetics/chemistry ; Databases, Nucleic Acid ; Nucleic Acid Conformation ; Databases, Genetic ; Introns/genetics ; Sequence Analysis, RNA/methods ; },
abstract = {Transfer-messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.},
}
@article {pmid40104595,
year = {2025},
author = {Galanis, A and Papadimitriou, K and Moloney, GM},
title = {Editorial: Omics technologies and bioinformatic tools in probiotic research.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577852},
pmid = {40104595},
issn = {1664-302X},
}
@article {pmid40104149,
year = {2025},
author = {Wu, W and Xu, J and Ruan, J and Tian, B and Xuan, N},
title = {Metagenomic next-generation sequencing identifies native valve Aspergillus fumigatus endocarditis with cerebral involvement: a case report.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1487543},
pmid = {40104149},
issn = {2297-055X},
abstract = {Aspergillus endocarditis is a rare but highly fatal condition, particularly in immunocompromised patients. This case report describes a 74-year-old male with native valve Aspergillus fumigatus endocarditis and intracranial infection. Diagnosis was complicated by atypical presentation and negative blood cultures, but metagenomic next-generation sequencing (mNGS) enabled rapid identification of the pathogen. This case is notable for being the first to document Aspergillus fumigatus endocarditis with cerebral involvement confirmed by mNGS, highlighting the importance of early diagnosis and advanced diagnostic tools in improving outcomes.},
}
@article {pmid40103993,
year = {2025},
author = {Rai, A and Sirotiya, V and Ahirwar, A and Singh, G and Kawatra, R and Sharma, AK and Harish, and Vinayak, V},
title = {Textile dye removal using diatomite nanocomposites: a metagenomic study in photosynthetic microalgae-assisted microbial fuel cells.},
journal = {RSC advances},
volume = {15},
number = {11},
pages = {8300-8314},
pmid = {40103993},
issn = {2046-2069},
abstract = {In this study, Coomassie brilliant blue (CBB), brilliant green (BG), and rhodamine (Rh) dyes were used to simulate dye-rich wastewater. Adsorption and degradation of these dyes (2 μM, 10 μM, and 30 μM) on diatomite (DE) were evaluated under light (L) and dark (D) conditions. The adsorption of dye-DE composites followed pseudo-second-order kinetics at all concentrations and conditions had R [2] > 0.99, thus showing a good fit. The calculated equilibrium adsorption amount q e,(cal) was coherent with the value of experimental q e,(exp). The poorest adsorption and photocatalysis occurred at 30 μM, prompting the functionalization of dyes with TiO2 and Fe3O4 nanoparticles (NP(s)). The highest dye degradation efficiencies (DGeff) for 30 μM dyes were 86.79% (CBB-DE-Fe3O4, 72 h), 96.10% (BG-DE-TiO2, 52 h), and 81.74% (Rh-DE-TiO2, 48 h), with Rh-DE-TiO2 showing the fastest degradation. Functionalized DE-dye (30 μM) nanocomposites were further tested in a photosynthetic microalgae-assisted microbial fuel cell with dye-simulated wastewater at the anode (PMA-MFC-1 with CBB-DE-Fe3O4, PMA-MFC-2 with BG-DE-TiO2 and PMA-MFC-3 with Rh-DE-TiO2) and Asterarcys sp. GA4 microalgae at the cathode. In dark anode chambers, PMA-MFC-3 achieved the highest DGeff value of Rh dye as 88.23% and a polarization density of 30.06 mW m[-2], outperforming PMA-MFC-2 with BG dye and PMA-MFC-1 with CBB dye. The molecular identifier analysis of microbes in wastewater at the anode showed the dominance of Sphingobacteria and Proteobacteria in PMA-MFC-3 (Rh-DE-TiO2) and COD removal of 61.36%, highlighting its potential for efficient dye degradation and bioelectricity generation. Furthermore, PMA-MFC-3 simultaneously demonstrated a superior microalgal lipid yield of 3.42 μg g[-1] and an algal growth of 8.19 μg g[-1] at the cathode.},
}
@article {pmid40103786,
year = {2025},
author = {Wang, KM and Mu, N and Wang, HB},
title = {Intracranial infection in an adult caused by Mycoplasma hominis, diagnosed using mNGS technology: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1560635},
pmid = {40103786},
issn = {2296-858X},
abstract = {Mycoplasma hominis is a rare cause of adult central nervous system infections, posing significant diagnostic challenges due to its fastidious growth requirements and high false-negative rate in conventional cultures. We report a case of Mycoplasma hominis meningoencephalitis in a postpartum female, diagnosed via metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The patient presented with fever, headache, and progressive neurological deficits following a cesarean section. Neuroimaging revealed a subdural hematoma, and CSF analysis demonstrated an inflammatory response. mNGS identified Mycoplasma hominis, prompting targeted antimicrobial therapy with moxifloxacin and doxycycline, which led to significant clinical improvement. This case underscores the utility of mNGS in detecting rare intracranial infections and highlights the critical role of early pathogen identification in optimizing treatment outcomes.},
}
@article {pmid40103293,
year = {2025},
author = {Rasmussen, AN and Tolar, BB and Bargar, JR and Boye, K and Francis, CA},
title = {Metagenome-Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70060},
doi = {10.1111/1462-2920.70060},
pmid = {40103293},
issn = {1462-2920},
support = {DE- AC02-76SF00515//SLAC Accelerator Laboratory, U.S. Department of Energy, Biological and Environmental Research/ ; //Watershed Function Science Focus Area/ ; },
mesh = {*Archaea/genetics/classification/metabolism ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Nitrification ; *Metagenome ; *Ammonia/metabolism ; *Phylogeny ; Rivers/microbiology ; Oxidation-Reduction ; Nitrites/metabolism ; Genome, Bacterial ; },
abstract = {Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.},
}
@article {pmid40102971,
year = {2025},
author = {Luo, Z and Ou, H and Tan, Z and Jiao, J},
title = {Rumen-protected methionine and lysine supplementation to the low protein diet improves animal growth through modulating colonic microbiome in lambs.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {46},
pmid = {40102971},
issn = {1674-9782},
abstract = {BACKGROUND: Dietary protein level and amino acid (AA) balance are crucial determinants of animal health and productivity. Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants. The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine (RPMet) and rumen-protected lysine (RPLys) supplementation, however, it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process. Here, we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet (CON), a low-protein diet (LP) or a LP diet supplemented with RPMet and RPLys (LR).<br><br>RESULTS: The LP treatment decreased the average daily weight gain (ADG) in lambs, while the LR treatment tended to elicit a remission in ADG. The butyrate molar concentration was greater (P&#x2009;<&#x2009;0.05), while acetate molar concentration (P&#x2009;<&#x2009;0.05) was lower for lambs fed the LP and LR diets compared to those fed the CON diet. Moreover, the LP treatment remarkably decreased total AA concentration (P&#x2009;<&#x2009;0.05), while LR treatment showed an improvement in the concentrations of methionine, lysine, leucine, glutamate, and tryptophan. Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids (VFAs) and AAs in the colon were remarkably altered by three dietary treatments. Metagenomic binning identified distinct microbial markers for the CON group (Alistipes spp., Phocaeicola spp., and Ruminococcus spp.), LP group (Fibrobacter spp., Prevotella spp., Ruminococcus spp., and Escherichia coli), and LR group (Akkermansia muciniphila and RUG099 spp.).<br><br>CONCLUSIONS: Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids, enriche the&#xa0;beneficial bacteria in the colon, and&#xa0;thereby improve the growth performance of lambs.},
}
@article {pmid40102641,
year = {2025},
author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J},
title = {Information storage across a microbial community using universal RNA barcoding.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40102641},
issn = {1546-1696},
support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; },
abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.},
}
@article {pmid40102546,
year = {2025},
author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T},
title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9288},
pmid = {40102546},
issn = {2045-2322},
mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Escherichia coli/genetics/isolation &amp; purification ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Germany ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Anti-Bacterial Agents/pharmacology ; },
abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.},
}
@article {pmid40102379,
year = {2025},
author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T},
title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2683},
pmid = {40102379},
issn = {2041-1723},
support = {OPP1175213//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; },
abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.},
}
@article {pmid40101714,
year = {2025},
author = {Lynn, HM and Gordon, JI},
title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101005},
doi = {10.1016/j.crmeth.2025.101005},
pmid = {40101714},
issn = {2667-2375},
abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.},
}
@article {pmid40101514,
year = {2025},
author = {Zhang, X and Wu, L and Gu, L and Jiang, Q and He, Z and Qi, Y and Zheng, X and Xu, T},
title = {Dietary areca nut extract supplementation modulates the growth performance and immunity of Jiaji ducks (Cairina moschata).},
journal = {Poultry science},
volume = {104},
number = {5},
pages = {104971},
doi = {10.1016/j.psj.2025.104971},
pmid = {40101514},
issn = {1525-3171},
abstract = {Areca nut extract (ANE) has a variety of pharmacological effects on animals. Here, we investigated the influence of ANE on the slaughter performance and immune function of Jiaji ducks. One hundred and fifty 42-day-old healthy Jiaji ducks were randomly divided into 2 groups (5 replicates of 15 ducks each), named DCK group (control) and DNT group (treatment), respectively. Ducks in the DCK group were fed a basal diet and ducks in the DNT group were fed a basal food supplemented with 0.08 g ANE per kg of basal diet. Additionally, using proteomics, untargeted metabolomics, and metagenomics, we analyzed the impact of ANE on the protein profile of the spleen, the composition of plasma metabolites, and the structure of the cecal microbiota. The results showed that the dietary inclusion of ANE significantly increased the slaughter rate of Jiaji ducks. Proteomic analysis revealed 78 differentially expressed proteins in the spleens of ANE-treated birds, including 54 proteins up-regulated and 24 proteins down-regulated in the DNT group, mainly enriched in cell adhesion molecules and glutathione metabolic pathways. Untargeted metabolomic analysis revealed that 117 serum metabolites were differentially regulated between the ANE and DCK groups; meanwhile, KEGG pathway analysis indicated that these metabolites were mainly involved in arachidonic acid metabolism, phospholipase D signaling pathway and eicosanoids. Furthermore, a metagenomic analysis showed that the genus Methanobrevibacter was significantly downregulated in the ANE supplementation group. Combined, the results of the metagenomic and metabolomic analyses showed that the relative abundance of Prevotella was significantly lower in the ANE group than in the DCK group and that Prevotella was negatively correlated with the levels of the anti-inflammatory compound hydrocinnamic acid and the lipid metabolism regulator ganoderic acid A. This study provides a reference for the application of ANE as a supplement in the diet of Jiaji ducks.},
}
@article {pmid40101486,
year = {2025},
author = {Sun, J and Geng, L and Zhou, D and Teng, X and Chen, M},
title = {Gut microbiota participates in polystyrene microplastics-induced defective implantation through impairing uterine receptivity.},
journal = {Journal of environmental management},
volume = {380},
number = {},
pages = {124997},
doi = {10.1016/j.jenvman.2025.124997},
pmid = {40101486},
issn = {1095-8630},
abstract = {Microplastics (MPs) are widespread in global ecosystems and could pose risks to human health. However, crucial information on the impact of MP exposure on female reproductive health remains insufficient. In this study, we constructed an MP-exposure mice model through oral administration of polystyrene microplastics (PS-MPs) and found that it resulted in impaired uterine receptivity and defective implantation. An accumulation of plastic particles was detected in MP mice intestines. Metagenomic sequencing of feces samples indicated a structural and functional alteration of gut microbiota. Alistipes played a prominent role in MP biodegradation, while among the biodegradable functional genes, ACSL made the greatest contribution. Both had a significant increase in MP group, suggesting a potential occurrence of ferroptosis. Ferroptosis, a form of programmed cell death, is closely associated with uterine receptivity impairment and defective implantation. We detected MDA contents and ferroptosis-related proteins, and the results indicated the activation of ferroptosis in the process. Our research is the first to elucidate that exposure to MPs impairs uterine receptivity and results in deficient implantation, while also providing initial evidence that gut microbiota plays a critical role in this process.},
}
@article {pmid40100955,
year = {2025},
author = {Davis, BC and Vikesland, PJ and Pruden, A},
title = {Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08284},
pmid = {40100955},
issn = {1520-5851},
abstract = {Metagenomics holds promise as a comprehensive, nontargeted tool for environmental monitoring. However, one key limitation is that the quantitative capacity of metagenomics is not well-defined. Here, we demonstrated a quantitative metagenomic technique and benchmarked the approach for wastewater-based surveillance of antibiotic resistance genes. To assess the variability of low-abundance oligonucleotide detection across sample matrices, we spiked DNA reference standards (meta sequins) into replicate wastewater DNA extracts at logarithmically decreasing mass-to-mass percentages (m/m%). Meta sequin ladders exhibited strong linearity at input concentrations as low as 2 × 10[-3] m/m% (R[2] > 0.95), with little to no reference length or GC bias. At a mean sequencing depth of 94 Gb, the limits of quantification (LoQ) and detection were calculated to be 1.3 × 10[3] and 1 gene copy per μL DNA extract, respectively. In wastewater influent, activated sludge, and secondary effluent samples, 27.3, 47.7, and 44.3% of detected genes were ≤LoQ, respectively. Volumetric gene concentrations and log removal values were statistically equivalent between quantitative metagenomics and ddPCR for 16S rRNA, intI1, sul1, CTX-M-1, and vanA. The quantitative metagenomics benchmark here is a key step toward establishing metagenomics for high-throughput, nontargeted, and quantitative environmental monitoring.},
}
@article {pmid40100697,
year = {2025},
author = {Sun, J and Hirai, M and Takaki, Y and Evans, PN and Nunoura, T and Rinke, C},
title = {Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001351},
pmid = {40100697},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Metagenome ; Phylogeny ; Pacific Ocean ; Microbiota/genetics ; },
abstract = {Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.},
}
@article {pmid40099977,
year = {2025},
author = {López-Sánchez, R and Aguilar-Vera, A and Castillo-Ramírez, S},
title = {Metagenome-assembled genomes reveal novel diversity and atypical sources of a superbug.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0010625},
doi = {10.1128/spectrum.00106-25},
pmid = {40099977},
issn = {2165-0497},
abstract = {The genomic epidemiology of Acinetobacter baumannii has been based on culture-dependent whole-genome sequencing. However, this approach neglects sources that are not amenable to microbial culture. Here, we show that metagenome-assembled genomes (MAGs) are useful in appraising the neglected diversity of A. baumannii from unconventional sources. We analyzed 22 MAGs in the context of genomes from the main human international clones and some animal and plant isolates. Given the known ecology of the species, some of these MAGs came from unexpected sources, such as the New York City subway or a kitchen counter. Our global phylogeny, with 240 genomes, demonstrated that although some MAGs were associated with some human international clones, most of them were not and were distantly related to the human clones. Furthermore, we found that these MAGs have antibiotic-resistance genes. Our results show that many MAGs represent novel lineages with some important resistance genes coming from unexpected sources. Our work illustrates a powerful approach to studying the neglected diversity of this superbug from uncommon sources. We anticipate that in the coming years, MAGs will be employed to analyze unconventional sources for other important superbugs.IMPORTANCEThe genomic epidemiology of Acinetobacter baumannii has been based on cultivated bacterial isolates. This disregards A. baumannii diversity from sources not amenable to microbial culture. In this study, we demonstrate that metagenome-assembled genomes (MAGs) are very helpful in assessing the understudied diversity of A. baumannii from atypical sources. Our results show that many MAGs represent novel lineages with important resistance genes coming from unexpected sources. We anticipate that in the coming years, approaches similar to ours will be employed to delve into different sources for other important superbugs.},
}
@article {pmid40099899,
year = {2025},
author = {Nakao, R and Yamaguchi, T and Shibasaki, H and Saeki, J and Takahashi, A and Tominaga, R and Abe, K and Akeda, Y and Nakagawa-Nakamura, T and Nishino, T and Ishihara, K and Jinno-Oue, A and Inoue, S},
title = {Assessment of periodontitis vaccine using three different bacterial outer membrane vesicles in canine model.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0103324},
doi = {10.1128/msphere.01033-24},
pmid = {40099899},
issn = {2379-5042},
abstract = {UNLABELLED: Canines frequently develop periodontitis, which is similar and relevant to immunopathology and microbiology of human periodontitis. The aim of this study was to investigate whether bacterial outer membrane vesicle (OMV)-based periodontal vaccines induced humoral immune response in canines from a human vaccine development perspective. Porphyromonas gingivalis (Pg) and Treponema denticola (Td), two major periodontal pathobionts, were chosen as vaccine targets. Intranasal (IN) immunization with Pg OMVs and Td OMVs strongly elicited humoral immune responses against the two respective species in preparative mouse experiments, particularly when adjuvanted with a probiotic Escherichia coli derivative (EcNΔflhD)-derived OMVs. However, in beagles, intranasal immunization with the same Pg/Td/EcNΔflhD OMV vaccine insufficiently elicits humoral immune responses. Nevertheless, the subcutaneous booster with the same OMVs dramatically improved antibody responses in both systemic blood circulation and mucosal sites such as eyes, oral cavity, and upper and lower respiratory tracts. Metagenomic analysis of salivary microbiota revealed that the OMV vaccine might change the microbial composition, while not reducing the number of any periodontal pathobionts at least during the timeframe of the present beagle study. In in vitro Pg growth inhibition assay, serum samples from OMV-immunized beagles significantly inhibited growth of the gingipain-deficient strain but not the gingipain-expressing wild-type strain. Taken together, our data offer the trivalent OMV vaccine strategy by IN-prime/SC-boost regimen, which could elicit robust mucosal immune responses, while suggesting the requirement of revised periodontal vaccine regimen toward achievement of sterilizing immunity in the oral cavity.<br><br>IMPORTANCE: Bacterial outer-membrane vesicles (OMVs) are attractive for use as novel nanoparticle adjuvants, as well as delivery platforms. Periodontal diseases are the most prevalent oral diseases in humans and have serious health and economic burdens, greatly reducing quality of life. The aim of this study is to investigate the humoral immune responses to an OMV-based periodontal disease vaccine in beagles. The vaccine elicited strong mucosal immune responses when administered to beagles by a four-dose heterologous immunization (IN-IN-IN prime and subcutaneous [SC] boost). The OMV vaccine significantly altered the composition of the microbial community in the oral cavity. These findings suggest the utility of the intranasal (IN) prime followed by the SC boost regimen as a rational option to elicit robust humoral immune responses in canines, and most probably in humans as well. We here discuss the outcomes of beagle experiments, the mechanism behind immunological escape of Pg from host immunity, and a rational perspective toward sterilizing immunity in the oral cavity.},
}
@article {pmid40099881,
year = {2025},
author = {de Kleine, RH and Carbo, EC and Lexmond, WS and Zhou, XW and de Kroon, A and Mei, H and Bontemps, STH and Hennevelt, R and Gard, L and Sidorov, IA and Boers, SA and van den Heuvel, MC and Buddingh, EP and Kroes, ACM and de Meijer, VE and Schölvinck, EH and von Eije, KJ and Jochems, SP and de Vries, JJC},
title = {Metagenomic and transcriptomic investigation of pediatric acute liver failure cases reveals a common pathway predominated by monocytes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0391324},
doi = {10.1128/mbio.03913-24},
pmid = {40099881},
issn = {2150-7511},
abstract = {UNLABELLED: In 2022, a cluster of severe childhood hepatitis was detected primarily in Europe and North America, leading to a global alert by the World Health Organization. An association with adeno-associated virus 2 (AAV2) in conjunction with human adenoviruses was found. Five percent of the cases progressed to acute liver failure, necessitating transplantation. The mechanism of disease that accounts for fulminant liver failure in these patients remains incompletely described. An upsurge was observed of in the five total cases of acute liver failure that presented to the Dutch national referral center for pediatric liver transplantation in the spring of 2022. An in-depth molecular analysis of the mechanism of pediatric acute liver failure was performed using targeted transcriptomics and metagenomics to identify any virus present in the cases, immune profile haplotypes, and differentially expressed gene groups. Explanted liver tissue and plasma samples (n = 15) were subjected to viral metagenomic and human transcriptomic profiling, targeting >600 inflammatory genes. Liver transcriptomic signatures of transplanted cases were compared with those of pediatric controls from a liver biobank (n = 6). AAV2, adenoviruses, and herpesviruses were detected in liver explant tissue and plasma samples of the cases. Epstein-Barr virus and varicella zoster virus infection with pathognomonic clinical symptomatology preceded liver failure in two respective cases. AAV2 was detected in one-third of control livers. Excessive activation of monocyte pathways was detected in liver explants from cases compared with controls. Remarkably, this signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases. Our multi-omic findings suggest a common transcriptomic profile, with an upregulation of monocyte pathways in the presented transplanted cases, which had similar severe clinical outcomes. In the cohort presented, AAV2 was not exclusively associated with acute liver failure, suggesting that other processes may have contributed to a uniform cascade of irreversible pathology.<br><br>IMPORTANCE: Since the appearance of the cluster of pediatric hepatitis of unknown origin in 2022, several groups have reported an association of adenoviruses and AAV2 in a high number of cases in contrast to controls. The adenoviruses detected were heterogeneous in both species-adenovirus C and F-and sequences. The mechanisms of disease that accounts for fulminant liver failure, occurring in 5% of pediatric hepatitis cases, remain incompletely described. The current study adds to previous data by including pediatric acute liver failure cases during the upsurge, enabling the analyses of inflammation expression profiles in cases with different viruses in relation to pediatric controls. This led to the discovery of transcriptome upregulation of monocyte pathways in liver explants from the cases. This inflammatory transcriptomic signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases.},
}
@article {pmid40099113,
year = {2025},
author = {Tomasella, F and Pizzi, C},
title = {MetaComBin: combining abundances and overlaps for binning metagenomics reads.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1504728},
pmid = {40099113},
issn = {2673-7647},
abstract = {INTRODUCTION: Metagenomics is the discipline that studies heterogeneous microbial samples extracted directly from their natural environment, for example, from soil, water, or the human body. The detection and quantification of species that populate microbial communities have been the subject of many recent studies based on classification and clustering, motivated by being the first step in more complex pipelines (e.g., for functional analysis, de novo assembly, or comparison of metagenomes). Metagenomics has an impact on both environmental studies and precision medicine; thus, it is crucial to improve the quality of species identification through computational tools.<br><br>METHODS: In this paper, we explore the idea of improving the overall quality of metagenomics binning at the read level by proposing a computational framework that sequentially combines two complementary read-binning approaches: one based on species abundance determination and another one relying on read overlap in order to cluster reads together. We called this approach MetaComBin (metagenomics combined binning).<br><br>RESULTS AND DISCUSSION: The results of our experiments with the MetaComBin approach showed that the combination of two tools, based on different approaches, can improve the clustering quality in realistic conditions where the number of species is not known beforehand.},
}
@article {pmid40098591,
year = {2025},
author = {Hernández-Trujillo, PN and Lopez-Barón, CA and Arévalo-Pinzón, G and Trujillo-Güiza, ML and González-Duque, MI and Flórez, AM and Franco, DC and Vanegas, J},
title = {Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach.},
journal = {HIV medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/hiv.70014},
pmid = {40098591},
issn = {1468-1293},
support = {2022218//Universidad Antonio Nari&#xf1;o/ ; },
abstract = {INTRODUCTION: The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.<br><br>MATERIALS AND METHODS: In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.<br><br>RESULTS: Initially, 90 samples were collected, with 20 discarded due to having less than 200&#x2009;ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p&#x2009;=&#x2009;0.45) and beta diversity (PERMANOVA R&#x2009;=&#x2009;-0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.<br><br>CONCLUSION: Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.},
}
@article {pmid40098558,
year = {2025},
author = {Di Rienzi, SC and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA},
title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {6},
pages = {e70408},
doi = {10.1096/fj.202401669R},
pmid = {40098558},
issn = {1530-6860},
support = {T15 LM007093/LM/NLM NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; //Weston Family Foundation (WFF)/ ; //BioGaia/ ; },
mesh = {*Limosilactobacillus reuteri/metabolism ; *Enteroendocrine Cells/metabolism ; *Enterocytes/metabolism/microbiology ; Humans ; Organoids/metabolism ; Gastrointestinal Hormones/metabolism/genetics ; Gastrointestinal Microbiome ; Animals ; },
abstract = {Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.},
}
@article {pmid40098182,
year = {2025},
author = {Rodríguez, V and Bartholomäus, A and Liebner, S and Oses, R and Scholten, T and Wagner, D},
title = {Microbial transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {31},
pmid = {40098182},
issn = {2524-6372},
support = {72200201//BECAS Chile (ANID)/ ; SCHO 739/17//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites. We characterized pedogenetic microbial processes and how their gene expression differs between soils from arid and semiarid sites under a sixteen-week climate simulation experiment using metagenomic and metatranscriptomic approaches.<br><br>RESULTS: We found that an intense functional response is triggered under humid climate conditions in the arid site compared to the semiarid site, which showed greater resilience. The arid site undergoes higher transcription of genes involved in soil aggregate formation, phosphorus metabolism, and weathering, potentially adapting the development of arid sites to climate change. Additionally, a transcriptional reconfiguration linked to soil carbon and nitrogen dynamics suggests that soil microorganisms use available organic resources alongside autotrophy in response to increased moisture. Pseudomonadota and Actinomycetota dominated the overall transcriptional profile and specific functions associated with the early stages of soil development in both sites.<br><br>CONCLUSIONS: Our findings highlight the rapid activation of pathways related to pedogenesis under humid conditions in arid sites, potentially driven by their metabolic requirements and environmental stressors, influencing soil development dynamics under global climate change.},
}
@article {pmid40098172,
year = {2025},
author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L},
title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {343},
pmid = {40098172},
issn = {1479-5876},
mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/drug therapy/microbiology ; *Immunotherapy ; Treatment Outcome ; Male ; Female ; Metagenome/genetics ; },
abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.<br><br>METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.<br><br>RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy&#x2009;>&#x2009;90% and AUC ROC&#x2009;>&#x2009;95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.<br><br>CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.},
}
@article {pmid40097931,
year = {2025},
author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D},
title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {150},
pmid = {40097931},
issn = {1471-2180},
mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; *Metagenomics/methods ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Microbiota/genetics/drug effects ; Aged ; Genome, Bacterial/genetics ; Adult ; },
abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.},
}
@article {pmid40097230,
year = {2025},
author = {Nair, SS and Kutty Narayanan, A and Nair, K and Mallick, S and Zackariah, NM and Biswas, L and Praseedom, R and G Nair, BK and Surendran, S},
title = {Microbiota-directed intervention in living donor liver transplant recipients: protocol for a randomised double-blind placebo-controlled trial.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e092984},
doi = {10.1136/bmjopen-2024-092984},
pmid = {40097230},
issn = {2044-6055},
mesh = {Humans ; *Liver Transplantation ; *Living Donors ; Double-Blind Method ; *Synbiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Acute-On-Chronic Liver Failure/therapy ; Probiotics/therapeutic use ; Adult ; Postoperative Complications/microbiology ; Male ; Female ; },
abstract = {INTRODUCTION: Acute-on-chronic liver failure (ACLF) patients have the highest propensity for post-liver transplantation (LT) infections and mortality. Liver-associated diseases have been one of the primary targets for synbiotic therapy to augment immunity and mitigate infections. However, despite multiple studies showing benefits of synbiotics in liver diseases, data on their use following LT are sparse.<br><br>METHODS AND ANALYSIS: This randomised placebo-controlled study aims to assess the impact of synbiotics in ACLF patients undergoing living donor liver transplantation (LDLT). Following randomisation by computer-generated block number sequence, 3&#x2009;days prior to LDLT, the intervention arm will receive standard medical treatment and synbiotics (VSL#3 a probiotic, and Yogut, prebiotic and probiotic combination) for 6&#x2009;weeks, while the control arm will receive standard medical treatment with a placebo. The patients will be followed up for 6&#x2009;months to study the clinical and biochemical outcomes. The primary objective is to compare the difference in the occurrence of infectious complications between the patients who receive synbiotics versus placebo during the 6-month period following LDLT. The secondary objectives include assessing the qualitative and quantitative change in microbiota with synbiotics and LDLT, adverse reactions due to synbiotics, and post-LT morbidity and mortality. The minimum sample size comes to 71 in each group. The first 50 patients in the study protocol will undergo gut microbiome analysis using 16s metagenomic and nanopore sequencing to analyse the microbial composition before starting synbiotics/placebo and at 6 weeks after LDLT.<br><br>ETHICS AND DISSEMINATION: The study is approved by the Research Ethics Committee of Amrita Institute of Medical Sciences, Kochi, India (IEC-AIMS-2022-GISUR-203) and registered in the Clinical Trial Registry of India (CTRI) CTRI/2022/10/046327. The results of the trial will be disseminated by presentation at national/international conferences and publication in peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBER: CTRI/2022/10/046327 - Clinical Trial Registry of India.},
}
@article {pmid40096869,
year = {2025},
author = {Xing, X and Zhu, J and Li, Z and Zhang, G and Li, W and Tan, H and Xie, B and Yang, Y and Zhao, S and Ding, Y and You, H},
title = {Increasing the light-dark ratio enhances nitrogen removal performance by altering the mechanism in photogranules.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132400},
doi = {10.1016/j.biortech.2025.132400},
pmid = {40096869},
issn = {1873-2976},
abstract = {Photogranules provide a cost-effective solution for treating mariculture wastewater. The impact of light: dark ratios on nitrogen removal needs further study. We tested four photogranular reactors with different light: dark ratios and found that higher ratios increased total inorganic nitrogen (TIN) removal rate, achieved 99 ± 0 % every 48 h at a 5.5 h:0.5 h ratio. Kinetic and metagenomic analyses showed that increased TIN removal was mainly due to a significant transformation in the nitrogen removal mechanism of photogranules. At 5.5 h:0.5 h, diatoms replaced the outer cyanobacteria, causing nitrifying bacteria to disappear via direct and indirect inhibition. In addition, the mechanisms by which photogranules remove nitrate nitrogen are diverse. Adjusting the light: dark ratio could change the nitrogen removal mechanism of photogranules in mariculture wastewater treatment and enhance their nitrogen removal performance. This offered insights into controlling light - related parameters of photogranules for practical engineering applications.},
}
@article {pmid40096540,
year = {2025},
author = {Zhang, Q and Li, J and Tuo, J and Liu, S and Liu, Y and Liu, P and Ye, L and Zhang, XX},
title = {Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf051},
pmid = {40096540},
issn = {1751-7370},
abstract = {Bacteria have evolved various antiviral defense systems to protect themselves, but how defense systems respond to the variation of bacteriophages in complex bacterial communities and whether defense systems function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge samples from two full-scale wastewater treatment plants over six years and found that defense systems were widespread in activated sludge, with 91.1% of metagenome-assembled genomes having more than one complete defense system. The stability of the bacterial community was maintained under the fluctuations of the phage community, and defense system abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of defense systems to phage fluctuations. The rapid turnover of CRISPR spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical metagenome-assembled genomes showing significant differences in defense system composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities, and reveals the key roles of defense systems in stabilizing bacterial community structure and function.},
}
@article {pmid40095061,
year = {2025},
author = {Laiho, JE and Oikarinen, S and Morfopoulou, S and Oikarinen, M and Renner, A and Depledge, D and Ross, MC and Gerling, IC and Breuer, J and Petrosino, JF and Plagnol, V and Pugliese, A and Toniolo, A and Lloyd, RE and Hyöty, H and , },
title = {Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.},
journal = {Diabetologia},
volume = {},
number = {},
pages = {},
pmid = {40095061},
issn = {1432-0428},
support = {R01-AI50237//National Institutes of Health, USA/ ; personal grant for JEL//Diabetestutkimuss&#xe4;&#xe4;ti&#xf6;/ ; personal grants for JEL//Yrj&#xf6; Jahnssonin S&#xe4;&#xe4;ti&#xf6;/ ; MO//Yrj&#xf6; Jahnssonin S&#xe4;&#xe4;ti&#xf6;/ ; Grant#2018PG-T1D053//Leona M. and Harry B. Helmsley Charitable Trust/ ; G-2108-04793//Leona M. and Harry B. Helmsley Charitable Trust/ ; 97013//European Foundation for the Study of Diabetes/ ; 25-2012-770//JDRF/United States ; JDRF 25-2012-516//JDRF/United States ; nPOD: 5-SRA-2018-557-Q-R//JDRF/United States ; RRID:SCR_014641//network for Pancreatic Organ donors with Diabetes, nPOD/ ; personal grant for JEL//Pirkanmaan Rahasto/ ; Persistent Virus Infection in Diabetes Network [PE//Seventh Framework Programme/ ; for HH//Sigrid Jus&#xe9;liuksen S&#xe4;&#xe4;ti&#xf6;/ ; 288671//Research Council of Finland/ ; personal grants for JEL//P&#xe4;ivikki ja Sakari Sohlbergin S&#xe4;&#xe4;ti&#xf6;/ ; MO//P&#xe4;ivikki ja Sakari Sohlbergin S&#xe4;&#xe4;ti&#xf6;/ ; },
abstract = {AIMS/HYPOTHESIS: The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas and other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of pancreas samples collected to date. The aim of the current work was to examine the presence of enterovirus RNA in pancreas and lymphoid tissues of organ donors with and without type 1 diabetes.<br><br>METHODS: We analysed pancreas, spleen, pancreatic lymph nodes and duodenum samples from the following groups: (1) donors with type 1 diabetes (n=71) with (n=35) or without (n=36) insulin-containing islets; (2) donors with single or double islet autoantibody positivity without diabetes (n=22); and (3) autoantibody-negative donors without diabetes (control donors) (n=74). Five research laboratories participated in this collaborative effort using approaches for unbiased discovery of RNA viruses (two RNA-Seq platforms), targeted detection of Enterovirus A-D species using RT-PCR, and tests for virus growth in cell culture.<br><br>RESULTS: Direct RNA-Seq did not detect virus signal in pancreas samples, whereas RT-PCR detected enterovirus RNA confirmed by sequencing in low amounts in pancreas samples in three of the five donor groups: donors with type 1 diabetes with insulin-containing islets, 16% (5/32) being positive; donors with single islet autoantibody positivity, 53% (8/15) being positive; and non-diabetic donors, 8% (4/49) being positive. Detection of enterovirus RNA was significantly more frequent in single islet autoantibody-positive donors compared with donors with type 1 diabetes with insulin-deficient islets (p<0.001) and control (non-diabetic) donors (p=0.004). In some donors, pancreatic lymph nodes were also positive. RT-PCR detected enterovirus RNA also in the spleen of a small number of donors and virus enrichment in susceptible cell lines before RT-PCR resulted in much higher rate in spleen positivity, particularly in donors with type 1 diabetes. Interestingly, the enterovirus strains detected did not cause a typical lytic infection, possibly reflecting their persistence-prone nature.<br><br>CONCLUSIONS/INTERPRETATION: This was the largest coordinated effort to examine the presence of enterovirus RNA in the pancreas of organ donors with type 1 diabetes, using a multitude of assays. These findings are consistent with the notion that donors with type 1 diabetes and donors with islet autoantibodies may carry a low-grade enterovirus infection in the pancreas and lymphoid tissues.},
}
@article {pmid40094563,
year = {2025},
author = {Cheng, W and Yi, L and Xu, T and Xie, Y and Zhu, J and Guan, X and Li, Q and Huang, Y and Zhao, Y and Zhao, S},
title = {The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs.},
journal = {Animal biotechnology},
volume = {36},
number = {1},
pages = {2471785},
doi = {10.1080/10495398.2025.2471785},
pmid = {40094563},
issn = {1532-2378},
mesh = {Animals ; *Panax notoginseng/microbiology ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves ; *Plant Stems ; Drug Resistance, Microbial/genetics ; Animal Feed/analysis ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/classification ; Genes, Bacterial/genetics ; Cecum/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.},
}
@article {pmid40094561,
year = {2025},
author = {Gai, Y and Liu, S and Zhang, Z and Wei, J and Wang, H and Liu, L and Bai, Q and Qin, Q and Zhao, C and Zhang, S and Xiang, N and Zhang, X},
title = {Integrative Approaches to Soybean Resilience, Productivity, and Utility: A Review of Genomics, Computational Modeling, and Economic Viability.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/plants14050671},
pmid = {40094561},
issn = {2223-7747},
abstract = {Soybean is a vital crop globally and a key source of food, feed, and biofuel. With advancements in high-throughput technologies, soybeans have become a key target for genetic improvement. This comprehensive review explores advances in multi-omics, artificial intelligence, and economic sustainability to enhance soybean resilience and productivity. Genomics revolution, including marker-assisted selection (MAS), genomic selection (GS), genome-wide association studies (GWAS), QTL mapping, GBS, and CRISPR-Cas9, metagenomics, and metabolomics have boosted the growth and development by creating stress-resilient soybean varieties. The artificial intelligence (AI) and machine learning approaches are improving genetic trait discovery associated with nutritional quality, stresses, and adaptation of soybeans. Additionally, AI-driven technologies like IoT-based disease detection and deep learning are revolutionizing soybean monitoring, early disease identification, yield prediction, disease prevention, and precision farming. Additionally, the economic viability and environmental sustainability of soybean-derived biofuels are critically evaluated, focusing on trade-offs and policy implications. Finally, the potential impact of climate change on soybean growth and productivity is explored through predictive modeling and adaptive strategies. Thus, this study highlights the transformative potential of multidisciplinary approaches in advancing soybean resilience and global utility.},
}
@article {pmid40094559,
year = {2025},
author = {Gao, S and Wei, G and Chang, Y and Yin, Y and Wei, Q and Shi, Y},
title = {Multiomic Analysis of Environmental Effects and Nitrogen Use Efficiency of Two Potato Varieties Under High Nitrogen Conditions.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/plants14050633},
pmid = {40094559},
issn = {2223-7747},
support = {CARS-09&#xff1b;2022ZXJ06B01&#xff1b;JD2023GJ01-09&#xff1b;LH2021C027//China Agriculture Research Systems&#xff1b;Heilongjiang Province Scientific and Technological Project&#xff1b;Key R&amp;D projects of Heilongjiang Province in 2023&#xff1b;Natural Science Foundation of Heilongjiang Province/ ; },
abstract = {Potato (Solanum tuberosum L.) has high nutritional value and strong adaptability and plays an extremely important role in global food security. Excessive use of nitrogen (N) fertilizer in potato production has increased costs and environmental pollution. In this study, the N use efficiency (NUE) of two potato varieties (DXY and DN310) was determined under high nitrogen conditions. The N use efficiency of DXY was relatively high. The differences between the rhizosphere microbial population groups of the two varieties were determined using the metagenomic sequencing method. The genes related to N efficiency were jointly identified using transcriptome and metabolome analyses. Significant difference was observed between the two varieties of microorganisms, leading to different rhizosphere microorganisms. Compared with DN310, the roots of DXY retained more available N and generated less NO. Additionally, DXY exhibited relatively low disease susceptibility. Combined transcriptome and metabolome analyses indicated that the differentially expressed metabolites in the two different varieties under high N conditions were mainly enriched in amino acid metabolism and sugar metabolism pathways. Using weighted gene co-expression network analysis, two genes associated with N fertilizer response were identified: PGSC0003DMG400025888 and PGSC0003DMG400017276. This study provided valuable insights into breeding potato varieties with high N efficiency.},
}
@article {pmid40094201,
year = {2025},
author = {Masaadeh, AH and Eletrebi, M and Parajuli, B and De Jager, N and Bosch, DE},
title = {Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2479774},
doi = {10.1080/19490976.2025.2479774},
pmid = {40094201},
issn = {1949-0984},
mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; *Disease Progression ; *Colorectal Neoplasms/microbiology/pathology ; *Bacteria/classification/isolation &amp; purification/genetics ; Inflammatory Bowel Diseases/microbiology/pathology/complications ; Colitis-Associated Neoplasms/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; Colitis/microbiology/pathology ; Metagenomics ; Intestinal Mucosa/microbiology/pathology ; },
abstract = {Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.},
}
@article {pmid40093613,
year = {2025},
author = {Huang, X and Yuan, T and Huang, Y and Qazi, IH and Liu, J},
title = {Analysis of causal pathogens of mulberry bacterial blight in samples collected from eight provinces of China using culturomics and metagenomic sequencing methods.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1517050},
pmid = {40093613},
issn = {1664-462X},
abstract = {Mulberry bacterial blight (MBB) is a complex and one of the devastating diseases of mulberry that causes serious reduction in the yield and quality of mulberry. In recent years, the transformation of sericulture industry, mulberry production system, and increasing seedling trade have resulted in the spread of MBB to different parts of China, posing a major economic threat to the farmers and industry. This study investigated the occurrence of MBB in eight provinces of China during years 2023 and 2024. The MBB disease samples were collected and the composition of the MBB pathogenic microbiome was analyzed by combining culturomics and metagenomic sequencing methods. A total of 498 bacterial strains were isolated and identified through culturomics, and then 109 suspected pathogen strains were preliminarily screened based on metagenomic sequencing data. Finally, 10 pathogens including, Pseudomonas syringae, P. fulva, P. fluorescens, Pantoea ananatis, Pectobacterium parvum, P. carotovorum, Flavobacterium fluviale, Citrobacter portucalensis, Klebsiella grimontii, Stenotrophomonas maltophilia, were identified through Koch's postulates. Based on the distribution pattern of pathogens and the changes in the microbiome community of mulberry following infection with P. syringae, we infer that P. syringae, and P. fulva are important pathogens of MBB. In addition, based on the analysis of meteorological data, different bacteria showed adaptability to different environments, leading to differences in the pathogens of MBB under different climate conditions and latitudes. The data presented herein provides a foundation for understanding the occurrence, spatial distribution and pathogenic mechanism of MBB and its major pathogens.},
}
@article {pmid40093185,
year = {2025},
author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, J and Kassaro, M and Holm, JB and Ma, B and Ravel, J},
title = {VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.04.641479},
pmid = {40093185},
issn = {2692-8205},
abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.},
}
@article {pmid40092793,
year = {2025},
author = {Abakumov, S and Ruppeka-Rupeika, E and Chen, X and Bouwens, A and Leen, V and Dedecker, P and Hofkens, J},
title = {DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.},
journal = {ACS omega},
volume = {10},
number = {9},
pages = {9224-9232},
pmid = {40092793},
issn = {2470-1343},
abstract = {DNA optical mapping is a powerful technique commonly used for structural variant calling and genome assembly verification. Despite being inherently high-throughput, the method has not yet been applied to highly complex settings such as species identification in microbiome analysis due to the lack of alignment algorithms that can both assign large numbers of reads in minutes and handle large database size. In this work, we present a novel genomic classification pipeline based on deep convolutional neural networks for optical mapping data (DeepMAP), which can perform fast and accurate assignment of individual optical maps to their respective genomes. We furthermore achieve a superior performance of DeepMAP in the presence of evolutionary divergent sequences, making it robust to the presence of unknown strains within metagenomic samples. We evaluate DeepMAP on genomic DNA extracted from bacterial mixtures, reaching species-level resolution with true positive rates of around 75% and a false positive rate of less than 1%, with measured classification speeds significantly outpacing those of previously developed approaches for high-density optical mapping data alignment.},
}
@article {pmid40092035,
year = {2025},
author = {Li, S and Liu, Y and Yang, X and Yang, Y and Peng, J and Xu, Y and Wei, J},
title = {Spatiotemporal composition and diversity of endophyte communities in Dracaena cambodiana on Hainan Island.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1540669},
pmid = {40092035},
issn = {1664-302X},
abstract = {INTRODUCTION: Dracaena cambodiana produces a red resin known as Dragon's blood, which is used worldwide in traditional medicine and as a dye. The role of endophytes in the resin-formation process remains underexplored. Understanding the endophyte communities and their functional roles in resin production could enable the development of efficient induction techniques for resin production.<br><br>METHODS: In this study, ITS and metagenomic sequencing analyzed endophyte communities' characteristics and functional traits in different tissues and D. cambodiana across multiple wild populations on Hainan Island.<br><br>RESULTS: We identified distinct fungal genera that were dominant in different tissues. Following injury, we observed significant changes in the expression of endophytic fungal genes. These changes indicated that metabolic pathways associated with resin metabolism, sucrose metabolism, signal transduction, and phenylalanine metabolism were likely involved in resin formation. Additionally, several glycosylation gene families were upregulated in the post-injury endophytic communities, which suggests a role in flavonoid transport and the reduction of autotoxic effects.<br><br>DISCUSSION: Our results suggest that endophytes play a vital role in the resin-formation process of D. cambodiana. Isolating specific endophytes or using synthetic communities could potentially improve resin yields and avoid pathogenic fungi, ensuring safety. The findings from this study provide a theoretical basis for the development of high-efficiency resin induction techniques by targeting the dynamic changes in endophyte communities across tissues, regions, and resin formation stages.},
}
@article {pmid40091996,
year = {2025},
author = {Chandra Nayak, S and Latha, PB and Kandanattu, B and Pympallil, U and Kumar, A and Kumar Banga, H},
title = {The Oral Microbiome and Systemic Health: Bridging the Gap Between Dentistry and Medicine.},
journal = {Cureus},
volume = {17},
number = {2},
pages = {e78918},
pmid = {40091996},
issn = {2168-8184},
abstract = {The oral microbiome, consisting of a mixture of bacteria, fungi, and viruses, is an important contributor to oral and systemic health. Microbial balance disruptions are associated with oral pathologies like dental caries and periodontitis as well as systemic diseases such as cardiovascular diseases, adverse pregnancy outcomes, and respiratory diseases. This review explores the mechanistic pathways linking oral dysbiosis to systemic inflammation, endothelial dysfunction, and immune modulation. The roles of key microbial species in health and disease are analyzed, with an emphasis on how hematogenous dissemination leads to systemic pathologies through inflammatory signaling. Also, advances in high throughput sequencing are discussed, as well as microbial diversity and its implications for diagnostics and therapeutics. The review highlights the potential of oral microbiota-targeted interventions to mitigate systemic diseases through dentistry and medicine integration, by throwing light on interdisciplinary strategies. Future work should focus on the evaluation of the mechanisms by which the oral microbiome plays a role in systemic diseases through the integration of multi-omics approaches such as metagenomics, transcriptomics, and metabolomics. Furthermore, clinical trials need to be designed in a way to evaluate the efficacy of microbiome-targeted therapies in the prevention of cardiovascular diseases, adverse pregnancy outcomes, and autoimmune disorders.},
}
@article {pmid40091534,
year = {2025},
author = {Lu, YM and Lu, JQ and Zhao, Q and Chen, J and Xiong, JB},
title = {Pathogenic mechanisms of Enterocytozoon hepatopenaei through the parasite-gut microbiome-shrimp (Litopenaeus vannamei) physiology axis.},
journal = {Zoological research},
volume = {46},
number = {2},
pages = {401-413},
doi = {10.24272/j.issn.2095-8137.2024.411},
pmid = {40091534},
issn = {2095-8137},
mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/physiology ; *Enterocytozoon/physiology/genetics ; Host-Parasite Interactions ; },
abstract = {The progressive impact of Enterocytozoon hepatopenaei (EHP) infection on gut microbial function in Litopenaeus vannamei remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.},
}
@article {pmid40091365,
year = {2025},
author = {Norgan, AP and Enninga, EAL and Fedyshyn, B and Wolf, M and Goldstein, JA and Shanes, ED},
title = {Enterovirus Placentitis is an Underrecognized Cause of Placental Pathology.},
journal = {The American journal of surgical pathology},
volume = {},
number = {},
pages = {},
doi = {10.1097/PAS.0000000000002378},
pmid = {40091365},
issn = {1532-0979},
abstract = {The placenta is susceptible to infection by a number of viral pathogens, including severe acute respiratory syndrome coronavirus 2, which is associated with poor fetal outcomes. The histologic pattern of injury, termed severe acute respiratory syndrome coronavirus 2 placentitis, is characterized by a triad of increased perivillous fibrin deposition, intervillous histiocytes, and trophoblast necrosis. While the etiology of massive perivillous fibrin deposition (MPVFD) is mostly unknown, previous case reports of MPVFD in association with maternal Enterovirus (ENT) suggest that a subset of these cases are a consequence of undiagnosed viral infection. We evaluated 46 placentas collected between 2011 and 2022 with a diagnosis of MPVFD (n = 41) or chronic histiocytic intervillositis (CHI; n = 4). Combining methods of pan-viral metagenomic sequencing and targeted viral PCR, we detected Enterovirus DNA in 8 of 45 (18%) MPVFD and/or CHI cases. Seven of these positive cases were from MPVFD, and 1 was associated with a CHI diagnosis. Enterovirus A species (n = 7) were commonly identified, whereas one case had Enterovirus B. Histologic evaluation of these cases, including immunohistochemical staining for CD68, demonstrated increased intervillous histiocytes in Enterovirus-positive MPVFD cases in comparison with Enterovirus-negative, as well as evidence of trophoblast necrosis. Thus, we favor the terminology Enterovirus placentitis to describe this pathology. Overall, these findings suggest that Enterovirus is an underrecognized etiology of histologic MPVFD and, possibly, CHI. Further study to evaluate the recurrence risk of Enterovirus placentitis in comparison to MPVFD may help inform future fertility planning in patients with these diagnoses.},
}
@article {pmid40091083,
year = {2025},
author = {Honda, H and Suzuki, T and Kitajima, M and Kondo, NI and Miyata, K and Utsumi, S and Yamada, M},
title = {The new era shaped by environmental genome monitoring - symposium of the japanese environmental mutagen and genome society (JEMS), 2024.},
journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society},
volume = {47},
number = {1},
pages = {6},
pmid = {40091083},
issn = {1880-7046},
abstract = {The symposium "The New Era Shaped by Environmental Genome Monitoring," held in December 2024 by the Japanese Environmental Mutagen and Genome Society (JEMS), aimed to explore the interdisciplinary collaborations that are essential for the development of new scopes in environmental genome monitoring. This event highlighted the necessity of integrating mutagenicity research with ecological assessments to enhance public health and biodiversity conservation. Presentations focused on the evolving landscape of environmental genomics, including metagenomic analyses for antibiotic resistance, viral genomic surveillance in wastewater, and innovations in noninvasive biodiversity and stress monitoring through environmental DNA and RNA. This report summarizes the key discussions and presentations from the symposium, underscoring the critical role of environmental genome monitoring in shaping future safety research.},
}
@article {pmid40090954,
year = {2025},
author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E},
title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2595},
pmid = {40090954},
issn = {2041-1723},
support = {2018-02835//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-05771//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-03482//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-00945//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; },
abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.},
}
@article {pmid40090735,
year = {2025},
author = {Yabuki, A and Fujii, C and Yazaki, E and Tame, A and Mizuno, K and Obayashi, Y and Takao, Y},
title = {Massive RNA Editing in Ascetosporean Mitochondria.},
journal = {Microbes and environments},
volume = {40},
number = {1},
pages = {},
doi = {10.1264/jsme2.ME24070},
pmid = {40090735},
issn = {1347-4405},
mesh = {*RNA Editing ; *Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing ; Eukaryota/genetics/classification ; Phylogeny ; Adenosine Deaminase/genetics/metabolism ; },
abstract = {Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.},
}
@article {pmid40090521,
year = {2025},
author = {Kitaya, S and Horiba, K and Kabata, T and Iyobe, T and Hashino, M and Yamazaki, H and Takahashi, Y and Zaimoku, Y and Oshima, M and Kanamori, H},
title = {The contribution of metagenomic next-generation sequencing to a diagnosis of gas-producing Fusobacterium-induced septic hip arthritis: A case report.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102681},
doi = {10.1016/j.jiac.2025.102681},
pmid = {40090521},
issn = {1437-7780},
abstract = {Pyogenic arthritis with gas gangrene triggered by intra-articular steroid injections can occasionally result in fatal complications. Clostridium perfringens is typically the causative pathogen, with infections caused by Fusobacterium sp. being relatively rare. Fusobacterium sp. are known to cause pyogenic infections, but due to their extreme sensitivity to oxygen, they can be difficult to detect with traditional culture methods. Recently, metagenomic next-generation sequencing (mNGS) has gained attention as an alternative diagnostic tool to traditional culture, enabling rapid identification of causative pathogens in infectious diseases, including pyogenic arthritis. Its use is illustrated in the following case report, which demonstrates the diagnostic utility of mNGS in pyogenic arthritis with gas gangrene triggered by an intra-articular steroid injection. Using mNGS as a complement to conventional culture testing allows for a more precise narrowing-down of causative pathogens, enabling targeted therapy and improving patient outcomes. This approach may also help reduce the use of broad-spectrum antibiotics and prevent the emergence of antibiotic-resistant bacteria.},
}
@article {pmid40090450,
year = {2025},
author = {Wu, H and Chen, S and Deng, Y and Shen, J and Xu, Y and Wen, T and Yuan, J and Shen, Q and Xue, C},
title = {Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126048},
doi = {10.1016/j.envpol.2025.126048},
pmid = {40090450},
issn = {1873-6424},
abstract = {Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1%. By contrast, ARG levels surged by 17.3% and 10.9% on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8% reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63% of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.},
}
@article {pmid40090148,
year = {2025},
author = {Dong, KY and Yang, CX and Pang, JL and Chang, RR and Chen, KY and Yao, W and Huang, BC and Jin, RC},
title = {Antibiotics shape the core microbial community distribution between floc and biofilm in an endogenous partial denitrification system: Insight from metabolic pathway.},
journal = {Water research},
volume = {280},
number = {},
pages = {123491},
doi = {10.1016/j.watres.2025.123491},
pmid = {40090148},
issn = {1879-2448},
abstract = {The response mechanism of microorganisms in partial denitrification (PD) system under antibiotic stress, particularly microbial energy metabolism and electron transfer, remain inadequately understood. This knowledge gap hinders the establishment of ecological links between microbial dynamics and macro-level reactor performance. To address this, moving bed biofilm reactors were employed to investigate the dynamic changes of microbial community and metabolism under sulfadiazine (SDZ) and ciprofloxacin (CIP) stress. Results showed that dosing 2 mg/L SDZ or CIP accelerated nitrite accumulation, achieving this milestone 15 days earlier than in the control group. At the end of the operational phase, nitrate removal efficiencies reached 90.3 ± 18.3 % (Control), 83.5 ± 16.2 % (SDZ-treated) and 93.9 ± 12.4 % (CIP-treated), with nitrate-to nitrite-transformation rates of 61.3 ± 12.7 %, 65.6 ± 13.1 % and 58.0 ± 21.2 %, respectively. The abundances of energy supply related genes, i.e., sucC and PK were higher in the CIP-treated group, while those in the other two groups were similar. The promoted tricarboxylic acid cycle and glycolysis led to NADH and ATP accumulation, accelerating nitrogen metabolism and benefiting early nitrite accumulation in the antibiotic-stressed system. More importantly, increasing antibiotics concentration from 2 mg/L to 4 mg/L induced selective migration of Thauera from floc to biofilm (abundance in floc reduced to < 2.01 %). Metagenomic sequencing indicated that the higher abundance of narGHI in biofilms, compared to flocs, was crucial for maintaining stable PD performance under antibiotic stress. The electron transport related genes, such as IDH1, DLD and DLAT, were more abundant in biofilms than in flocs after SDZ and CIP addition. These findings provide a theoretical basis for understanding the response mechanism of PD consortia to antibiotic.},
}
@article {pmid40090144,
year = {2025},
author = {Deng, B and Ren, Z and Li, Q and Zhang, Z and Xu, C and Wang, P and Zhao, H and Yuan, Q},
title = {Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system.},
journal = {Water research},
volume = {280},
number = {},
pages = {123483},
doi = {10.1016/j.watres.2025.123483},
pmid = {40090144},
issn = {1879-2448},
abstract = {Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.},
}
@article {pmid40089680,
year = {2025},
author = {Wang, S and Niu, W and Lv, T and Xie, K},
title = {Traceability of septic shock caused by phocaeicola vulgatus: a rare case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {364},
pmid = {40089680},
issn = {1471-2334},
mesh = {Humans ; *Shock, Septic/microbiology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Phocaeicola vulgatus (P.vulgatus) is a member of Bacteroides fragilis Group(BFG). Septic shock caused by P.vulgatus has not been reported yet. In recent years, BFG have attracted much clinical attention. BFG are the commensal microbiota residing in human mucosal sites, most notably the gut, that provide several benefits to healthy hosts. Yet BFG can cause devastating infections when they gain access to normally sterile body compartments following trauma, surgery, or mucosal barrier disruption.<br><br>CASE PRESENTATION: We report a case of septic shock event in a middle-aged male who underwent surgical intervention for a gallbladder mass incidentally detected during routine abdominal CT screening. P.vulgatus was isolated and cultured from blood sample and abdominal drainage fluid after surgery. We further performed the Metagenomic Next-Generation Sequencing (mNGS) with pathological slices of colon and hepatobiliary tissue, and result of mNGS also showed P.vulgatus. The patient was treated with comprehensive therapies and had a good outcome.<br><br>CONCLUSION: To the best of our knowledge, septic shock secondary to P.vulgatus infection originating from non-gastrointestinal area represents an rare clinical condition. We realized that research on BFG should not only focus on its positive effects on the intestine, but also on its potential pathogenicity, including intra-abdominal infections, abscesses, and bloodstream infection.},
}
@article {pmid40089034,
year = {2025},
author = {Zhang, Z and Liu, Y and Yang, X and Luo, Q and Huang, W and Zhao, Z},
title = {Impacts of hydraulic retention time on organic removal in treating liquor wastewater via algal-bacterial granular sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132394},
doi = {10.1016/j.biortech.2025.132394},
pmid = {40089034},
issn = {1873-2976},
abstract = {This study optimized hydraulic retention time (HRT) to improve p-cresol and chemical oxygen demand (COD) removal and promote algal-bacterial granular sludge (ABGS) formation in Chinese fermented liquor wastewater treatment. At an HRT of 4 h, no granules formed in the sequential batch reactor, and after 30 days, the removal efficiencies were low for both COD (58.5 %) and p-cresol (21.6 %). In contrast, compact granules developed at HRT 8 and 12 h. The HRT of 8 h achieved the highest removal efficiencies (COD: 96.0 %, p-cresol: 91.3 %), outperforming the HRT of 12 h (COD: 95.1 %, p-cresol: 82.7 %). Microbial analysis identified Rhodobacteraceae and Pseudomonas as key p-cresol degraders. Metagenomic analysis revealed a higher abundance of benzoate degradation genes at an HRT of 8 h compared to 12 h, with Acidovorax predominantly contributing at 8 h and Hydrogenophaga at 12 h. These findings provide insights into the optimization of liquor wastewater treatment.},
}
@article {pmid40088533,
year = {2025},
author = {Kim, HR and Kim, SH and Le, HD and Kim, JK and Her, M},
title = {The complete genome sequence of quail coronavirus identified in disease surveillance on quail farms in South Korea.},
journal = {Poultry science},
volume = {104},
number = {5},
pages = {105007},
doi = {10.1016/j.psj.2025.105007},
pmid = {40088533},
issn = {1525-3171},
abstract = {Avian carcasses collected from 103 flocks on 14 quail farms in Korea between 2022 and 2023 were diagnosed with viral diseases (22 flocks), bacterial disease (58 flocks), parasitic diseases (28 flocks) and non-infectious diseases (60 flocks). The only viral disease identified was viral enteritis in quails that showed pathological lesions in duodenum and appeared to be caused by quail coronavirus (QcoV) through viral metagenomics and RT-PCR assay. Two complete genomes of QCoV from samples diagnosed as viral enteritis were obtained using amplicon-based whole genome sequencing. The two QcoVs were gammacoronavirus, but were distinct from other avian coronaviruses. The spike genes of QCoV have 86.2 ∼ 87.1 % identity with that of American turkey coronavirus, but other gene sequences of QcoV was found to be similar to those of Korean infectious bronchitis virus. Genetic analysis based on the complete genomic sequences found QCoVs had a genetic structure similar to avian coronaviruses, yet it seems to be a unique pathogen specific to quail. This is the first report about the complete genome and genetic analysis of QCoV and the result of disease surveillance in quail in South Korea.},
}
@article {pmid40087960,
year = {2025},
author = {Sabba, F and Farmer, M and Dunlap, P and Qin, C and Kozak, J and Barnard, J and Wells, G and Downing, L},
title = {Unlocking the potential of sidestream EBPR: exploring the coexistence of PAO, GAO and DGAO for effective phosphorus and nitrogen removal.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {91},
number = {5},
pages = {469-481},
pmid = {40087960},
issn = {0273-1223},
mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Waste Disposal, Fluid/methods ; Bioreactors ; Denitrification ; Anaerobiosis ; Glycogen/metabolism ; Water Pollutants, Chemical/metabolism ; },
abstract = {Wastewater treatment facilities use enhanced biological phosphorus removal (EBPR) to meet discharge quality limits. However, the EBPR process can experience upsets due to a lack of influent carbon or inadequate anaerobic zones. By using a sidestream EBPR (S2EBPR) process, carbon can be generated internally through fermentation processes and a higher anaerobic mass fraction can be attained in smaller volumes. This study investigates nutrient removal and microbial community trends in a full-scale S2EBPR demonstration at the Calumet Water Reclamation Plant. The study aims to improve a process model of the system by better representing the activity of glycogen-accumulating organisms (GAO) and potential competitors of phosphorus-accumulating organisms (PAO), which were found in high abundance in this study. Modifying anaerobic hydrolysis, GAO glycogen storage and ORP activity parameters resulted in model prediction improvements of approximately 5% for nitrate and nitrite and 10-60% for phosphorus. The study also uses shotgun metagenomic sequencing to profile denitrification pathways of PAO and GAO. It shows that denitrifying GAO may contribute to nitric oxide reduction to a greater degree than denitrifying PAO. This study improves process modeling predictions for S2EBPR and highlights the potential role of denitrifying PAO and GAO in combined phosphorus and nitrogen removal in S2EBPR.},
}
@article {pmid40087791,
year = {2025},
author = {Centeno-Delphia, RE and Glidden, N and Long, E and Ellis, A and Hoffman, S and Mosier, K and Ulloa, N and Cheng, JJ and Davidson, JL and Mohan, S and Kamel, M and Szasz, JI and Schoonmaker, J and Koziol, J and Boerman, JP and Ault, A and Verma, MS and Johnson, TA},
title = {Nasal pathobiont abundance is a moderate feedlot-dependent indicator of bovine respiratory disease in beef cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {27},
pmid = {40087791},
issn = {2524-4671},
support = {2020-68014-31302//National Institute of Food and Agriculture/ ; 2018-006//Purdue University's Colleges of Agriculture and Engineering Collaborative Projects Program/ ; },
abstract = {BACKGROUND: Bovine respiratory disease (BRD) poses a persistent challenge in the beef cattle industry, impacting both animal health and economic aspects. Several risk factors make an animal susceptible to BRD, including bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Despite efforts to characterize and quantify these bacteria in the nasal cavity for disease diagnosis, more research is needed to understand if there is a pathobiont abundance threshold for clinical signs of respiratory disease, and if the results are similar across feedlots. This study aims to compare the nasal microbiome community diversity and composition, along with the abundance of four bacterial pathogens and associated serotypes, in apparently healthy and BRD-affected beef cattle. Nasal swabs were collected from four beef feedlots across the US, covering the years 2019 to 2022. The study included post-weaned beef cattle with diverse housing conditions.<br><br>RESULTS: Quantification of BRD-associated pathogens effectively distinguished BRD-affected from apparently healthy beef cattle, surpassing the efficacy of 16S rRNA gene sequencing of the nasal microbiome community. Specifically, H. somni, M. bovis, and M. haemolytica had higher abundance in the BRD-affected group. Utilizing the abundance of these pathobionts and analyzing their combined abundance with machine learning models resulted in an accuracy of approximately 63% for sample classification into disease status. Moreover, there were no significant differences in nasal microbiome diversity (alpha and beta) between BRD-affected and apparently healthy cattle; instead, differences were detected between feedlots.<br><br>CONCLUSIONS: Notably, this study sheds light on the beef cattle nasal microbiome community composition, revealing specific differences between BRD-affected and apparently healthy cattle. Pathobiont abundance was increased in some, but not all farms. Nonetheless, more research is needed to determine if these differences are consistent across other studies. Additionally, future research should consider bacterial-viral interactions in the beef nasal metagenome.},
}
@article {pmid40087775,
year = {2025},
author = {Duret, M and Wallner, A and Besaury, L and Aziz, A},
title = {Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {30},
pmid = {40087775},
issn = {2524-6372},
support = {1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; },
abstract = {BACKGROUND: Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.<br><br>RESULTS: Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.<br><br>CONCLUSIONS: This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.},
}
@article {pmid40087699,
year = {2025},
author = {Gu, D and Liu, J and Wang, J and Yi, Y and Chu, Y and Gao, R and Liu, H and She, J and Lu, B},
title = {Integrating DNA and RNA sequencing for enhanced pathogen detection in respiratory infections.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {325},
pmid = {40087699},
issn = {1479-5876},
support = {L222073//Beijing Natural Science Foundation/ ; CFH, 2024-1-4063//Alpha Foundation for the Improvement of Mine Safety and Health/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; },
mesh = {Humans ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; Male ; Female ; Sequence Analysis, RNA/methods ; Middle Aged ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Sequence Analysis, DNA/methods ; Aged ; Reproducibility of Results ; Retrospective Studies ; Young Adult ; Metagenomics/methods ; Adolescent ; },
abstract = {BACKGROUND: The clinical value of shotgun metagenomic next-generation sequencing (mNGS) in improving the detection rates of respiratory pathogens is well-established. However, mNGS is complex and expensive. This study designed and evaluated the performance of targeted NGS (tNGS) in diagnosing respiratory infections.<br><br>METHODS: We retrospectively included samples from 281 patients with lower respiratory tract infections to establish thresholds of pathogens. Subsequently, target pathogens were selected and a probe hybridization system was established. The performance and clinical manifestations of tNGS for 306 pathogens were evaluated using clinical and simulated samples.<br><br>RESULTS: The tNGS method took 16&#xa0;h with sequencing data sizes of 5&#xa0;M reads. The limit-of-detection of tNGS was 100-200 CFU/mL, respectively. Bioinformatics simulation confirmed the method's high specificity and robustness. In 281 patients of clinical validation cohort, tNGS exhibited a sensitivity of 97.73% and specificity of 75.41% compared to the composite reference standard, which notably surpasses those of culture-based and conventional microbiological methods (CMT). In detecting bacterial and viral infection, tNGS demonstrated superior sensitivity relative to CMT. Notably, 61.40% of target viruses were subtype-resolved with the initial establishment of reliable typing cutoffs, with the subtyping results being completely consistent with the PCR results. tNGS allowed for concurrent identification of antimicrobial resistance (AMR) markers and viral subtyping. 80.56% of AMR markers identified by tNGS were consistent with antimicrobial susceptibility testing.<br><br>CONCLUSION: This research established the robust performance of our tailored tNGS assay in the simultaneous detection of DNA and RNA pathogens, underscoring its prospective suitability for widespread use in clinical diagnostics.},
}
@article {pmid40087607,
year = {2025},
author = {Meng, B and Liu, H and Wu, Q and Qu, L and Mao, C and Yang, F and Lan, T and Fang, J and Hu, Z and Fang, Y},
title = {Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {360},
pmid = {40087607},
issn = {1471-2334},
support = {2020-55//Wuhan Young and Middle-aged Medical Backbone Talent Project 2020/ ; ZZ20231693//Young Talent Project of General Hospital of Center Theater/ ; JCZRYB202500657//Natural Science Foundation of Hubei Province/ ; },
mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; *Respiratory Tract Infections/drug therapy/microbiology ; Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Adult ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; },
abstract = {BACKGROUND: Immunocompromised patients with Lower Respiratory Tract Infections (LRTI) frequently encounter a diverse range of pathogenic infections, characterized by rapid disease progression and significant mortality rates due to reckless or excessive utilization of antibiotics. Therefore, it is crucial to promptly and accurately identify the causative microorganisms for pathogen diagnosis and clinical decision-making. The objective of this study is to evaluate the clinical applicability of metagenomic next-generation sequencing (mNGS) in the diagnosis and management of LRTI, as well as its impact on empirical antibacterial therapy for patients with varying immune statuses.<br><br>METHODS: We conducted a comparative analysis of positivity rate, detection accuracy, pathogen spectrum, duration of treatment (DOT), and antibiotic management in a cohort of 283 patients diagnosed with lower respiratory tract infections.<br><br>RESULTS: The positive detection rate was higher in mNGS compared to conventional culture in both immunocompetent group (89.92% vs. 28.57%, P&#x2009;<&#x2009;0.001) and immunocompromised group (84.44% vs. 33.33%, P&#x2009;<&#x2009;0.001). The antibiotic escalation in the immunocompromised group was more frequent than that in the immunocompetent group (49.00% vs. 31.00%, P&#x2009;=&#x2009;0.018), but no difference was observed for antibiotic de-escalation (20.00% vs. 15.00%, P&#x2009;=&#x2009;0.458).<br><br>CONCLUSIONS: The application of mNGS can significantly enhance the pathogen detection rate and optimize antimicrobial drug management in immunocompromised patients with LRTI.},
}
@article {pmid40087598,
year = {2025},
author = {Lu, S and Li, H and Ma, C and Li, X},
title = {Systemic and localized infections in humans caused by Paenibacillus: a case report and literature review.},
journal = {BMC ophthalmology},
volume = {25},
number = {1},
pages = {133},
pmid = {40087598},
issn = {1471-2415},
support = {LHGJ20220370//Joint Construction Project of Henan Medical Science and Technology/ ; LHGJ20220370//Joint Construction Project of Henan Medical Science and Technology/ ; 232300420237//Natural Science Foundation of Henan/ ; 232300420237//Natural Science Foundation of Henan/ ; },
mesh = {Humans ; Male ; Adult ; *Eye Infections, Bacterial/diagnosis/microbiology/drug therapy ; *Paenibacillus/isolation &amp; purification ; *Gram-Positive Bacterial Infections/diagnosis/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: As opportunistic pathogens, Paenibacillus organisms rarely induce human infections. This research paper details the clinical manifestations, treatment, and prognosis of an intraocular infection caused by Paenibacillus in a 43-year-old male patient.<br><br>CASE PRESENTATION: In this case, the patient initially presented with persistent ocular redness and a sensation of foreign bodies following trauma surgery. Upon admission, we performed intraocular fluid metagenomic next generation sequencing (mNGS) testing and systemic blood sampling for infection-related assessments. The results revealed a localized ocular infection with Paenibacillus organisms. Consequently, the patient received daily levofloxacin injections (500&#xa0;mg) and clindamycin (300&#xa0;mg) for systemic anti-infective therapy, along with subconjunctival injections of gentamicin (2 WIU) and dexamethasone (5&#xa0;mg) for topical application. The infection was effectively managed, and their ocular symptoms showed improvement during the treatment course.<br><br>CONCLUSIONS: We conducted a comprehensive review of previously reported cases involving Bacillus-like organisms causing human infections, exploring mechanisms, diagnostic approaches, and treatment strategies.},
}
@article {pmid40087549,
year = {2025},
author = {Wang, X and Shang, Y and Xing, Y and Chen, Y and Wu, X and Zhang, H},
title = {Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {142},
pmid = {40087549},
issn = {1471-2180},
support = {2022KJ177//the Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 32001228//the National Natural Science Foundation of China/ ; 32270444//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Virulence Factors/genetics ; *Wolves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/enzymology ; Dogs ; *Foxes/microbiology ; Animals, Zoo/microbiology ; Animals, Wild/microbiology ; Carbohydrate Metabolism ; Metagenomics ; },
abstract = {Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.},
}
@article {pmid40087199,
year = {2025},
author = {Zhang, Y and Xu, S and Xu, Y},
title = {Clinical Analyses of 4 Cases of Microsporidial Keratoconjunctivitis.},
journal = {Acta parasitologica},
volume = {70},
number = {2},
pages = {71},
pmid = {40087199},
issn = {1896-1851},
mesh = {Humans ; *Keratoconjunctivitis/microbiology/drug therapy/diagnosis ; Male ; Adult ; Female ; Middle Aged ; China ; Microsporidiosis/diagnosis/drug therapy/microbiology ; Encephalitozoon/isolation &amp; purification/genetics ; Antifungal Agents/therapeutic use ; Eye Infections, Fungal/drug therapy/microbiology/diagnosis ; Encephalitozoonosis/drug therapy/diagnosis ; },
abstract = {OBJECTIVE: To report four cases of microsporidial keratoconjunctivitis (MKC) from The Affiliated Eye Hospital of Nanjing Medical University (from May 2023 to October 2024) and to aid ophthalmologists in diagnosing and treating MKC, as MKC has been increasingly reported in Asian healthy individuals but not much in Mainland China.<br><br>METHODS: Four patients with MKC were studied. Demographic information, symptoms, and clinical data were collected. Diagnosis involved ophthalmic examinations, corneal scraping microscopy (including Giemsa staining, modified Ziehl-Neelsen staining, Calcofour white staining), bacterial and fungal cultures, and metagenomic next-generation sequencing (mNGS). Treatment included various topical medications like polyhexamethylene biguanide (PHMB), fluconazole, tacrolimus, sodium hyaluronate, and systemic medication such as albendazole.<br><br>RESULTS: Three cases were caused by Encephalitozoon hellem proved by mNGS. Patients had symptoms like eye redness, swelling, pain, foreign body sensation, and vision loss. Risk factors included improper contact lens - wearing habits, contact with birds, or exposure to potentially contaminated environments. All patients showed improvements after treatment, with 3 cases cured and 1 case improved.<br><br>CONCLUSION: MKC is a unilateral, acute, non-purulent ocular surface infectious disease. Clinicians should be more aware of it. Diagnosis depends on recognizing clinical signs, exploring risk factors, and laboratory tests. There is no consensus on treatment, but combined topical and systemic anti-protozoal drugs showed good results. Further large-scale validation is needed. Relevant departments should strengthen water source management, and patients should pay attention to personal hygiene.},
}
@article {pmid40087044,
year = {2025},
author = {Chen, B and Li, Y and Li, Z and Hu, X and Zhen, H and Chen, H and Nie, C and Hou, Y and Zhu, S and Xiao, L and Li, T},
title = {Vitamin E ameliorates blood cholesterol level and alters gut microbiota composition: A randomized controlled trial.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {103964},
doi = {10.1016/j.numecd.2025.103964},
pmid = {40087044},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Antioxidants, including vitamin E (VE) and grape seed extract (GSE), as anti-aging supplementation have been widely used to improve human health. The gut microbiota plays a crucial role in health and affects the treatment effect of various interventions. However, the role of gut microbiota in VE remains unclear. This study aimed to assess the longitudinal impact of VE treatment on body health and the gut microbiota.<br><br>METHODS AND RESULTS: A randomized controlled trial was conducted with 90 healthy individuals. The participants were randomly assigned to three groups: a treatment group receiving VE, another antioxidant treatment group receiving GSE, and a control group receiving a placebo. We found that VE ameliorated blood cholesterol levels by reducing the levels of low-density lipoprotein cholesterol (LDL-C) in healthy volunteers. After the intervention, there was an increase in the relative abundance of short-chain fatty acid (SCFA)-producing bacteria and bile acid metabolizers. Specifically, the abundances of Lachnospira sp. and Faecalibacterium spp. increased in the VE. Interestingly, the gut microbiota of poor responders harbored a greater proportion of disease-associated bacterial species.<br><br>CONCLUSIONS: VE could promote health by lowering LDL-C, partly and indirectly by affecting gut bacteria with the ability to produce SCFAs or metabolize bile acids.<br><br>The clinical trial was registered on August 28, 2021. Registration number was ChiCTR2100050567 (https://www.chictr.org.cn).},
}
@article {pmid40086988,
year = {2025},
author = {Peng, Q and Quan, L and Zheng, H and Li, J and Xie, G},
title = {Analyzing the contribution of top-down and bottom-up methods to the construction of synthetic microbial communities in Jiuyao.},
journal = {Food microbiology},
volume = {129},
number = {},
pages = {104759},
doi = {10.1016/j.fm.2025.104759},
pmid = {40086988},
issn = {1095-9998},
mesh = {*Fermentation ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Food Microbiology ; Fermented Foods/microbiology ; Metagenomics ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; Saccharomyces cerevisiae/genetics/metabolism ; Taste ; },
abstract = {The construction of synthetic microbial communities is a crucial strategy for improving the stability of microbial populations and the quality of fermented foods. Jiuyao, an essential saccharification and fermentation starter in Huangjiu production, was the focus of this study. Using metagenomics combined with culture-dependent methods, we identified 11 microbial species involved in Huangjiu fermentation. Through metagenomic analysis and simulated fermentation, Rhizopus delemar, Rhizopus microspores, Rhizopus stolonife, Rhizopus azygosporus, Saccharomycopsis fibuligera, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Pediococcus pentosaceus were determined to be the core microbial species driving the Jiuyao fermentation process. A synthetic microbial community was constructed based on these species, successfully reproducing the flavor and sensory qualities of Huangjiu while enhancing fermentation efficiency. This study provides valuable insights into the functional roles of Jiuyao-associated microbes and offers a framework for improving microbial community stability and fermentation quality in Huangjiu production.},
}
@article {pmid40086981,
year = {2025},
author = {Kothe, CI and Renault, P},
title = {Metagenomic driven isolation of poorly culturable species in food.},
journal = {Food microbiology},
volume = {129},
number = {},
pages = {104722},
doi = {10.1016/j.fm.2025.104722},
pmid = {40086981},
issn = {1095-9998},
mesh = {*Metagenomics ; *Cheese/microbiology ; *Food Microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Metagenome ; Phylogeny ; },
abstract = {Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.},
}
@article {pmid40086705,
year = {2025},
author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X},
title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.},
journal = {Gene},
volume = {},
number = {},
pages = {149414},
doi = {10.1016/j.gene.2025.149414},
pmid = {40086705},
issn = {1879-0038},
abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.},
}
@article {pmid40086585,
year = {2025},
author = {Rawat, N and Sivanesan, S and Kanade, GS and Bafana, A},
title = {Interaction of environmental fluoride exposure and gut microbes: potential implication in the development of fluorosis in human subjects.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115388},
doi = {10.1016/j.fct.2025.115388},
pmid = {40086585},
issn = {1873-6351},
abstract = {Fluoride exposure primarily occurs through contaminated water and leads to fluorosis, which is a global health concern. After ingestion, fluoride is absorbed via gastrointestinal tract, where it interacts with the gut microbiota. While animal studies have explored fluoride's effects on gut microbiota, no human studies have yet been conducted. Most research emphasizes metagenomic diversity, neglecting isolation and characterization of pure cultures for further applications. Additionally, the association between gut microbiota with fluorosis outcomes in fluoride-exposed populations is unexplored. This study characterizes and compares the cultivable gut microbiota in the fluoride-exposed population with (symptomatic, group II) or without (asymptomatic, group I) signs of skeletal fluorosis along with unexposed control (group III). Group I displayed higher abundance of Firmicutes (58.58%), group II had predominance of Proteobacteria (61.25%) while group III showed similar abundance of Proteobacteria (50.38%) and Firmicutes (49.51%). On analyzing short-chain fatty acid (SCFA) profiles, group I isolates produced higher isobutyric acid (1.31 ± 0.9 mM) than group II (0.71 ± 0.35 mM), while group II produced more isovaleric acid (0.8 ± 0.41 mM) than group I (0.61 ± 0.08 mM) (p < 0.05). These findings suggest that gut microbiota and SCFAs alteration may influence bone metabolism, affecting the fluorosis progression.},
}
@article {pmid40086354,
year = {2025},
author = {Can Yilmaz, E and Barnes, MA},
title = {Comparative study of rates of environmental DNA (eDNA) accumulation and degradation in water and sediment from model plant (Egeria densa) and animal (Daphnia magna) species.},
journal = {The Science of the total environment},
volume = {971},
number = {},
pages = {179057},
doi = {10.1016/j.scitotenv.2025.179057},
pmid = {40086354},
issn = {1879-1026},
abstract = {Understanding of the ecology of environmental DNA (eDNA)-its origin, state, transport, and fate- is critical for interpreting the results of eDNA applications ranging from single-species presence/absence monitoring to whole-community analysis via metabarcoding and metagenomics. Accumulation and degradation of eDNA can be most accurately measured by conducting systematic manipulative experiments under controlled conditions. We compared eDNA accumulation and degradation in a laboratory setting for two different taxa (Daphnia magna and Egeria densa) across two different substrates (water and sediment). In accumulation experiments, both D. magna and E. densa showed increased eDNA levels in both water and sediment over 24 h. Daphnia magna eDNA concentrations were twice as high in sediment compared to water, whereas E. densa eDNA remained consistent between the two substrates. Degradation kinetic models were applied to our data for the two model organisms to characterize eDNA decay rates, inadvertently introducing an additional nutrient treatment with three different levels. The degradation of D. magna and E. densa eDNA varied based on nutrient concentrations and substrate types, with different models providing the best fit for different scenarios. Overall, we have demonstrated the importance of taxonomic, sample type, and environmental differences in eDNA ecological processes such as accumulation and degradation. These and similar processes require further study to enhance the interpretation of eDNA results in both research and management contexts.},
}
@article {pmid40086306,
year = {2025},
author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D},
title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.},
journal = {The Science of the total environment},
volume = {972},
number = {},
pages = {179109},
doi = {10.1016/j.scitotenv.2025.179109},
pmid = {40086306},
issn = {1879-1026},
abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.},
}
@article {pmid40086246,
year = {2025},
author = {Han, NN and Yang, JH and Wu, GG and Yang, JH and Jin, JA and Fan, NS and Jin, RC},
title = {Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137886},
doi = {10.1016/j.jhazmat.2025.137886},
pmid = {40086246},
issn = {1873-3336},
abstract = {Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.},
}
@article {pmid40086153,
year = {2025},
author = {Huang, JN and Liu, ZQ and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Stocking filter-feeder in fed fish aquaculture pond: Unexpected Aggravation of nitrous oxide emission.},
journal = {Water research},
volume = {280},
number = {},
pages = {123475},
doi = {10.1016/j.watres.2025.123475},
pmid = {40086153},
issn = {1879-2448},
abstract = {Intensive farming of fed fish could produce large amounts of uneaten feed and feces, potentially leading to increased nitrous oxide (N2O) emissions. Filter-feeding fish can ingest residual feed and feces, but it is unclear whether introducing them into fed fish farming ponds could reduce N2O emissions. This study employed monoculture of fed largemouth bass (Micropterus salmoides, LB) and polyculture of LB with filter-feeding silver carp (Hypophthalmichthys molitrix, SC) at density ratios of 18:1, 9:1 and 4.5:1 to compare the N2O emission characteristics. The results showed that silver carp could indeed feed on largemouth bass feces, and isotope mixing model indicated that feces was the second largest contributor to the food of silver carp, reaching 14.75 %-15.56 %. However, polyculture of the two species did not or even increased N2O emission flux at water-air interface and its release potential in sediment. Increased mineralization, nitrification and denitrification rates were observed in polyculture systems, particularly at high stocking densities of silver carp. Also, the higher NH4[+] accumulation were found across sediment-water interface within polyculture systems. Metagenome revealed that polyculture disturbed the microbial community structure and increased the abundance of Burkholderiales and Steroidobacteraceae. Moreover, polyculture increased the abundance of nitrogen-cycling functional genes, including gdhA, hao, nirB and norB, potentially contributing to the elevated N2O emissions. Structural equation model highlighted that polyculture of largemouth bass and silver carp could drive N2O emissions, mainly through increased sedimental NH4[+] concentration and microbial activity. These findings indicate that the introduction of extractive filter-feeding fish into fed fish farming ponds could not reduce N2O emissions, implying the need for optimized management strategies to balance aquaculture productivity with environmental sustainability.},
}
@article {pmid40085365,
year = {2025},
author = {Makarani, N and Kaushal, RS},
title = {Advances in actinobacteria-based bioremediation: mechanistic insights, genetic regulation, and emerging technologies.},
journal = {Biodegradation},
volume = {36},
number = {2},
pages = {24},
pmid = {40085365},
issn = {1572-9729},
mesh = {*Biodegradation, Environmental ; *Actinobacteria/metabolism/genetics ; *Metals, Heavy/metabolism ; },
abstract = {Untreated wastewater from sewage, industries, and agriculture contaminates ecosystems due to rapid population growth and industrialization. It introduces hazardous pollutants, including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals, which pose serious health risks such as cancer, lung disorders, and kidney damage, threatening both environmental and human well-being. Using microorganisms for bioremediation is thought to be safer and more effective. Compared to other approaches, bioremediation is the most effective way to absorb heavy metals. Due to the high cost and unreliability of traditional remediation techniques, such as chemical and physical treatments, interest in bioremediation as an environmentally benign substitute has grown. Through the use of microorganisms, bioremediation successfully removes heavy metals and breaks down organic contaminants from contaminated circumstances. Actinobacteria are unique among these microbes because of their flexibility in metabolism and capacity to endure severe environments. They create secondary metabolites, such as enzymes, that help break down a variety of pollutants. Actinobacteria also produce siderophores and extracellular polymeric substances (EPS), which aid in trapping organic contaminants and immobilizing heavy metals. This review explores the diverse applications of actinobacteria in bioremediation, with a focus on their mechanisms for breaking down and neutralizing pollutants. We highlighted the advancements in bioremediation strategies, including the use of mixed microbial cultures, biosurfactants, nanoparticles and immobilized cell technologies which enhance the efficiency and sustainability of pollutant removal. The integration of omics technologies such as metagenomics, meta-transcriptomics, and meta-proteomics provides deeper insights into the genetic and metabolic pathways involved in bioremediation, suggesting the way for the development of genetically optimized strains with enhanced degradation capabilities. By leveraging these emerging technologies and microbial strategies, actinobacteria-mediated bioremediation presents a highly promising approach for mitigating environmental pollution. Ongoing research and technological advancements in this field can further enhance the scalability and applicability of bioremediation techniques, offering sustainable solutions for restoring contaminated ecosystems and protecting human health.},
}
@article {pmid40085274,
year = {2025},
author = {Rono, JK and Zhang, Q and He, Y and Wang, S and Lyu, Y and Yang, ZM and Feng, Z},
title = {Biochemical characterization of a bilfunctional endoglucanase/glucomannanase derived from mountain soil.},
journal = {Biotechnology letters},
volume = {47},
number = {2},
pages = {33},
pmid = {40085274},
issn = {1573-6776},
support = {32370089//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Enzyme Stability ; *Cellulase/genetics/metabolism/chemistry ; *Mannans/metabolism ; Hydrogen-Ion Concentration ; Substrate Specificity ; *Recombinant Proteins/genetics/metabolism/chemistry/isolation &amp; purification ; Temperature ; Escherichia coli/genetics ; Carboxymethylcellulose Sodium/metabolism ; Metagenome/genetics ; Kinetics ; Hydrolysis ; Cloning, Molecular ; },
abstract = {Metagenomics is increasingly recognized as a vital technique for exploring uncultured microorganisms, with one key application being the discovery of novel enzymes for industrial use. This study identified an endoglucanase gene from soil metagenome, termed ZFEG1801, which was expressed in E. coli BL21, purified, and characterized for its biochemical properties. The 72.8 kDa recombinant protein exhibited hydrolytic activity against sodium carboxymethyl cellulose (CMC) and konjac glucomannan (KG), with activities of 12.1 U/mg and 42.1 U/mg, respectively. The enzyme displayed optimal activity at pH 5 for CMC and pH 6 for KG, with broad pH stability ranging from 5 to 9. The optimal temperature was 40 °C, and it remained thermally stable between 20 and 40 °C, retaining over 60% of its activity. The enzyme activity remained stable in the presence of most metal ions; however, CMCase activity was inhibited by Cu[2+], while glucomannanase activity was inhibited by Mn[2+], Fe[3+], and Ca[2+]. The catalytic efficiency towards both substrates was reduced by addition of SDS, DMSO, ethanol, isopropanol and acetonitrile. The Vmax and Km of the purified recombinant enzyme were 106.4 μmol/L/min and 4.9 mg/mL for CMC, and 833.3 μmol/L/min and 11.1 mg/mL for KG, respectively. The dual catalytic properties of ZFEG1801, broad pH stability and resistance to additives, demonstrate its potential for use in various biomass degradation processes.},
}
@article {pmid40084919,
year = {2025},
author = {Baalbaki, N and Slob, EMA and Kazer, SW and I Abdel-Aziz, M and Bogaard, HJ and Golebski, K and Maitland-van der Zee, AH},
title = {The Omics Landscape of Long COVID-A Comprehensive Systematic Review to Advance Biomarker, Target and Drug Discovery.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16526},
pmid = {40084919},
issn = {1398-9995},
support = {//Health~Holland/ ; },
abstract = {An estimated 10% of coronavirus disease (COVID-19) survivors suffer from persisting symptoms referred to as long COVID (LC), a condition for which approved treatment options are still lacking. This systematic review (PROSPERO: CRD42024499281) aimed to explore the pathophysiological mechanisms underlying LC and potential treatable traits across symptom-based phenotypes. We included studies with primary data, written in English, focusing on omics analyses of human samples from LC patients with persistent symptoms of at least 3 months. Our search in PubMed and Embase, conducted on January 8, 2024, identified 642 studies, of which 29 met the inclusion criteria after full-text assessment. The risk of bias was evaluated using the Joanna Briggs Institute appraisal tool. The synthesis of omics data, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics, revealed common findings associated with fatigue, cardiovascular, pulmonary, neurological, and gastrointestinal phenotypes. Key findings included mitochondrial dysfunction, dysregulated microRNAs associated with pulmonary dysfunction, tissue impairment, blood-brain barrier disruption, coagulopathy, vascular dysfunction, microbiome disturbances, microbial-derived metabolite production and persistent inflammation. Limitations include cross-study heterogeneity and variability in sampling methods. Our review emphasizes the complexity of LC and the need for further longitudinal omics-integrated studies to advance the development of biomarkers and targeted treatments.},
}
@article {pmid40084893,
year = {2025},
author = {Yuan, S and Wu, Y and Balcazar, JL and Wang, D and Zhu, D and Ye, M and Sun, M and Hu, F},
title = {Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0029625},
doi = {10.1128/aem.00296-25},
pmid = {40084893},
issn = {1098-5336},
abstract = {The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.},
}
@article {pmid40084890,
year = {2025},
author = {Sarkar, P and Beebe, M and Bhandari, G and Wielinski, J and Lowry, GV and Gulliver, D},
title = {Novel anaerobic selenium oxyanion reducers native to FGD wastewater for enhanced selenium removal.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0122224},
doi = {10.1128/aem.01222-24},
pmid = {40084890},
issn = {1098-5336},
abstract = {Biological treatment is a recognized approach for removing selenate and selenite oxyanions present in flue gas desulfurization (FGD) wastewater. However, the knowledge of the specific microbial species or communities responsible for reducing water-soluble selenium oxyanions to insoluble elemental selenium remains limited. In addition, the selenium oxyanion reduction genes and pathways have yet to be understood in these wastewaters. This study characterizes selenium oxyanion-reducing bacteria (SeRB) native to FGD wastewater, and the resulting elemental selenium particles formed. By selecting native SeRB microbes in a defined media, a novel resolution of these organisms has been achieved. This research identifies previously unrecognized selenium oxyanion-reducing capabilities in Anaerosolibacter, alongside predominant SeRB from Mesobacillus and Tepidibacillus genera. This work encompasses both 16S and metagenomic techniques to recover novel metagenome-assembled genomes, distinct to this environment. The biogenic selenium produced by these organisms was predominantly of elemental selenium, either amorphous or with a hexagonal structure. This study identifies the SeRB present in FGD wastewater and characterizes their selenium products, offering crucial insights to enhance the efficiency of biological treatment strategies and the potential of selenium recovery from this industrial waste.IMPORTANCEThis is the first report on the culturability and recovery of taxonomic and metabolic information of the anaerobic selenium oxyanion-reducing bacteria (SeRB) in flue gas desulfurization (FGD) wastewater. Selenium is a regulated contaminant in FGD wastewater found on average to be 3,130 µg/L that must be removed to meet EPA discharge limits of 16 µg/L (D. B. Gingerich, E. Grol, and M. S. Mauter, Environ Sci Water Res Technol 4:909-925, 2018, https://doi.org/10.1039/C8EW00264A; also see U.S. EPA EPA-821-R-20-001, 2020). Better understanding of anaerobic SeRB and the microbial community in FGD wastewater is needed to harness their full potential for the bioremediation and recovery of selenium from FGD wastewater. Optimizing the biotreatment strategies for these wastewaters promises to yield cleaner and healthier waterways and ecosystems, even as the United States undergoes a shift in its energy landscape.},
}
@article {pmid40084855,
year = {2025},
author = {Brock, ML and Tavares-Reager, JF and Dong, J and Larkin, AA and Lam, T and Pineda, N and Olivares, CI and Mackey, KRM and Martiny, AC},
title = {Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0226724},
doi = {10.1128/spectrum.02267-24},
pmid = {40084855},
issn = {2165-0497},
abstract = {An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus. Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure.IMPORTANCEOil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill's impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.},
}
@article {pmid40083791,
year = {2025},
author = {, },
title = {Erratum: Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1576969},
doi = {10.3389/fmicb.2025.1576969},
pmid = {40083791},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1452423.].},
}
@article {pmid40083784,
year = {2025},
author = {Yang, D and Wuyunsiqin, and YanNiu, and Hashentuya, and Tana, and Anna, and Ma, M and Zhao, W and Menggenduxi, and Wang, M},
title = {Traditional Mongolian Medicine Qiqirigan-8 alleviates non-alcoholic fatty liver disease via restoring gut microbiota and metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1517082},
pmid = {40083784},
issn = {1664-302X},
abstract = {BACKGROUND: Mongolian Medicine Qiqirigan-8 (MMQ-8) is a traditional Mongolian medicine formula used to treat fatty liver disease. However, the material basis and in vivo metabolic process of the therapeutic effect of MMQ-8 on non-alcoholic fatty liver disease (NAFLD) remain unclear.<br><br>METHODS: The chemical composition of MMQ-8 was determined using Ultra-high-performance liquid chromatography-quadrupole Exactive Mass spectrometry analysis (UHPLC-QE-MS). C57BL/6J mice were fed a choline-deficient diet for 12 weeks to induce a NAFLD model. Hematoxylin and Eosin (H&amp;E)-staining, combined with serum biochemical indexes, was used to observe liver appearance and characterize the pathological changes and functions of the liver. HE staining and Alcian Blue-Phosphoric Acid Schiff (AB-PAS) staining of the colon, along with ZO-1 immunofluorescence expression in the colon were used to reveal the effect of MMQ-8 on the disruption of the intestinal epithelial mucosal barrier in the NAFLD. The expression of intestinal tight junction genes was analyzed by qRT-PCR to observe the protective effect of MMQ-8 against intestinal epithelial mucosal barrier disruption. Fecal metagenomics and serum non-targeted metabolomics were used to reveal the effects of MMQ-8 on the gut microbiota and metabolism in mice with NAFLD. Finally, we emphasize the interaction between gut microbiota and metabolites through Spearman correlation coefficient analysis.<br><br>RESULTS: Mongolian Medicine Qiqirigan-8 contains 17 active ingredients, which can reduce hepatic steatosis and lobular inflammation in mice with NAFLD, and have protective effects against liver injury. MMQ-8 reduced the infiltration of inflammatory cells in the colon epithelium of model mice while restoring the number of goblet cells. MMQ-8 significantly enhanced ZO-1 protein expression in the colon, as well as the mRNA expression of both ZO-1 and Occludin. Fecal metagenomics results showed that MMQ-8 reduced the Bacillota/Bacteroidota ratio in NAFLD mice. Increased the abundance of beneficial bacteria such as Porphyromonadaceae, Prevotella, and Bacteroidota. and suppressed the abundance of dysfunctional bacteria, such as Bacillota, Acetatifactor, and Erysipelotrichaceae. Furthermore, metabolomics studies revealed that MMQ-8 intervention significantly regulated the expression of metabolites related to glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, and glycerophospholipid metabolism in NAFLD mice compared to the model group. These metabolic pathways play key roles in NAFLD. According to Spearman's correlation coefficient analysis, up-regulation of Porphyromonadaceae, Prevotella, and Bacteroidota after MMQ-8 intervention was negatively correlated with LPC levels in glycerophospholipid metabolic pathways, while positively correlated with PC levels. In contrast, the relationship between Bacillota and Acetatifactor, which were down-regulated after MMQ-8 intervention, was the opposite. In addition, the up-regulation of Porphyromonadaceae, Prevotella, and Bacteroidota after MMQ-8 intervention was positively correlated with fumaric acid, 2-oxoglutaric acid, adenosine, and L-glutathione levels, while those down-regulated after MMQ-8 intervention were positively correlated with the levels of Bacillota, Acetatifactor were negatively correlated with all the above metabolites. Thus, glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism and gut microbial ecosystem are tightly intertwined in this process.<br><br>CONCLUSION: In summary, these findings indicate that MMQ-8 has a synergistic anti-NAFLD effect through its multi-component, multi-target, gut microbiota-modulating and multi metabolic pathway characteristics. The host's regulation of specific gut microbiota and involvement in multiple metabolic pathways may be one of the important mechanisms by which MMQ-8 exerts its therapeutic effects on NAFLD. It is worth noting that metabolic pathways such as glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism, and the gut microbiota ecosystem are closely intertwined in this process.},
}
@article {pmid40083550,
year = {2025},
author = {Ng, HY and Liao, Y and Cheung, CL and Zhang, R and Chan, KH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS},
title = {Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1534787},
pmid = {40083550},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; Adult ; *BNT162 Vaccine/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology ; Antibodies, Neutralizing/blood/immunology ; Immunogenicity, Vaccine ; Prospective Studies ; Antibodies, Viral/blood/immunology ; Hong Kong ; Feces/microbiology ; },
abstract = {INTRODUCTION: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity.<br><br>METHODS: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day 180 after first dose, and tested for neutralizing antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day 180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites.<br><br>RESULTS: Of 242 subjects (median age: 50.2 years [IQR:42.5-55.6]; male:85 [35.1%]), 61 (25.2%) were high-responders while 33 (13.6%) were extreme-high responders (defined as NAb&#x2265;200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans-aOR: 1.87, 95% CI: 1.02-3.51; P. excrementihominis-aOR: 2.2, 95% CI: 1.18-4.18; S. salivarius-aOR: 2.09, 95% CI: 1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00, 95% CI:1.81-107.2) and isoleucine (aOR:1.17, 95% CI:1.04-1.35) significantly associated with extreme-high vaccine response.<br><br>CONCLUSION: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.},
}
@article {pmid40083506,
year = {2025},
author = {Zhou, Y and Ren, D and Chen, Y and Wen, S and Zhang, Y and Song, F and Yang, M and Eisenhut, M and O'Rourke, J and Li, Y and Gui, S},
title = {Presepsin, procalcitonin, interleukin-6, and high-sensitivity C-reactive protein for predicting bacterial DNAaemia among patients with sepsis.},
journal = {Journal of thoracic disease},
volume = {17},
number = {2},
pages = {991-1001},
pmid = {40083506},
issn = {2072-1439},
abstract = {BACKGROUND: Anti-infective therapy against pathogens is the key to treatment of sepsis. Metagenomic next-generation sequencing (mNGS) has higher sensitivity than blood culture. The aim of this study was to use mNGS to identify DNAaemia of pathogens and to assess the diagnostic accuracy of presepsin (PSEP), procalcitonin (PCT), interleukin-6 (IL-6), and high-sensitivity C-reactive protein (hsCRP) in differentiating between bacterial and nonbacterial infections in patients with sepsis.<br><br>METHODS: This retrospective study included patients with sepsis from November 2020 to September 2022 in the Shenzhen Second People's Hospital. Blood samples were sent for blood culture and mNGS when the patients were diagnosed with sepsis. Plasma PSEP, PCT, and IL-6 levels were measured using whole blood specimens that were collected and analyzed after a diagnosis of sepsis. Area under the receiver operating characteristic curve (AUC) was used to evaluate the accuracy of PSEP, PCT, IL-6, and hsCRP for prediction of bacterial DNAaemia detected by mNGS in patients with sepsis.<br><br>RESULTS: This study included 230 patients with sepsis. The bacterial DNAaemia rate was 53.0% [Gram-positive DNAaemia (GPD), Gram-negative DNAaemia (GND), and fungi DNAaemia rate was 18.2%, 37.8%, and 10.9%, respectively]. Among GND, Klebsiella was the most common, followed by Escherichia coli; meanwhile, the GPD were mainly Enterococcus, and Aspergillus was identified in 5 patients with sepsis. The PSEP median values were significantly higher in GND than in non-GND [GND: 1,291 pg/mL, interquartile range (IQR) 456-3,502 pg/mL; non-GND: 707 pg/mL, IQR 332-2,417 pg/mL; P=0.035]. There was no significant difference in PSEP values between GPD and non-GPD groups, or between fungi DNAaemia and non-fungi DNAaemia groups. Receiver operating characteristics analysis indicated that the best cutoff values for PSEP, PCT, IL-6, and hsCRP were 869 pg/mL, 1.14 ng/mL, 85.5 pg/mL, and hsCRP 96.2 mg/L, respectively. Logistic regression indicated that PSEP, PCT, IL-6, and hsCRP had significant predictive value for GND in patients with sepsis. The levels of PCT and IL-6 were different between patients with GPD and those with non-GPD. Only PCT levels differed significantly between fungal DNAaemia and nonfungal DNAaemia.<br><br>CONCLUSIONS: Bacterial-DNAaemia was detected in half of the patients with sepsis. PSEP, PCT, IL-6, and hsCRP demonstrated significant predictive value for GND, PCT and IL-6 levels demonstrated significant predictive value for GPD. Meanwhile, only PCT demonstrated significant predictive value for fungal DNAaemia.},
}
@article {pmid40083031,
year = {2025},
author = {Wang, H and Li, Y and You, J and Feng, N and Wang, D and Su, Y and Feng, X},
title = {Diurnal oscillations of amino acids dynamically associate with microbiota and resistome in the colon of pigs.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {26},
pmid = {40083031},
issn = {2524-4671},
support = {2023YFD1301304//National Key R&amp;D Program of China/ ; 32072688//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Nutrients are one of the key determinants of gut microbiota variation. However, the intricate associations between the amino acid (AA) profile and the dynamic fluctuations in the gut microbiota and resistome remain incompletely elucidated. Herein, we investigated the temporal dynamics of AA profile and gut microbiota in the colon of pigs over a 24-hour period, and further explored the dynamic interrelationships among AA profile, microbiota, and resistome using metagenomics and metabolomics approaches.<br><br>RESULTS: JTK_circle analysis revealed that both the AA profile and the gut microbiota exhibited rhythmic fluctuations. With respect to the feed intake, all AAs except L-homoserine (PAdj = 0.553) demonstrated significant fluctuations. Over 50% of Lactobacillaceae, Ruminococcaceae, Clostridiaceae, and Eubacteriaceae species reached their peaks during T15&#x2009;&#x223c;&#x2009;T21 when 50% of Lachnospiraceae species experienced a trough. The eLSA results showed that most AAs positively correlated with Prevotellaceae species but negatively correlated with Lactobacillaceae and Lachnospiraceae species. Moreover, most of the AAs negatively correlated with the mobile genetic elements Tn916 and istA group but positively correlated with plasmids. Further partial least squares structural equation model analysis indicated that AAs affected the antibiotic resistance gene dynamics through mobile genetic elements and the gut microbiota.<br><br>CONCLUSIONS: Taken together, the AA profile and the gut microbiota exhibit robust fluctuations over a day. The AA profile can affect the gut microbiota and resistome in a direct or indirect manner. These findings may provide new insights into a potential strategy for manipulating the gut microbiota and resistome.},
}
@article {pmid40082992,
year = {2025},
author = {Edminster, SY and Rebbe, RW and Khatchadourian, C and Hurth, KM and Mathew, AJ and Huss-Bawab, J and Shiroishi, MS and Clark, D and Norgan, AP and Butler-Wu, SM and Hiniker, A},
title = {The role of plasma metagenomic sequencing in identification of Balamuthia mandrillaris encephalitis.},
journal = {Acta neuropathologica communications},
volume = {13},
number = {1},
pages = {60},
pmid = {40082992},
issn = {2051-5960},
mesh = {Humans ; Female ; *Balamuthia mandrillaris/genetics/isolation &amp; purification ; Middle Aged ; *Amebiasis/diagnosis/cerebrospinal fluid ; *Metagenomics/methods ; Encephalitis/diagnosis/parasitology/cerebrospinal fluid ; High-Throughput Nucleotide Sequencing ; Infectious Encephalitis/diagnosis/cerebrospinal fluid ; Central Nervous System Protozoal Infections/diagnosis/parasitology ; Brain/pathology/parasitology ; },
abstract = {Balamuthia mandrillaris is a rare, free-living amoeba (FLA) that causes granulomatous amoebic encephalitis, a disease with close to 90% mortality. The geographical ranges of many FLA are expanding, potentially increasing human exposure to B. mandrillaris. Here, we report a case of a 58-year-old woman with progressive neurological symptoms, ultimately diagnosed postmortem with B. mandrillaris encephalitis through plasma metagenomic next-generation sequencing (mNGS) despite negative results on both cerebrospinal fluid (CSF) mNGS and CSF PCR testing. Histologic analysis and real-time PCR (qPCR) studies on postmortem brain tissue confirmed B. mandrillaris infection with significant vascular clustering of trophozoites. Retrospective analysis of CSF mNGS data demonstrated subthreshold reads for B. mandrillaris, emphasizing the challenges of interpreting low-level pathogen signals. A systematic review of 159 published B. mandrillaris cases revealed only two reports of B. mandrillaris diagnosed using plasma mNGS, both of which also had diagnostic CSF studies. This case demonstrates the diagnostic challenges of B. mandrillaris infections, highlights its vascular tropism, and suggests that plasma mNGS may warrant evaluation as a diagnostic tool for B. mandrillaris.},
}
@article {pmid40082612,
year = {2025},
author = {Đokić, J and Dinić, M and Soković Bajić, S and Bisenić, A and Mitrović, H and Jakovljević, S and Radojević, D and Brdarić, E and Lukić, J and Živković, M and Tolinački, M and Terzić-Vidojević, A and Golić, N},
title = {High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8741},
pmid = {40082612},
issn = {2045-2322},
support = {Grant IDEAS No. 7744507, NextGenBiotics//Science Fund of the Republic of Serbia/ ; Grant No. 451-03-66/2024-03/200042//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Brain-Gut Axis ; Anti-Inflammatory Agents/metabolism/pharmacology ; Workflow ; Bacteria/metabolism/classification/genetics ; Brain/metabolism ; Probiotics ; Metagenome ; },
abstract = {The gut microbiota is deeply interconnected with the brain, a phenomenon often referred to as the gut-brain axis. Dysfunction in the microbiota-gut-brain axis can cause various neurological and psychiatric disorders associated with chronic inflammation and gut microbiota dysbiosis. Therefore, cultivation of anaerobic human gut microbiota strains, and characterization of their safety status and immunomodulatory potential could contribute to deciphering the molecular mechanisms underlying the microbiota-gut-brain communication and revealed their biotherapeutic potential. However, poor cultivability of gut microbiota members, makes research into their physiological role challenging. Hence, we report a high-throughput workflow based on targeted cultivation linked to metagenome sequencing, combined with the bioinformatic search for gut members with anti-inflammatory properties which produce the most important microbial metabolites that affect brain function. With this approach, we isolated 147 bacterial strains, and 41 were characterized for their immunomodulatory status with 12 strains showing immunosuppressive features with ability of producing brain important metabolites. Through this workflow we established the best growing conditions essential for cultivation, archiving, phenotyping, and characterization of anaerobic gut bacteria important for microbiota-gut-brain-axis research, and characterized the safety and probiotic potential of 7 extremely oxygen-sensitive strains.},
}
@article {pmid40082593,
year = {2025},
author = {Cardona, ST and Rahman, ASMZ and Novomisky Nechcoff, J},
title = {Innovative perspectives on the discovery of small molecule antibiotics.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {19},
pmid = {40082593},
issn = {2731-8745},
support = {169121//Canadian Institutes of Health Research (CIHR)/ ; },
abstract = {Antibiotics are essential to modern medicine, but multidrug-resistant (MDR) bacterial infections threaten their efficacy. Resistance evolution shortens antibiotic lifespans, limiting investment returns and slowing new approvals. Consequently, the WHO defines four innovation criteria: new chemical class, target, mode of action (MoA), and lack of cross-resistance. This review explores innovative discovery approaches, including AI-driven screening, metagenomics, and target-based strategies, to develop novel antibiotics that meet these criteria and combat MDR infections.},
}
@article {pmid40082238,
year = {2025},
author = {Yong-Chun, R and Yi-Qing, Z and Hai-Wang, Z and Jie, Z and Jin-Nan, D and Xiao-Jing, Z and Ming-Hui, LI},
title = {Metagenomic Next-Generation Sequencing-Assisted Diagnosis of Japanese Spotted Fever: Report of One Case.},
journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae},
volume = {47},
number = {1},
pages = {146-149},
doi = {10.3881/j.issn.1000-503X.15997},
pmid = {40082238},
issn = {1000-503X},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Rickettsia/genetics/isolation &amp; purification ; *Metagenomics/methods ; Spotted Fever Group Rickettsiosis/diagnosis/microbiology ; Male ; Doxycycline/therapeutic use ; },
abstract = {Japanese spotted fever(JSF)is an infectious disease caused by Rickettsia japonica,with nonspecific clinical symptoms and a high risk of misdiagnosis.We reported a case of JSF,in which Rickettsia japonica was detected in blood cells by metagenomic next-generation sequencing.The patient recovered after treatment with doxycycline.This report provides a reference for the clinical diagnosis and treatment of JSF.},
}
@article {pmid40082172,
year = {2025},
author = {Wang, ZJ and Zhang, J and Shi, YY},
title = {Successful Oral Isavuconazole Monotherapy for Invasive Pulmonary Mucormycosis in Kidney Transplant Recipients: Case Reports and Literature Review.},
journal = {Transplantation proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.transproceed.2025.02.047},
pmid = {40082172},
issn = {1873-2623},
abstract = {This study represents 2 cases of kidney transplant recipients (KTRs) with invasive pulmonary Rhizopus infection, successfully treated with oral isavuconazole monotherapy without lobectomy. The rapid detection via mNGS of bronchoalveolar lavage fluid enabled early diagnosis and timely intervention, resulting in complete recovery and stable graft function. The literature review revealed a 16.7% mortality rate among 13 cases, with a higher mortality rate of 66.7% among patients receiving antifungal treatment without surgical intervention. Our findings underscore the efficacy of isavuconazole as a first-line monotherapy, characterized by lower nephrotoxicity and fewer interactions with immunosuppressants, and emphasize the crucial role of metagenome next-generation sequencing (mNGS) in early diagnosis of invasive mucormycosis in high-risk population.},
}
@article {pmid40082024,
year = {2025},
author = {Yin, F and Ge, T and Zalucki, MP and Xiao, Y and Peng, Z and Li, Z},
title = {Gut symbionts affect Plutella xylostella (L.) susceptibility to chlorantraniliprole.},
journal = {Pesticide biochemistry and physiology},
volume = {209},
number = {},
pages = {106327},
doi = {10.1016/j.pestbp.2025.106327},
pmid = {40082024},
issn = {1095-9939},
mesh = {Animals ; *ortho-Aminobenzoates/pharmacology ; *Moths/drug effects/microbiology ; *Insecticides/pharmacology ; *Insecticide Resistance/genetics ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; Bacteria/drug effects/genetics/metabolism ; Larva/drug effects/microbiology ; },
abstract = {Plutella xylostella, a globally economically important pest of cruciferous crops, has varying degrees of resistance to almost all insecticides. Insect gut microbiotas have a variety of physiological functions, and recent studies have shown that they have some potential connection with insecticide resistance. Here, we use metagenomics to analyze the differences in gut microbiota among 5 different populations of P. xylostella resistant to chlorantraniliprole. Differential gene expression was enriched in various metabolic pathways including carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, nucleotide metabolism and so on. Proteobacteria was the dominate phyla, and the relative abundance of common dominant genera in the treated group (CL, Bt, and BtCL) was higher than that in susceptible controls. We successfully isolated 15 species of bacteria, in which the Enterobacter hormaechei was associated with enhanced insecticide resistance. The population we isolated can metabolize chlorantraniliprole in vitro, with a metabolic rate of 34.8 % within 4 days. Our work advances understanding of the evolution of insecticide resistance and lays a foundation for the further exploration of symbiotic microbial associations of lepidopteran insects and their ecological consequences.},
}
@article {pmid40082000,
year = {2025},
author = {Massaro, CA and Meade, S and Lemarié, FL and Kaur, G and Bressler, B and Rosenfeld, G and Leung, Y and Williams, AJ and Lunken, G},
title = {Gut microbiome predictors of advanced therapy response in Crohn's disease: protocol for the OPTIMIST prospective, longitudinal, observational pilot study in Canada.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e094280},
doi = {10.1136/bmjopen-2024-094280},
pmid = {40082000},
issn = {2044-6055},
mesh = {Humans ; *Crohn Disease/microbiology/therapy ; *Gastrointestinal Microbiome ; Pilot Projects ; Prospective Studies ; Longitudinal Studies ; Observational Studies as Topic ; Feces/microbiology ; British Columbia/epidemiology ; Canada ; },
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis, is characterised by chronic and relapsing inflammation of the gastrointestinal tract, leading to significant morbidity and reduced quality of life. The global rise in IBD incidence is driven by a complex interplay of genetic, environmental, dietary and microbiome-related factors. Despite advancements in treatment, such as biologics, response rates remain variable, highlighting the need for personalised approaches. Recent research suggests that specific microbiome signatures may serve as biomarkers for predicting therapeutic efficacy, offering a potential tool for optimising treatment strategies in CD. The aim of the Optimising IBD Patient Treatment with Integrated Microbiome Investigation for Specialised Therapeutics (OPTIMIST) study is to evaluate microbiome profiles across various sample types in a Canadian CD cohort starting or already on advanced therapy, with the goal of developing predictive models for personalised therapeutics.<br><br>METHODS AND ANALYSIS: This study is a two-phase, longitudinal, prospective observational pilot study conducted in British Columbia, Canada, involving both CD patients and non-IBD controls. Phase 1 focuses on baseline microbiome differences across participant cohorts through cross-sectional analysis. Phase 2 follows participants over 12 months to assess microbiome changes and their association with treatment response. Stool samples, intestinal biopsies from the left colon, right colon and ileum, as well as mucosal wash samples from the proximal part of the distal colon, will undergo metagenomics, metaproteomics and metabolomics analyses to explore compositional and functional differences. Data will be analysed using alpha and beta diversity metrics, differential abundance analyses and multivariate analyses to identify microbiome-based predictors of therapeutic response.<br><br>ETHICS AND DISSEMINATION: Ethical approval was received by the Research Ethics Board (REB) of University of British Columbia-Providence Healthcare (UBC-PHC) with a REB number H23-02927. All amendments to the protocol are reported and adapted based on the requirements of the REB. The results of this study will be submitted to peer-reviewed journals and will be communicated in editorials/articles by the IBD Centre of BC and BC Children's Hospital Research Institute.<br><br>TRIAL REGISTRATION NUMBER: NCT06453720.<br><br>PROTOCOL VERSION: 2024-06-21, version 3.0.},
}
@article {pmid40081757,
year = {2025},
author = {Armengaud, J},
title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105430},
doi = {10.1016/j.jprot.2025.105430},
pmid = {40081757},
issn = {1876-7737},
abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.},
}
@article {pmid40081368,
year = {2025},
author = {Dai, R and Zhang, J and Liu, F and Xu, H and Qian, JM and Cheskis, S and Liu, W and Wang, B and Zhu, H and Pronk, LJU and Medema, MH and de Jonge, R and Pieterse, CMJ and Levy, A and Schlaeppi, K and Bai, Y},
title = {Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.02.013},
pmid = {40081368},
issn = {1097-4172},
abstract = {Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.},
}
@article {pmid40081359,
year = {2025},
author = {Ali, MJ},
title = {Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.},
journal = {Ophthalmic plastic and reconstructive surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/IOP.0000000000002931},
pmid = {40081359},
issn = {1537-2677},
abstract = {PURPOSE: To study the metagenomics of microbes isolated from the lacrimal sacs of patients with congenital nasolacrimal duct obstruction (CNLDO).<br><br>METHODS: A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from the patients with CNLDO who underwent endoscopic dacryocystorhinostomy at a tertiary care dacryology service. Immediately after a full-length lacrimal sac marsupialization, the samples were collected and transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina platform following DNA extraction and library preparation. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in the SqueezeMeta pipeline, and the functional annotation was performed using the MetaCerberus, v1.3.1.<br><br>RESULTS: The taxonomic hit distribution across the samples showed that bacteria were the most common isolates, followed by fungi and viruses. The major bacterial phyla identified across the samples of CNLDO were proteobacteria, firmicutes, actinobacteria, and bacteroidetes. The prevalent organisms include Haemophilus influenzae, Streptococcus pneumoniae, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Staphylococcus aureus, and Ochrobactrum anthropi, among others. The predominant fungal species identified include Botrytis cinerea, Aspergillus oryzae, and Fusarium fujikuroi. Several species of pandoravirus were the common viruses recognized.<br><br>CONCLUSIONS: This is the first whole metagenome sequencing of the lacrimal sac contents from patients with CNLDO, which showed that the sacs harbored diverse microbial communities of bacteria, fungi, and viruses. Further work is needed to decipher the polymicrobial interactions and their relationship with CNLDO.},
}
@article {pmid40081035,
year = {2025},
author = {Qv, M and Dai, D and Wu, Q and Wang, W and Li, L and Zhu, L},
title = {Metagenomic insight into the horizontal transfer mechanism of fluoroquinolone antibiotic resistance genes mediated by mobile genetic element in microalgae-bacteria consortia.},
journal = {Journal of environmental management},
volume = {380},
number = {},
pages = {124946},
doi = {10.1016/j.jenvman.2025.124946},
pmid = {40081035},
issn = {1095-8630},
abstract = {Antibiotics could accumulate in the environment with the discharge of wastewater from families, hospitals and livestock farms, which intensifies the spread of resistance genes around the world. Although microalgae-bacteria consortia (MBC) can efficiently remove antibiotics, the horizontal transfer mechanism of antibiotics resistance genes in MBC is still rarely reported. In this study, the removal efficiency of ofloxacin, norfloxacin and enrofloxacin by MBC under different antibiotic concentrations was investigated, while resistance genes in the MBC were identified and the mechanism of horizontal transfer was disclosed. The results showed that norfloxacin removal efficiency (up to 56.35 %) surpassed that of ofloxacin and enrofloxacin. The abundance of the fluoroquinolone resistance gene QnrS8 was the highest at 1331. The horizontal transfer of resistance gene QnrS8 and QnrS11 were mainly mediated by transposons. Fluoroquinolones increased the abundance of Brevundimonas (<0.10 % up to 9.63 %) and Bosea (0.96 % up to 17.67 %) involved in antibiotic removal. Arthrobacter and Acidovorax might be potential hosts which carried fluoroquinolone resistance genes. Structural equation model indicated that the key factor influencing the fluoroquinolone resistance genes abundance in MBC was transposons. These findings drew an insightful understanding of MBC application for fluoroquinolone antibiotics removal and the horizontal transfer mechanism of fluoroquinolone resistance genes.},
}
@article {pmid40080648,
year = {2025},
author = {Starcevic, A and Figueredo, RTA and Naldoni, J and Corrêa, LL and Okamura, B and Adriano, EA and Long, PF},
title = {Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa).},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf014},
pmid = {40080648},
issn = {2047-217X},
support = {2019/17427-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 307485/2023-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*DNA Methylation ; *Myxozoa/genetics ; Animals ; *Cytosine/metabolism ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled 5 myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.},
}
@article {pmid40080343,
year = {2025},
author = {Birkeland, KW and Mostert, L and Claas, ECJ and Aamot, HV and Demuyser, T},
title = {The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {40080343},
issn = {1439-0973},
abstract = {BACKGROUND: The diversity of pathogens causing central nervous system (CNS) infections presents a diagnostic challenge. Patient demographics and geographical location affect the likelihood of certain pathogens causing infection. Current diagnostic methods rely on labour-intensive cultivation or targeted detection. Metagenomic next-generation sequencing (mNGS) is a promising tool for detecting pathogens in CNS infections, offering an unbiased approach. To enhance our understanding of patient demographics and the range of pathogens identified through mNGS, we conducted a systematic review of case reports.<br><br>METHODS: The PubMed database was searched in March 2024. Case reports on CNS infections and mNGS published from January 2014 through February 2024 were included based on predefined criteria.<br><br>RESULTS: The search yielded 649 articles, of which 76 were included, encompassing 104 patients. Most patients were male (75%), the median age was 31,5 years [0-75] and 28% were immunocompromised. The most common diagnosis was encephalitis (36%), followed by meningitis (23%) and meningoencephalitis (22%). 53 unique pathogens were identified, comprising 27 different viruses, 19 bacteria, 5 parasites, and 2 fungi. Syndromic encephalitis/meningitis panels would only have detected four of the viruses and five of the bacteria. Additionally, 14 of the bacterial species are considered slow-growing or fastidious and could be challenging to detect by culture.<br><br>CONCLUSION: The application of mNGS in diagnosing CNS infections reveals the diversity of pathogens responsible for these severe infections, thereby improving diagnostics and facilitating targeted treatment. While case reports may be subjected to bias, they provide valuable insights into the use of mNGS in this clinical context.},
}
@article {pmid40079640,
year = {2025},
author = {Passos, GS and Pellegrinetti, TA and Fiore, MF},
title = {Metagenome-assembled bacterial genomes from long accurate reads associated with Capilliphycus salinus ALCB114379.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0080724},
doi = {10.1128/mra.00807-24},
pmid = {40079640},
issn = {2576-098X},
abstract = {We report the complete genome sequences of five bacteria associated with the marine cyanobacterium Capilliphycus salinus ALCB114379 of the phylum Pseudomonadota. This genetic diversity offers insights into the cyanosphere, shedding light on potential relationships between these microorganisms and their cyanobacterial hosts.},
}
@article {pmid40078981,
year = {2024},
author = {Hu, T and Cheng, Y and Wan, J and Liu, Y and Zhuang, Y and Zhou, M and Zhang, X and Tan, X and Deng, A and Zhang, M and Wang, P and Li, X and Zong, J and Cheng, L and Kang, M},
title = {Q fever diagnosed using metagenomic next-generation sequencing in Guangdong Province, China.},
journal = {Biosafety and health},
volume = {6},
number = {6},
pages = {337-340},
pmid = {40078981},
issn = {2590-0536},
abstract = {Q fever is a zoonotic disease caused by infection with Coxiella burnetii (C. burnetii). Due to its atypical symptoms and the absence of specific detection methods, Q fever is underdiagnosed commonly. Herein, we report a case of Q fever confirmed by metagenomic next-generation sequencing (mNGS) in March 2024 in Guangdong Province, China. The patient initially experienced fever and was admitted to hospital six days later. Despite a series of laboratory tests conducted at the hospital, the pathogen remained undetermined. Ten days after admission, mNGS revealed that the patient was infected with C. burnetii. The patient subsequently underwent treatment with doxycycline and recovered well. Epidemiological investigation revealed that the patient had been exposed to sheep infected with C. burnetii without any protective measures in Jiangxi Province, China. Based on the comprehensive results of mNGS, exposure history, clinical manifestations and treatment response, the patient was confirmed as a Q fever case. As a neglected and underestimated illness, Q fever necessitates an elevation in awareness among medical staff and the public. The public should be encouraged to take personal protective measures when exposed to livestock. Further research is needed to explore the rational application of mNGS in the diagnosis of uncommon and unknown diseases.},
}
@article {pmid40078947,
year = {2024},
author = {Fan, Q and Jiang, M and Zhang, J and Tang, G and Gao, M and Wen, Y and Deng, X and Dai, J and Lai, H and Qian, P and Lin, Y and He, R and Li, L and Li, Y and Li, Z and Liu, X and Li, Y and Yu, N and Lan, Y and Hu, F and Li, F},
title = {Prevalence of bacteria, fungi, and virus coinfections with SARS-CoV-2 Omicron variant among patients with severe COVID-19 in Guangzhou, China, winter 2022.},
journal = {Biosafety and health},
volume = {6},
number = {2},
pages = {92-97},
pmid = {40078947},
issn = {2590-0536},
abstract = {The status of coinfection during the national outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.5.2 or BF.7 in China in the winter of 2022, which is suspected to contribute substantially to the overloaded severe cases, needs to be investigated. We analyzed the coinfection status of 385 severe patients infected with the Omicron variant in Guangzhou using metagenomic sequencing. We found that 317 (82.3 %) patients were coinfected with at least one additional pathogen(s), including bacteria (58.7 %), fungi (27.1 %) and viruses (73.5 %). Pseudomonas aeruginosa (P. aeruginosa) (24.2 %), Staphylococcus aureus (S. aureus) (14.0 %), and Klebsiella pneumoniae (K. pneumonia) (13.4 %) ranked as the top three coinfected bacteria. Aspergillus fumigatus (A. fumigatus) (39.5 %), Pneumocystis jirovecii (P. jirovecii) (24.4 %) and Canidia albicans (C. albicans) (22.1 %) were the top three coinfected fungi. Epstein-Barr virus (EBV) (63.1 %), Human herpesvirus 7 (HHV-7) (34.8 %), and Herpes simplex virus 1 (HSV-1) (32.6 %) were the top three coinfected viruses. Of note, the detection of multiple coinfections of potential pathogenic bacteria, fungi, and viruses, despite lacking consistent patterns, highlighted a complicated synergistic contribution to disease severity. Our study presents the most comprehensive spectrum of bacterial, fungal, and viral coinfections in Omicron-associated severe coronavirus disease 2019 (COVID-19), implying that the coinfection of conditional pathogens might synergistically deteriorate the Omicron infection outcomes.},
}
@article {pmid40078943,
year = {2024},
author = {Wang, Y and Qu, M and Bi, Y and Liu, WJ and Ma, S and Wan, B and Hu, Y and Zhu, B and Zhang, G and Gao, GF},
title = {The multi-kingdom microbiome catalog of the chicken gastrointestinal tract.},
journal = {Biosafety and health},
volume = {6},
number = {2},
pages = {101-115},
doi = {10.1016/j.bsheal.2024.02.006},
pmid = {40078943},
issn = {2590-0536},
abstract = {Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries. We found that 812 and 240 MAGs in our dataset were putative novel species and genera, respectively, far beyond what was previously reported. The newly unclassified MAGs were predominant in Phyla Firmicutes_A (n = 263), followed by Firmicutes (n = 126), Bacteroidota (n = 121), and Proteobacteria (n = 87). Most of the classified species-level viral operational taxonomic units belong to Caudovirales. Approximately, 63.24 % of chicken gut viromes are predicted to infect two or more hosts, including complete circular viruses. Moreover, we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses. Together, our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date, functional insights into the chicken gastrointestinal tract microbiota, and paves the way for microbial interventions for better chicken health and productivity.},
}
@article {pmid40078550,
year = {2025},
author = {Wang, G and Haenelt, S and Corrêa, FB and da Rocha, UN and Musat, F and Zhang, J and Müller, JA and Musat, N},
title = {Riverine antibiotic resistome along an anthropogenic gradient.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1516033},
doi = {10.3389/fmicb.2025.1516033},
pmid = {40078550},
issn = {1664-302X},
abstract = {The introduction of antibiotic-resistant bacteria into riverine systems through the discharge of wastewater treatment plant (WWTP) effluent and agricultural waste poses significant health risks. Even when not pathogenic, these bacteria can act as reservoirs for antibiotic resistance genes (ARGs), transferring them to pathogens that infect humans and animals. In this study, we used fluorescence in situ hybridization, qPCR, and metagenomics to investigate how anthropogenic activities affect microbial abundance and the resistome along the Holtemme River, a small river in Germany, from near-pristine to human-impacted sites. Our results showed higher bacterial abundance, a greater absolute and relative abundance of ARGs, and a more diverse ARG profile at the impacted sites. Overall, the ARG profiles at these sites reflected antibiotic usage in Germany, with genes conferring resistance to drug classes such as beta-lactams, aminoglycosides, folate biosynthesis inhibitors, and tetracyclines. There were also variations in the ARG profiles of the impacted sites. Notably, there was a high abundance of the oxacillin resistance gene OXA-4 at the downstream site in the river. In the metagenome assembly, this gene was associated with a contig homologous to small plasmids previously identified in members of the Thiotrichaceae. The likely in-situ host of the putative plasmid was a close relative of Thiolinea (also known as Thiothrix) eikelboomii, a prominent member of WWTP microbiomes worldwide. Our results show that the effluent from WWTPs can introduce bacteria into the environment that act as shuttle systems for clinically relevant ARG.},
}
@article {pmid40078542,
year = {2025},
author = {Zhang, C and Liu, Z and Yu, H and Shen, Y and Lu, L and Kong, F and Sun, W and Wei, X and Jin, L and Ge, L and Zeng, B},
title = {Dynamic changes in the gut microbiota of SPF Bama piglets during breast and formula feeding.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537286},
doi = {10.3389/fmicb.2025.1537286},
pmid = {40078542},
issn = {1664-302X},
abstract = {The gut microbiota plays a crucial role in the growth performance, health status, and welfare of pigs. Breast milk is a key factor in the colonization of gut microbiota and the overall health of newborn piglets. With advancements in breeding technology, formula milk has been widely adopted as a substitute for breast milk. This study aims to investigate the effects of sow feeding (natural breastfeeding) and formula milk feeding on the gut microbiota of specific pathogen-free (SPF) Bama pigs. Using metagenomic sequencing technology, we analyzed 114 fecal samples to uncover the impacts of different feeding methods on gut microbial diversity, dominant microbial populations, metabolic functions, carbohydrate-active enzymes (CAZymes), and antibiotic resistance genes (ARGs). The results revealed significant differences in the structure and function of gut microbiota between the breast milk (BM) group and the formula milk (FM) group at day 21. The BM group exhibited higher gut microbial diversity compared to the FM group, along with more extensive metabolic functions at both the gene and species levels. Notably, the FM group demonstrated higher activity in galactose metabolism and glycan metabolism, particularly at day 21. Additionally, the FM group showed significantly higher levels of ARGs against glycopeptide antibiotics at days 21 and 28 compared to the BM group. This study also found that breastfeeding and formula feeding differentially regulate the metabolic activity of gut microbiota and the expression of related enzymes, which may have long-term effects on nutrient absorption and disease resistance in pigs. These findings provide new insights into how different feeding methods shape the gut microbiota of pigs and offer a scientific basis for optimizing feeding strategies and improving breeding efficiency.},
}
@article {pmid40078316,
year = {2025},
author = {Zhao, C and Escalante, C and Jacobson, AL and Balkcom, KS and Conner, KN and Martin, KM},
title = {Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1461588},
doi = {10.3389/finsc.2025.1461588},
pmid = {40078316},
issn = {2673-8600},
}
@article {pmid40077957,
year = {2025},
author = {Ma, Z and Wen, X and Zhang, Y and Ai, Z and Zhao, X and Dong, N and Dou, X and Shan, A},
title = {Thymol Alleviates Colitis by Modulating Intestinal Barrier Damage, Gut Microbiota, and Amino Acid Metabolic Pathways.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c10406},
pmid = {40077957},
issn = {1520-5118},
abstract = {Thymol (THY) is a phenolic monoterpene compound that has garnered attention due to its various biological properties, including antioxidant, anti-inflammatory, and immune-regulatory effects. The purpose of this study was to determine the therapeutic and protective effects of THY in colitic mice, with a particular focus on the mechanisms involving gut microbiota. The results showed that early intervention with THY (40 and 80 mg/kg) not only alleviated the clinical symptoms and colonic damage in mice with dextran sodium sulfate (DSS)-induced colitis but also suppressed the colonic production of inflammatory cytokines (IL-1β, IL-6, and IL-18) and enhanced the expression of mucins (MUC1 and MUC2) and trefoil factor family 3 (TFF3), thereby improving the integrity of the intestinal epithelial barrier. In addition, THY altered the composition of the gut microbiota in colitis mice by increasing the abundance of Bacteroides and reducing the abundance of Proteobacteria. Fecal microbial transplantation (FMT) results demonstrated that FM from THY donor mice significantly improved symptoms of inflammatory bowel disease (IBD), confirming the crucial role of the gut microbiota. Metagenomic and untargeted metabolomic studies found that the characteristic microbiota of THY is Prevotellaceae, and THY significantly upregulated the amino acid metabolic pathways related to arginine and proline metabolism, arginine biosynthesis, and glycerophospholipid metabolism. In summary, THY holds significant potential as a functional additive to enhance host intestinal activity.},
}
@article {pmid40077671,
year = {2025},
author = {Gao, Y and Borjihan, Q and Zhang, W and Li, L and Wang, D and Bai, L and Zhu, S and Chen, Y},
title = {Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.},
journal = {Nutrients},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/nu17050801},
pmid = {40077671},
issn = {2072-6643},
support = {2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; 2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Probiotics/pharmacology ; Mice ; *Feces/microbiology ; *Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Dysbiosis/therapy ; Serotonin/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Acetic Acid ; Constipation/therapy/microbiology/metabolism ; Butyric Acid/metabolism ; Tryptophan/metabolism ; },
abstract = {Background/Objectives: Irritable bowel syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Emerging evidence implicates gut microbiota dysbiosis in IBS pathogenesis, and probiotic interventions targeting microbial modulation hold therapeutic promise. Methods: this study used fecal microbiota transplantation to establish a mouse model of IBS before evaluating the effects of the complex probiotic by using metagenomics and targeted metabolomics to explore the potential mechanism. Results: After 14 days, the probiotic relieved constipation, reduced inflammation and intestinal permeability, lowered 5-HT levels and increased serotonin transporter (SERT) expression in tissues. Metagenomic analysis showed a reduced inflammation-related species abundance. It also decreased fecal butyric acid, acetic acid and tryptophan levels in IBS mice. Conclusions: The probiotic complex effectively alleviated IBS symptoms in mice by modulating gut microbiota and fecal metabolites, providing insights for future IBS research and treatment.},
}
@article {pmid40077516,
year = {2025},
author = {Li, W and Xu, M and Liu, Y and Zhang, S and Wang, J and Zhang, Z and Xiao, G and Wang, R and Zhang, J and Xue, H},
title = {Lactiplantibacillus plantarum GOLDGUT-HNU082 Alleviates CUMS-Induced Depressive-like Behaviors in Mice by Modulating the Gut Microbiota and Neurotransmitter Levels.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/foods14050813},
pmid = {40077516},
issn = {2304-8158},
support = {No. 32222066//National Natural Science Foundation of China/ ; THAITS-4//Earmarked Fund for Tropical High-efficiency Agricultural Industry Technology System of Hainan University/ ; },
abstract = {Emerging evidence links depressive disorders to the gut microbiota via the gut-brain axis. Probiotics, which are microorganisms that modulate the gut microbiota, have shown promising results in alleviating depression and are increasingly recognized as functional food components with potential health benefits. This study examines the effects of Lactiplantibacillus plantarum GOLDGUT-HNU082 (Lp082), a probiotic strain with potential applications in functional foods, on chronic unpredictable mild stress (CUMS)-induced depression in mice. Behavioral tests, measurements of the neurotransmitters and inflammatory cytokines in the serum and colon tissue, and the metagenomic sequencing of the gut microbiota were used to investigate potential mechanisms. The results demonstrated that Lp082 significantly alleviated depressive-like behaviors in CUMS mice, restored the balance of key neurotransmitters like serotonin (5-HT), reduced the levels of inflammatory cytokines like TNF-α, and enhanced brain neuroplasticity by promoting hippocampal neurogenesis. Additionally, Lp082 altered the composition of the gut microbiota in CUMS mice and promoted the growth of Bifidobacterium, improving metabolic pathways related to neurotransmitter synthesis. These findings indicate that Lp082, as a potential functional food ingredient, alleviates depressive-like behaviors in mice by reshaping the gut microbiota, offering new insights into the use of probiotics in functional foods for mental health management.},
}
@article {pmid40077458,
year = {2025},
author = {Jing, Y and Wang, Z and Cheng, W and Fan, H and Zheng, K and Zheng, Y and Wu, L},
title = {Structure Characterization and Treatment Effect of Zingiber officinale Polysaccharide on Dextran Sulfate Sodium-Induced Ulcerative Colitis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/foods14050753},
pmid = {40077458},
issn = {2304-8158},
support = {HBCT2023080201, HBCT2023080205//the Innovation Team of Hebei Province Modern Agricultural Industry Technology System/ ; H2024423098//the Hebei Natural Science Foundation/ ; 2024107//the Science and Technology Program of Hebei Administration of Traditional Chinese Medicine/ ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is on the rise all over the world. Zingiber officinale polysaccharide (ZOP-1) has good anti-inflammatory and antioxidant effects, but the therapeutic effect and mechanism of ZOP-1 on UC are still unclear.<br><br>METHODS: ZOP-1 obtained by water extraction and alcohol precipitation was analyzed by methylation and NMR. At the same time, the mechanism of ZOP-1 in the treatment of UC was clarified by hematoxylin-eosin (HE) staining, metagenomics, immunohistochemistry, and protein blot (Wb).<br><br>RESULTS: ZOP-1 was the structure of the by &#x2192;4,6)-&#x3b2;-Glcp-1&#x2192; and &#x2192;3,6)-&#x3b1;-Galp-(1&#x2192; constitute the main chain, there were two branched chain by &#x2192;4)-&#x3b2;-Glcp(1&#x2192;, and &#x3b1;-Araf(1&#x2192; as the end group. ZOP-1 significantly improved the shortening and thickening of the colon, changed the index of immune organs, inhibited the production of inflammatory factors in mice with ulcerative colitis, changed the intestinal flora of mice, increased the content of short-chain fatty acids (SCFAs) in the intestine, and controlled the TLR4/NF-&#x3ba;B/MAPK signaling pathway, thus preventing and treating DSS-induced ulcerative colitis in mice.<br><br>CONCLUSIONS: ZOP-1 alleviated UC by controlling the expression of cytokines, thereby reducing intestinal inflammation and oxidative stress, enhancing intestinal integrity, modulating intestinal flora, and regulating the levels of SCFAs.},
}
@article {pmid40076957,
year = {2025},
author = {Kumagai, K and Ishikawa, S and Iino, M and Edamatsu, K and Okuyama, N and Yusa, K and Shimizu, Y and Aoki, R and Masuda, C and Ohashi, Y and Horie, A and Hoshi, K and Hamada, Y},
title = {Characterization of Salivary Microbiota in Japanese Patients with Oral Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
doi = {10.3390/ijms26052339},
pmid = {40076957},
issn = {1422-0067},
support = {JP 22K10113//JSPS KAKENHI Grant-in-Aid for Scientific Research (C)/ ; },
mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Mouth Neoplasms/microbiology ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Japan ; Case-Control Studies ; Adult ; Metagenomics/methods ; East Asian People ; },
abstract = {This study aimed to characterize salivary microbiota in patients with oral cancer using 16S rRNA amplicon sequencing. DNA was extracted from saliva samples of 23 patients with oral cancer and 95 age-matched controls. A metagenomic analysis was performed using 16S rRNA amplicon sequencing. Patients with oral cancer exhibited lower α-diversity, as indicated by the Chao-1 index, compared to the control group, and significant differences in β-diversity were observed between the two groups. At the genus level, 25 bacterial species such as Lautropia, Megasphaera, Lactobacillus, Kingella, Gemella, Staphylococcus, and Propionibacterium were identified in patients with oral cancer, with more than half being Gram-positive facultative anaerobes or anaerobes. The reduced bacterial diversity in saliva of patients with oral cancer suggests dysbiosis during oral carcinogenesis may contribute to changes in bacterial distribution within the oral cavity.},
}
@article {pmid40076673,
year = {2025},
author = {Velazquez-Meza, ME and Galarde-López, M and Cornejo-Juárez, P and Bobadilla-Del-Valle, M and Godoy-Lozano, E and Aguilar-Vera, E and Carrillo-Quiroz, BA and Ponce de León-Garduño, A and Velazquez Acosta, C and Alpuche-Aranda, CM},
title = {Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
doi = {10.3390/ijms26052051},
pmid = {40076673},
issn = {1422-0067},
support = {682339//CONAHCYT, M&#xe9;xico/ ; },
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Hospitals ; Bacteria/genetics/pathogenicity ; Metagenome ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Genes, Bacterial ; Humans ; Microbiota/genetics ; },
abstract = {Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.},
}
@article {pmid40076252,
year = {2025},
author = {Gao, Y and Xu, Y and Dong, Z and Guo, Y and Luo, J and Wang, F and Yan, L and Zou, X},
title = {Endophytic Fungal Diversity and Its Interaction Mechanism with Medicinal Plants.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {5},
pages = {},
doi = {10.3390/molecules30051028},
pmid = {40076252},
issn = {1420-3049},
support = {BS0050//Heilongjiang Province Postdoctoral Research Fund/ ; LH2022H001//Heilongjiang Natural Science Foundation Joint Guidance Project/ ; ZYW2023-073//Heilongjiang Province Traditional Chinese Medicine Research Project/ ; GZ20210110//Key Research and Development Guidance Project of Heilongjiang Province/ ; },
mesh = {*Plants, Medicinal/microbiology/chemistry ; *Endophytes/metabolism ; *Fungi/metabolism ; Biodiversity ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; },
abstract = {This paper reviewed the diversity of endophytic fungi and their interactions with medicinal plants, along with the research methodologies utilized to investigate these interactions. It mainly includes the diversity of endophytic fungi, as well as distribution diversity, species diversity, and the diversity of their metabolites and functions, including antibacterial, anti-inflammatory, anti-tumor, insecticidal, antioxidant capabilities, and so on. The research methodologies employed to investigate the interactions between endophytic fungi and medicinal plants are categorized into metagenomics, transcriptomics, metatranscriptomics, proteomics, and metabolomics. Furthermore, this study anticipates the potential applications of secondary metabolites derived from endophytic fungi in both medicine and agriculture.},
}
@article {pmid40076036,
year = {2025},
author = {Bai, X and Gu, Y and Li, D and Li, M},
title = {Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/ani15050753},
pmid = {40076036},
issn = {2076-2615},
support = {National Key R &amp; D Program of China (2020YFA0509500 and 2023YFD1301302)//Mingzhou Li/ ; the Biological Breeding-Major Projects in National Science and Technology (2023ZD0404404)//Mingzhou Li/ ; the Sichuan Science and Technology Program (2021ZDZX0008 and 2021YFYZ0009)//Mingzhou Li/ ; the National Natural Science Foundation of China (32421005, 32225046 and 32494802)//Mingzhou Li/ ; },
abstract = {The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.},
}
@article {pmid40075266,
year = {2025},
author = {Cao, H and Xu, J and Wang, H and Yi, W and Yang, D and Yang, J and Sun, J and Wang, Y and Zhang, F and Yan, J and Li, D},
title = {Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {135},
pmid = {40075266},
issn = {1471-2180},
support = {2023YFF1104305//National Key Research and Development Program of China/ ; 2022YFF1100601//National Key Research and Development Program of China/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; Y2021001//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; K20221026//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; CXTD2021003//Key discipline construction program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; KX-23-C196//Soft Science Project of Wuxi Science and Technology Association/ ; YJZ202305//Medical research projects in research-oriented hospitals of Affiliated Hospital of Jiangnan University/ ; HB2023062//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023063//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023061//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; LCYJ202347//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202310//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202322//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202303//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; BK20210468//Natural Science Foundation of Jiangsu Province/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; *Weight Gain ; *Liver/metabolism ; Male ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Mice, Inbred C57BL ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; Fatty Acids, Volatile/metabolism ; Lipid Metabolism ; },
abstract = {BACKGROUND: Dysbiosis of the microbiome is strongly associated with weight rebound after dieting. However, the interactions between the host and microbiome and their relevance to the pathogenesis of post-diet weight rebound remain unclear.<br><br>PURPOSE: This study aimed to evaluate the effects of fecal microbiota transplantation (FMT) on post-diet weight regain and to investigate the underlying mechanisms by which FMT inhibits weight regain.<br><br>METHODS: FMT was administered once daily to mice for 5 weeks. Gas chromatography tandem mass spectrometry was employed to analyze short-chain fatty acid levels in serum, ultrahigh-performance liquid chromatography tandem mass spectrometry was utilized for analyzing hepatic lipid metabolites, and shotgun metagenomic sequencing was applied to examine the intestinal microbiome.<br><br>RESULTS: FMT reduced weight regain and prevented lipid accumulation in both liver and adipose tissue while also improving glucose intolerance in mice. Furthermore, FMT increased the abundance of Enterorhabdus caecimuris and decreased the abundances of Burkholderiales, Sutterellaceae, Turicimonas muris, Bacteroides stercorirosoris, and Acetivibrio ethanolgignens within the gut microbiota. Additionally, elevated propionic acid levels and significant alterations in hepatic lipid metabolites were observed following FMT administration.<br><br>CONCLUSIONS: Our findings demonstrate that FMT effectively mitigates post-diet weight regain and associated complications. These effects are mediated through interactions between the gut microbiota and the liver via the gut-propionic acid-liver axis.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40075219,
year = {2025},
author = {Sun, Y and Huang, S and Li, M and Yang, Y and Ma, J and Xie, R and Wang, J and Zhao, Q and Qin, S and He, L and Jiang, J and Zhao, Q and Jin, G and Liu, X and Huang, H and Yang, Y and Wei, J and Liu, W and Wang, B and Yang, R and Su, X and Cao, H},
title = {Maternal high-fat diet disrupts intestinal mucus barrier of offspring by regulating gut immune receptor LRRC19.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {420},
pmid = {40075219},
issn = {2399-3642},
support = {82270574//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82070545//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400632//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81970488//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Female ; Mice ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Mice, Inbred C57BL ; Pregnancy ; Mice, Knockout ; Male ; Interleukin-22 ; Receptors, Immunologic/metabolism/genetics ; },
abstract = {Maternal high fat diet (MHFD) increased colitis susceptibility in adulthood. However, the mechanism remains unclear. We sought to explore whether novel gut immune receptor leucine-rich repeat C19 (LRRC19) contributed to the impaired mucus barrier of offspring exposed to MHFD via gut immune response and microbiota. The results showed that MHFD significantly impaired the intestinal mucus barrier of offspring, and up-regulated the expression of LRRC19. Lrrc19 deletion alleviated the mucus barrier disruption. Mechanistically, metagenome sequencing revealed that the MHFD-induced gut microbiota alteration was partly restored in Lrrc19[-/-] offspring. Muc2-associated bacteria were decreased in the MHFD group, such as Akkermansia_muciniphila_CAG_154, which increased in the Lrrc19-deficient offspring. Moreover, Lrrc19[-/-] offspring had a higher rate of indole-3-acetic acid (IAA)-producing bacterium, such as Lactobacillus reuteri. A targeted metabolomics analysis revealed that IAA emerged as the top candidate that might mediate the protective effects. IAA was found to improve the mucus barrier function by increasing the ratio of interleukin-22 (IL-22)[+] ILC3 cells in an aryl hydrocarbon receptor (AhR)-dependent manner. These results suggest that MHFD disrupts the intestinal mucus barrier of offspring through regulating gut immune receptor LRRC19 and inducing an imbalance of gut microbiota and microbiota-derived metabolites.},
}
@article {pmid40074067,
year = {2025},
author = {Pragasam, AK and Maurya, S and Jain, K and Pal, S and Raja, C and Yadav, R and Kumar, S and Purohit, A and Pradhan, D and Kajal, K and Talukdar, D and Singh, AN and Verma, J and Jana, P and Rawat, S and Kshetrapal, P and Krishna, A and Kumar, S and Bansal, VK and Das, B and Srikanth, CV and Garg, PK},
title = {Invasive Salmonella Typhimurium Colonizes Gallbladder and Contributes to Gallbladder Carcinogenesis through Activation of Host Epigenetic Modulator KDM6B.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217621},
doi = {10.1016/j.canlet.2025.217621},
pmid = {40074067},
issn = {1872-7980},
abstract = {Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.},
}
@article {pmid40073489,
year = {2025},
author = {Han, NN and Wang, XP and Jin, JA and Li, WH and Yang, WY and Fan, NS and Jin, RC},
title = {Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system.},
journal = {Water research},
volume = {279},
number = {},
pages = {123463},
doi = {10.1016/j.watres.2025.123463},
pmid = {40073489},
issn = {1879-2448},
abstract = {Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.},
}
@article {pmid40072902,
year = {2025},
author = {Varsani, A and Custer, JM and Cobb, IN and Harding, C and Collins, CL and Suazo, C and Schreck, J and Fontenele, RS and Stainton, D and Dayaram, A and Goldstein, S and Kazlauskas, D and Kraberger, S and Krupovic, M},
title = {Bacilladnaviridae: refined taxonomy and new insights into the biology and evolution of diatom-infecting DNA viruses.},
journal = {The Journal of general virology},
volume = {106},
number = {3},
pages = {},
doi = {10.1099/jgv.0.002084},
pmid = {40072902},
issn = {1465-2099},
mesh = {*Diatoms/virology/genetics ; *Phylogeny ; *Genome, Viral ; *DNA Viruses/genetics/classification ; New Zealand ; Metagenomics ; Animals ; Evolution, Molecular ; DNA, Viral/genetics ; Capsid Proteins/genetics ; },
abstract = {Bacilladnaviruses are single-stranded DNA viruses that infect diatoms that, so far, have been primarily identified in marine organisms and environments. Using a viral metagenomics approach, we discovered 13 novel bacilladnaviruses originating from samples of mud-flat snail (Amphibola crenata; n=3 genomes) and benthic sediments (n=10 genomes) collected from the Avon-Heathcote Estuary in New Zealand. Comparative genomics and phylogenetic analysis of the new bacilladnavirus sequences in the context of the previously classified members of the family helped refine and further expand the Bacilladnaviridae taxonomy. Here, based on the replication-associated protein phylogeny and pairwise identities, we established 4 new genera - Aberdnavirus, Keisodnavirus, Puahadnavirus and Seawadnavirus - and 13 new species within the family. Comparison of the bacilladnavirus capsid protein sequences suggests that the positively charged N-terminal region (R-arm) is required for encapsidation of the larger genomes, whereas the smaller bacilladnavirus genomes can be packaged in the absence of the R-arm subdomain. Furthermore, analysis of the bacilladnavirus genomes revealed that members of three genera encode a highly derived variant of a phospholipase A1, which is predicted to be involved in the lysis of the infected diatoms and/or facilitates the entry of the virions into the host cells. Collectively, our results allow refining of the taxonomy of bacilladnaviruses and provide new insights into the biology and evolution of this understudied group of diatom viruses.},
}
@article {pmid40078515,
year = {2023},
author = {Li, Z and Wu, C and Tang, LA and Liang, Y and A, R and Huang, D and Ning, C and Wang, W and Tan, W},
title = {mNGS-based dynamic pathogen monitoring for accurate diagnosis and treatment of severe pneumonia caused by fungal infections.},
journal = {Biosafety and health},
volume = {5},
number = {3},
pages = {138-143},
doi = {10.1016/j.bsheal.2023.04.004},
pmid = {40078515},
issn = {2590-0536},
abstract = {Metagenomic next-generation sequencing (mNGS) has been widely applied to identify pathogens associated with infectious diseases. However, limited studies have explored the use of mNGS-based dynamic pathogen monitoring in intensive care unit patients with severe pneumonia. Here, we present a clinical case of an 86-year-old male patient with severe pneumonia caused by a fungal infection. During the clinical treatment, four mNGS analyses were performed within two consecutive weeks. Various respiratory fungal pathogens, including Candida orthopsilosis, Candida albicans, and Aspergillus fumigatus were detected by mNGS of bronchoalveolar lavage fluid (BALF). Based on conventional pathogen identification and clinical symptoms, the patient was diagnosed with severe pneumonia caused by a fungal infection. The abundance of fungal species decreased gradually in response to antifungal and empirical therapies, and the fungal infections were effectively controlled. In summary, our results demonstrated that mNGS could effectively identify pathogens in patients with severe pneumonia. Additionally, dynamic pathogen monitoring based on mNGS could assist in the precise diagnosis of complex infections and may facilitate rapid induction of the most appropriate therapy.},
}
@article {pmid40072675,
year = {2025},
author = {Verma, N and Chavan, N and Aulakh, KS and Sharma, A and Shouche, Y and Ramana, VV},
title = {Temporal Dynamics of Microbial Community Composition and Antimicrobial Resistance in a Mass Gathering Setting Using Culturomics and Metagenomic Approaches.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {41},
pmid = {40072675},
issn = {2210-6014},
support = {OLP-805//CSIR - Institute of Microbial Technology/ ; GAP-233//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Humans ; India/epidemiology ; *Metagenomics/methods ; Microbiota/drug effects ; Bacteria/drug effects/genetics/isolation &amp; purification/classification ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the major global concerns in the current scenario. Mass-gathering events in fast-developing and densely populated areas may contribute to antibiotic resistance. Despite meticulous planning and infrastructure development, the effect of mass gatherings on microbial ecosystems and antibiotic resistance must be investigated. This study used culture and metagenome-based methods to investigate and compare the bacterial diversity, AMR profile &amp; mechanism of resistance for bacteria in water samples collected from the mass gathering event (2019 Prayagraj Kumbh Mela in Uttar Pradesh, India) with the control samples, collected during no mass gathering.<br><br>METHODS: This study analyzed the water samples collected from a mass gathering event held in February 2019. Water samples collected in this study were grouped into "Test" (mass gathering event) and "Control" (no mass gathering event) groups. This study involved methods including culturomics, antibiotyping, phenotypic &amp; genotypic identification methods, and metagenomics.<br><br>RESULTS: There is a significant variation observed in the evenness and richness of bacterial diversity and MDR profile, expressed in terms of the relative abundance of the bacterial species between test and control samples. Out of the total multi-drug resistant (MDR) strains identified in the Prayagraj sample, the majority were derived from the test sample. A pathway-based analysis of MDR strains revealed the highest levels of acquired resistance were related to the inhibition of cell wall synthesis primarily in Pseudomonas spp., followed by resistance to protein synthesis and nucleic acid synthesis pathways. Additionally, the overall resistance profile of the test sample demonstrated a significantly elevated resistome for beta-lactams, particularly in the Pseudomonas spp. Additionally, several ESBL (Extended-spectrum beta-lactamase)-associated gene variants were identified. The test sample showed a two-fold increase in the prevalence and diversity of common beta-lactam gene variants in addition to the presence of unique variants. Using the metagenomics approach, we investigated the mechanism of antibiotic resistance, and it revealed a dominant trend in antibiotic efflux and inactivation pathways within both the test and control samples. Overall, the bacterial diversity, abundance (including AMR strains of human origin), and ARGs were relatively higher in the Test sample compared to the control sample which was collected 3 months after the mass gathering event.<br><br>CONCLUSION: Our study found significant variations in microbial communities, MDR strains, and ARGs due to environmental and human influences. Pseudomonas spp. was the most abundant MDR strain, primarily resistant to cell wall synthesis inhibitors. The test sample showed an increased resistome for beta-lactams, while the control sample had reduced bacterial species, ARGs, and MDR strains linked to human microflora. This shift could be due to the re-establishment of native bacterial communities in the Ganges River which may be attributed to its bacteriophage activity, biomolecules, and inherent antimicrobial properties. The study highlights the need for surveillance, monitoring AMR emergence to develop new strategies to combat it.},
}
@article {pmid40072088,
year = {2025},
author = {Świdnicka-Siergiejko, A and Daniluk, J and Miniewska, K and Daniluk, U and Guzińska-Ustymowicz, K and Pryczynicz, A and Dąbrowska, M and Rusak, M and Ciborowski, M and Dąbrowski, A},
title = {Inflammatory Stimuli and Fecal Microbiota Transplantation Accelerate Pancreatic Carcinogenesis in Transgenic Mice, Accompanied by Changes in the Microbiota Composition.},
journal = {Cells},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/cells14050361},
pmid = {40072088},
issn = {2073-4409},
support = {No NCN 2017/27/B/NZ5/02904//National Science Center/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation ; *Mice, Transgenic ; *Pancreatic Neoplasms/microbiology/genetics/pathology ; Mice ; *Inflammation/pathology/microbiology ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Pancreatic Ductal/microbiology/genetics/pathology ; Carcinogenesis/genetics/pathology ; Feces/microbiology ; Proto-Oncogene Proteins p21(ras)/genetics ; Pancreas/pathology ; },
abstract = {An association between gut microbiota and the development of pancreatic ductal adenocarcinoma (PDAC) has been previously described. To better understand the bacterial microbiota changes accompanying PDAC promotion and progression stimulated by inflammation and fecal microbiota transplantation (FMT), we investigated stool and pancreatic microbiota by 16s RNA-based metagenomic analysis in mice with inducible acinar transgenic expressions of KrasG12D, and age- and sex-matched control mice that were exposed to inflammatory stimuli and fecal microbiota obtained from mice with PDAC. Time- and inflammatory-dependent stool and pancreatic bacterial composition alterations and stool alpha microbiota diversity reduction were observed only in mice with a Kras mutation that developed advanced pancreatic changes. Stool Actinobacteriota abundance and pancreatic Actinobacteriota and Bifidobacterium abundances increased. In contrast, stool abundance of Firmicutes, Verrucomicrobiota, Spirochaetota, Desulfobacterota, Butyricicoccus, Roseburia, Lachnospiraceae A2, Lachnospiraceae unclassified, and Oscillospiraceae unclassified decreased, and pancreatic detection of Alloprevotella and Oscillospiraceae uncultured was not observed. Furthermore, FMT accelerated tumorigenesis, gradually decreased the stool alpha diversity, and changed the pancreatic and stool microbial composition in mice with a Kras mutation. Specifically, the abundance of Actinobacteriota, Bifidobacterium and Faecalibaculum increased, while the abundance of genera such as Lachnospiraceace A2 and ASF356, Desulfovibrionaceace uncultured, and Roseburia has decreased. In conclusion, pancreatic carcinogenesis in the presence of an oncogenic Kras mutation stimulated by chronic inflammation and FMT dynamically changes the stool and pancreas microbiota. In particular, a decrease in stool microbiota diversity and abundance of bacteria known to be involved in short-fatty acids production were observed. PDAC mouse model can be used for further research on microbiota-PDAC interactions and towards more personalized and effective cancer therapies.},
}
@article {pmid40072031,
year = {2025},
author = {Huang, YJ},
title = {The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations.},
journal = {Immunological reviews},
volume = {330},
number = {1},
pages = {e70015},
doi = {10.1111/imr.70015},
pmid = {40072031},
issn = {1600-065X},
support = {U01TR004066/TR/NCATS NIH HHS/United States ; 75N92024D00012-0-759202400001-1/HL/NHLBI NIH HHS/United States ; },
mesh = {*Asthma/microbiology/immunology/etiology ; Humans ; *Microbiota/immunology ; Animals ; Biomarkers ; Genomics/methods ; Proteomics ; Metabolomics/methods ; Disease Susceptibility ; Metagenomics/methods ; Multiomics ; },
abstract = {Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.},
}
@article {pmid40071918,
year = {2025},
author = {Foysal, MJ and Neilan, BA and Timms, V},
title = {The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0231724},
doi = {10.1128/aem.02317-24},
pmid = {40071918},
issn = {1098-5336},
abstract = {UNLABELLED: This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes (n = 10) than the pristine site (n = 4). Metal and multicompound resistance was more frequent in rural (14%) compared to urban samples (5%). Pristine samples lacked multidrug and multicompound resistance and had lower resistance to aminoglycosides and the MLS group. Multiresistance was evidenced by copper and aminocoumarin resistance in rural samples and aminoglycoside and mercury resistance in Pseudomonas in all environments. These findings highlight the impact of human activities on AMR and MR spread, emphasizing the need for environmental monitoring and management.<br><br>IMPORTANCE: Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.},
}
@article {pmid40071515,
year = {2025},
author = {Medina, JS and Zhang, S and Narayanasamy, S and Wang, C and Al-Gashgari, B and Hong, PY},
title = {Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10879},
pmid = {40071515},
issn = {1520-5851},
abstract = {Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.},
}
@article {pmid40071205,
year = {2025},
author = {Park, J and Park, T},
title = {Composite quantile regression approach to batch effect correction in microbiome data.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1484183},
doi = {10.3389/fmicb.2025.1484183},
pmid = {40071205},
issn = {1664-302X},
abstract = {BACKGROUND: Batch effects refer to data variations that arise from non-biological factors such as experimental conditions, equipment, and external factors. These effects are considered significant issues in the analysis of biological data since they can compromise data consistency and distort actual biological differences, which can severely skew the results of downstream analyses.<br><br>METHOD: In this study, we introduce a new approach that comprehensively addresses two types of batch effects: "systematic batch effects" which are consistent across all samples in a batch, and "nonsystematic batch effects" which vary depending on the variability of operational taxonomic units (OTUs) within each sample in the same batch. To address systematic batch effects, we apply a negative binomial regression model and correct for consistent batch influences by excluding fixed batch effects. Additionally, to handle nonsystematic batch effects, we employ composite quantile regression. By adjusting the distribution of OTUs to be similar based on a reference batch selected using the Kruskal-Walis test method, we consider the variability at the OTU level.<br><br>RESULTS: The performance of the model is evaluated and compared with existing methods using PERMANOVA R-squared values, Principal Coordinates Analysis (PCoA) plots and Average Silhouette Coefficient calculated with diverse distance-based metrics. The model is applied to three real microbiome datasets: Metagenomic urine control data, Human Immunodeficiency Virus Re-analysis Consortium data, and Men and Women Offering Understanding of Throat HPV study data. The results demonstrate that the model effectively corrects for batch effects across all datasets.},
}
@article {pmid40070462,
year = {2025},
author = {Amevor, FK and Uyanga, VA and Wu, L and Xu, D and Shu, G and Wang, Y and Zhao, X},
title = {Enhancing poultry health and productivity through the liver-gut axis with integrated nutritional and immunological approaches: a mini-review.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1537099},
doi = {10.3389/fphys.2025.1537099},
pmid = {40070462},
issn = {1664-042X},
abstract = {The liver-gut axis plays a central role in maintaining the health and productivity of poultry. In addition, the liver-gut axis serves as a key regulator of digestion, metabolism, immunity, and detoxification. The gut, with its diverse microbiota, is the primary site for nutrient absorption and immune modulation, while the liver metabolizes nutrients, detoxifies harmful substances, and acts as a frontline defense against pathogens translocated from the gut. Disruptions in this interconnected system, including gut dysbiosis or liver inflammation, can lead to compromised immunity and reduced productivity. This mini-review explores integrated nutritional and immunological strategies aimed at optimizing the liver-gut axis to enhance poultry performance. Nutritional interventions, such as the use of flavonoids, vitamins, amino acids, micronutrients, probiotics, prebiotics, and synbiotics, have demonstrated their potential to support liver and gut health. Dietary components such as phytogenic additives, fiber, and fatty acids further contribute to immune modulation and systemic health. Immunological approaches, such as beta-glucans and in ovo stimulation, and molecular approaches, including advanced genetic techniques, offer additional avenues for improving disease resistance and organ function. Despite notable advancements, challenges including antibiotic resistance, environmental stressors, and implementation costs persist. Emerging technologies like metagenomics, metabolomics, and precision breeding offer innovative solutions to enhance liver-gut interactions. This review underscores recent advancements in understanding the liver-gut axis and calls for holistic strategies to improve sustainable poultry production. Future research should integrate these approaches to enhance resilience, productivity, and sustainability in the poultry industry.},
}
@article {pmid40069804,
year = {2025},
author = {Ye, X and Sahana, G and Lund, MS and Li, B and Cai, Z},
title = {Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {24},
pmid = {40069804},
issn = {2524-4671},
abstract = {BACKGROUND: Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies.<br><br>RESULTS: This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles.<br><br>CONCLUSIONS: The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.},
}
@article {pmid40069605,
year = {2025},
author = {Zhang, H and Wang, Y and Luo, Z and Zhang, B and Lan, X and Xu, L and Li, X and Huang, Z and Bai, J and Hu, D},
title = {Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {128},
pmid = {40069605},
issn = {1471-2180},
support = {YC-20018//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; 2023I0046//Supported by Science and Technology Planning Project of Fujian Province, China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; China ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Phylogeny ; Forests ; Metagenomics ; Sympatry ; Adaptation, Physiological ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Ruminants/microbiology ; },
abstract = {BACKGROUND: The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.<br><br>RESULTS: The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.<br><br>CONCLUSION: These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.},
}
@article {pmid40069560,
year = {2025},
author = {Breselge, S and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Cotter, PD},
title = {The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {415},
pmid = {40069560},
issn = {2399-3642},
support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; USIRL-2019-1//Science Foundation Ireland (SFI)/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine (DAFM)/ ; TC/2018/0025//Enterprise Ireland/ ; },
mesh = {*Fermentation ; *Kefir/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/metabolism/genetics/classification ; Metabolomics/methods ; Food Microbiology ; Water/metabolism ; Multiomics ; },
abstract = {Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. WK grains can be reused to start new fermentations. Here we investigate the microbial composition and function of 69 WK grains and their ferments by shotgun metagenomics. A subset of samples was subjected to metabolomic, including volatilomic, analysis. The impact of different fermentation practices on microbial composition and fermentation characteristics was analysed and it was noted that, for example, the common practice of drying water kefir grains significantly reduces microbial diversity and negatively impacts subsequent grain growth. Metagenomic analysis allowed the detection of 96 species within WK, the definition of core genera and the detection of different community states after 48 h of fermentation. A total of 485 bacterial metagenome assembled genomes were obtained and 18 putatively novel species were predicted. Metabolite and volatile analysis show associations between key species with flavour compounds. We show the complex microbial composition of WK and links between fermentation practices, microbes and the fermented product. The results can be used as a foundation for the selection of species for large scale WK production with desired flavour profiles and to guide the regulatory framework for commercial WK production.},
}
@article {pmid40068786,
year = {2025},
author = {Wang, L and Zhao, G and Guo, W and Li, Y and Chen, J and Niu, L},
title = {Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121363},
doi = {10.1016/j.envres.2025.121363},
pmid = {40068786},
issn = {1096-0953},
abstract = {Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.},
}
@article {pmid40068396,
year = {2025},
author = {Guo, M and Wu, Y and Huang, H and Li, S and Zhao, L and Cao, J and Wang, C},
title = {Revealing the critical role of rare bacterial communities in shaping antibiotic resistance genes in saline soils through metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137848},
doi = {10.1016/j.jhazmat.2025.137848},
pmid = {40068396},
issn = {1873-3336},
abstract = {Salinity is considered one of the basic abiotic factors influencing the diversity and distribution of antibiotic resistance genes (ARGs) in soils, yet little is known about the distribution and driving factors of ARGs in naturally saline soils. In this study, metagenomic analysis was conducted to explore the intricate dynamics among soil salinity, microbial community structure and ARGs propagation, with a particular focus on the key contribution of rare potential-hosts of ARGs in light and heavy saline soils. The findings revealed that salinity was significantly negatively correlated with the abundance of ARGs, light saline soils hosted a greater abundance of ARGs than high saline soils, with particularly significant enrichment in genes conferring resistance to multidrug, vancomycin, bacitracin and tetracenomycin C. Proteobacteria and Actinobacteria were identified as primary hosts for ARGs. Notably, rare potential hosts of ARGs play a crucial role in shaping the abundance of ARGs despite their low relative abundance (0.85 %), significantly influencing the relative abundance of ARGs in light and heavy saline soils. The average degree of rare potential-hosts of ARGs was found to be higher in light saline soils (average degree = 45.729 and 25.923 in light and heavy saline soils, respectively), and there was stronger interaction connected between microorganisms (edges = 35,760 and 20,259 in light and heavy saline soils, respectively). Also, microbial community niche width and niche overlap of rare potential-hosts of ARGs in light saline soils were significantly greater than that in heavy saline soils. This work emphasizes the importance of bacterial communities of rare potential-hosts of ARGs on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.},
}
@article {pmid40068378,
year = {2025},
author = {Weng, YT and Huang, CK and Cheng, A and Ruan, SY and Wang, JT},
title = {Next-generation sequencing for rapid etiologic diagnosis of acute respiratory distress syndrome: A case of life-threatening leptospirosis.},
journal = {Journal of infection and public health},
volume = {18},
number = {6},
pages = {102727},
doi = {10.1016/j.jiph.2025.102727},
pmid = {40068378},
issn = {1876-035X},
abstract = {Leptospirosis is a zoonotic infection with public health implications and diverse clinical presentations, ranging from mild symptoms to severe, life-threatening disease. In critical cases, it can cause multiorgan failure and death. Diagnosis is typically based on clinical suspicion and confirmed by laboratory testing. However, in acute, life-threatening cases, obtaining a history of exposure and recognizing early symptoms may be challenging. Traditional diagnostic methods for identifying causative pathogens are time-consuming and limited. Next-generation sequencing (NGS) has emerged as a novel diagnostic tool that identifies pathogens using DNA or RNA from bodily fluids, offering more timely, unbiased results, especially for fastidious or non-culturable organisms.},
}
@article {pmid40068343,
year = {2025},
author = {Almarhabi, H and Sarhan, A and Alharbi, A and Al-Amri, A and Ahamed, MF and Hala, S},
title = {Multifocal osteolytic lesions as an initial presentation of mycobacterium riyadhense: Case report and literature review.},
journal = {Journal of infection and public health},
volume = {18},
number = {5},
pages = {102741},
doi = {10.1016/j.jiph.2025.102741},
pmid = {40068343},
issn = {1876-035X},
abstract = {Mycobacterium riyadhense is a newly discovered, slow-growing nontuberculous mycobacterium with an emerging global distribution. We report a case of multifocal osteolytic lesions as the first sign of infection in a previously healthy 39-year-old female. M. riyadhense was detected in this case using next-generation metagenomic sequencing after it failed to be identified with conventional methods. The patient received 12 months of therapy with isoniazid, rifampin, and ethambutol, with the addition of moxifloxacin and clarithromycin in the first four months, and had a full return to health with no detectable disease at the last follow-up.},
}
@article {pmid40068342,
year = {2025},
author = {Song, R and Lv, B and He, Z and Li, H and Wang, H},
title = {Rhizosphere metabolite dynamics in continuous cropping of vineyards: Impact on microflora diversity and co-occurrence networks.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128134},
doi = {10.1016/j.micres.2025.128134},
pmid = {40068342},
issn = {1618-0623},
abstract = {The metabolism of the crop rhizosphere affects microflora diversity and nutrient cycling. However, understanding rhizosphere metabolism in suitable crops within arid desert environments and its impact on microflora interactions remains limited. Through metagenomic and non-targeted metabolomic sequencing of rhizosphere soils from one uncultivated land and four vineyards with cropping years of 5, 10, 15 and 20 years, the critical importance of rhizosphere metabolites in maintaining bacterial and fungal diversity was elucidated. The results revealed that Nocardioides, Streptomyces, and Solirubrobacter were the relatively abundant bacterial genera in rhizosphere soils, while Rhizophagus, Glomus, and Pseudogymnoascus were the relatively abundant fungal genera. The composition of rhizosphere metabolic changed significantly during the continuous cropping of grapevines. Dimethylglycine, Formononetin, and Dehydroepiandrosterone were the most important metabolites. Enrichment analysis revealed significant involvement of metabolic pathways such as biosynthesis of amino acids, unsaturated fatty acids, and linoleic acid metabolism. Procrustes analysis highlighted stronger correlations between rhizosphere metabolites and bacterial community compared to those of fungal community. This suggests distinct responses of microflora to crop-released chemical elements across different soil habitats. Co-occurrence network analysis demonstrated complex associations between rhizosphere metabolites and soil microflora, the positive correlations between rhizosphere metabolites and microflora networks predominated over negative correlations. Partial least squares path model indicated that the effect of cropping years on rhizosphere metabolites was greater than that on bacterial microflora diversity. Futhermore, pH, total phosphorus, and alkali-hydrolyzed nitrogen were the key environmental factors affecting rhizosphere metabolites and microbial diversity. These results deepen our valuable insights into the complex biological processes that rhizosphere metabolites influence on microorganisms, and provide strong support for maintaining microbial diversity in farmland soils in arid regions.},
}
@article {pmid40068284,
year = {2025},
author = {Corbera-Rubio, F and Boersma, AS and de Vet, W and Pabst, M and van der Wielen, PWJJ and van Kessel, MAHJ and van Loosdrecht, MCM and van Halem, D and Lücker, S and Laureni, M},
title = {Biological methane removal by groundwater trickling biofiltration for emissions reduction.},
journal = {Water research},
volume = {279},
number = {},
pages = {123450},
doi = {10.1016/j.watres.2025.123450},
pmid = {40068284},
issn = {1879-2448},
abstract = {Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration-submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.},
}
@article {pmid40067770,
year = {2025},
author = {Dominguez, EG and McDonald, BR and Zhang, H and Stephens, MD and Dietmann, EC and Nedden, M and Byington, N and Thompson, S and Junak, M and Pepperell, CS and Kisat, MT},
title = {Enrichment of Microbial DNA in Plasma to Improve Pathogen Detection in Sepsis: A Pilot Study.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf011},
pmid = {40067770},
issn = {1530-8561},
support = {//the American Association for Surgery of Trauma Research and Education Fund Trauma Critical Care Scholarship/ ; K08GM148858/GF/NIH HHS/United States ; R01-AI113287//NIH/NIAID/ ; },
abstract = {BACKGROUND: Diagnosis of sepsis and timely identification of pathogens in critically ill patients remains challenging. Plasma metagenomic sequencing to detect microbial cell-free DNA (mDNA) has shown promise, but low abundance of mDNA in plasma limits sensitivity and necessitates high sequencing depth. mDNA is shorter and more fragmented than human cell-free DNA. Here, we evaluated whether combining single-stranded DNA (ssDNA) sequencing library preparation and size selection can enrich mDNA and improve pathogen detection.<br><br>METHODS: We prospectively enrolled 48 trauma patients and collected daily blood samples during the first 10 days of intensive care unit (ICU) admission. For patients with culture-proven infections, we extracted plasma DNA, prepared double-stranded DNA (dsDNA) and ssDNA sequencing libraries, and applied size selection to exclude fragments >110&#x2005;bp. Following sequencing, we performed taxonomic classification, and evaluated differences in mDNA fractions and in sensitivity for pathogen detection (compared to background noise).<br><br>RESULTS: We analyzed 46 plasma samples from 5 patients who developed culture-proven infections, including 17 samples coincident with positive microbial cultures. Size-selected ssDNA libraries showed the total mDNA fraction 204-fold higher on average than conventional dsDNA libraries (P < 0.0001). However, for pathogen-specific DNA (at the genus level), the highest sensitivity was observed in size-selected dsDNA (82%), compared to dsDNA (41%), ssDNA (71%), and size-selected ssDNA (35%) library preparations.<br><br>CONCLUSIONS: Our results demonstrate that combining ssDNA library preparation together with fragment size selection improves mDNA yield, potentially reducing sequencing requirements. However, at the genus level, this combination also increases background noise, which limits sensitivity for pathogen detection.},
}
@article {pmid40067020,
year = {2025},
author = {Kaminsky, LM and Burghardt, L and Bell, TH},
title = {Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0208524},
doi = {10.1128/aem.02085-24},
pmid = {40067020},
issn = {1098-5336},
abstract = {UNLABELLED: Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts microbial in-soil fitness, particularly focusing on incubation in liquid culture as an unavoidable phase of inoculant production and on pre-incubation in target soils as a potential method to improve performance. We conducted experimental evolution on a phosphorus-solubilizing bacterial species, Priestia megaterium, in (i) soil only, (ii) liquid media only, and (iii) soil followed by liquid media, using population metagenomic sequencing to track mutations over time. Several typical in vitro evolutionary phenomena were observed in liquid media-incubated populations, including clonal interference, genetic hitchhiking, and mutation parallelism between replicate populations, particularly in the sporulation transcription factor spo0A. Liquid media-incubated populations also developed a clear fitness reduction in soil compared to the ancestral isolate. However, soil-incubated populations grew slowly, experienced far fewer generations despite longer absolute time, and accumulated minimal mutational changes. Correspondingly, soil-incubated populations did not display improved survival compared to the ancestral isolate in their target soils, though there did appear to be minor fitness reductions in unfamiliar soil. This work demonstrates that adaptation to liquid media and/or a native soil can impact bacterial fitness in new soil and that bacterial evolution in more complex real-world habitats does not closely resemble bacterial evolution in liquid media.<br><br>IMPORTANCE: Innovative solutions are needed to address emerging challenges in agriculture while reducing its environmental footprint. Management of soil microbiomes could contribute to this effort, as plant growth-promoting microorganisms provide key ecosystem services that support crops. Yet, inoculating beneficial microbes into farm soils yields unreliable results. We require a greater knowledge of the ecology of these taxa to improve their functioning in sustainable agroecosystems. In this report, we demonstrate that exposure to laboratory media and lingering adaptation to another soil can negatively impact the in-soil survival of a phosphorus-solubilizing bacterial species. We go further to highlight the underlying mutations that give rise to these patterns. These insights can be leveraged to improve our understanding of how soil-dwelling beneficial microorganisms adapt to different evolutionary pressures.},
}
@article {pmid40066816,
year = {2025},
author = {Karchmer, AW and Kaufman, NJ and Park, SY and Modi, RM and Abdul-Azim, A and van den Berg, P and Matos, JD and Kramer, DB and Zimetbaum, PJ},
title = {Quantitative Microbial Cell-Free DNA Sequencing from Plasma: A Potential Biomarker for the Diagnosis of Staphylococcal Infection of Cardiac Implantable Electronic Devices.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf113},
pmid = {40066816},
issn = {1537-6591},
abstract = {BACKGROUND: Staphylococcus aureus bacteremia in patients with cardiac implantable electronic devices (CIED) is often associated with infective endocarditis (CIED-IE). The CIED-IE diagnosis is syndromic. Diagnostic uncertainty is common. Frequently, these patients are classified possible CIED-IE, resulting in guideline non-compliant treatment and heterogeneous outcomes. Improved outcomes require accurate diagnoses. In these patients, we evaluated whether metagenomic sequencing of microbial cell-free DNA (mcfDNA) in serial plasma specimens could improve diagnostic precision.<br><br>METHODS: We studied 16 patients with staphylococcal bacteremia who were classified definite or possible CIED-IE and recommended for device removal, if there was a positive blood culture within 7 days and no concurrent deep infection. Plasma specimens obtained at consent, before extraction, and during 96 hours after extraction underwent metagenomic sequencing and quantification of staphylococcal mcfDNA.<br><br>RESULTS: In 10 of 11 definite CIED-IE patients, mcfDNA persisted during antibiotic therapy for prolonged durations (median 11 days, IQR 7.5 days [7.5,15]). In these cases, mcfDNA concentration in plasma obtained early after lead extraction increased significantly and thereafter decreased rapidly. In 5 cases of possible CIED-IE, mcfDNA was undetectable after 6 days (IQR 2 days [5.5,7.5]) of antibiotic therapy and remained undetectable after CIED extraction. These mcfDNA patterns differ significantly (p=0.001), suggesting two distinct patient populations: one with definite CIED-IE and one without lead infection.<br><br>CONCLUSIONS: If confirmed, these mcfDNA patterns can serve as biomarkers, together with clinical features, to improve precision in diagnosing or rejecting S. aureus CIED-IE. Strategically timed mcfDNA testing before and after CIED extraction may aid in planning therapy.},
}
@article {pmid40066307,
year = {2025},
author = {Ci, X and Zhang, J and Lu, J and Qi, X and Ma, Y and Liu, W and Shi, J},
title = {Clinical characteristics of varicella-zoster virus central nervous system infection in 108 unimmunocompromised patients.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1554954},
pmid = {40066307},
issn = {1664-2295},
abstract = {BACKGROUND: Varicella-zoster virus (VZV) central nervous system infection is typically observed in immunocompromised patients, and there is a lack of studies involving large samples of non-immunocompromised individuals. In this study, we retrospectively analyzed 108 non-immunocompromised patients diagnosed with VZV central nervous system infection.<br><br>METHODS: This retrospective study was conducted in the Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, China. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) revealed a positive result for VZV with a sequence number greater than 3, leading to a clinical diagnosis of VZV central nervous system infection. We analyzed the patients' age, gender, clinical manifestations, blood routine, erythrocyte sedimentation rate (ESR), CSF examination, magnetic resonance imaging (MRI), electroencephalogram (EEG), and Activities of Daily Living (ADL) scale scores (Barthel Index) on the day of admission and 3&#x202f;month post-discharge.<br><br>RESULTS: The study involved 108 patients, average age was 47.58&#x202f;&#xb1;&#x202f;2.91&#x202f;years old (16 to 80), 33 were female (30.60%) and 75 were male (69.40%). Clinical manifestations were fever (63.9%), headache (88.9%), nausea (50%), vomiting (27.8%), fatigue (50%), dizziness (25.0%), herpes zoster (47.2%), chickenpox (0.9%), peripheral facial paralysis (19.4%), encephalopathy (5.6%), and myelitis (2.8%). The average white blood cell (WBC) count was 7.40&#x202f;&#xb1;&#x202f;0.48*10[9]/l, the average CRP was 6.58&#x202f;&#xb1;&#x202f;0.69&#x202f;mg/L, and the average ESR was 7.79&#x202f;&#xb1;&#x202f;0.53&#x202f;mm/h. 28.1% of patients exhibited elevated lumbar puncture pressure, the average lumbar puncture pressure was 155.41&#x202f;&#xb1;&#x202f;2.38&#x202f;mmH2O; the average CSF WBC count was 196.60&#x202f;&#xb1;&#x202f;3.98*10^6/l, the average CSF protein was 1.35&#x202f;&#xb1;&#x202f;0.03&#x202f;g/L, the average CSF glucose was 3.41&#x202f;&#xb1;&#x202f;0.03&#x202f;mmoL/L, the average CSF chloride was 116.62&#x202f;&#xb1;&#x202f;0.15&#x202f;mmoL/L, the average CSF IgG index was 0.66&#x202f;&#xb1;&#x202f;0.01, the average mNGS examination of VZV sequence count was 626.25&#x202f;&#xb1;&#x202f;5402.17. Head MRI scans revealed no new lesions; three patients' spinal cord MRI displayed short-segment, non-transverse, and non-continuous patchy long T1 and long T2 signals in the thoracic or cervical spinal cord. On the first day of admission, 41.7% of the patients achieved ADL score of 100 points, 19.4% scored between 41 and 99 points, and 38.9% of the patients scored less than 40 points. All patients received intravenous infusions of acyclovir with low-dose corticosteroids. An outpatient review conducted 3&#x202f;months after discharge indicated 98.15% of the patients recovered well without any sequelae.<br><br>CONCLUSION: VZV encephalitis in immunocompetent individuals typically presents with mild clinical symptoms and has a favorable prognosis. VZV should be considered the common pathogen in the management of patients without immunocompeted condition with encephalitis.},
}
@article {pmid40066275,
year = {2025},
author = {Negrete-Méndez, H and Valencia-Toxqui, G and Sepúlveda-Robles, OA and Ríos-Castro, E and Hurtado-Cortés, JC and Flores, V and Cázares, A and Kameyama, L and Martínez-Peñafiel, E and Fernández-Ramírez, F},
title = {Genomic and proteomic analyses of Nus-dependent non-lambdoid phages reveal a novel coliphage group prevalent in gut: mEpimmI.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1480411},
pmid = {40066275},
issn = {1664-302X},
abstract = {INTRODUCTION: Nus-dependent Mexican Escherichia coli phages (mEp) were previously isolated from clinical samples of human feces. Approximately 50% corresponded to non-lambdoid temperate phages integrating a single immunity group, namely immunity I (mEpimmI), and these were as prevalent as the lambdoid phages identified in such collection.<br><br>METHODS: In this work, we present the structural and functional characterization of six representative mEpimmI phages (mEp010, mEp013, mEp021, mEp044, mEp515, and mEp554). In addition, we searched for homologous phages and prophages in the GenBank sequence database, and performed extensive phylogenetic analyses on the compiled genomes.<br><br>RESULTS: A biological feature-based characterization of these phages was carried out, focusing on proteins relevant to phage biological activities. This included mass spectrometry analysis of mEp021 virion structural proteins, and a series of infection assays to characterize the function of the main repressor protein and the lipoproteins associated with superinfection-exclusion; to identify the main host receptor proteins recognized by these phages and the prophage insertion sites within the host genome, which were associated with specific integrase sequence-types present in the viral genomes. Further, we compiled 42 complete homologous genomes corresponding to 38 prophages from E. coli strains and 4 phages from metagenomes, displaying a wide geographical distribution. Intergenomic distance analyses revealed that these phages differ from previously established phage clades, and whole-proteome similarity analyses yielded a cohesive and monophyletic branch, when compared to >5,600 phages with dsDNA genomes.<br><br>DISCUSSION: According to current taxonomic criteria, our results are consistent with a novel family demarcation, and the studied genomes correspond to 9 genera and 45 distinct species. Further, we identified 50 core genes displaying high synteny among the mEpimmI genomes, and these genes were found arranged in functional clusters. Furthermore, a biological feature-based characterization of these phages was carried out, with experiments focusing on proteins relevant to phage biological activities, revealing common traits as well as diversity within the group. With the integration of all these experimental and bioinformatics findings, our results indicate that the mEpimmI phages constitute a novel branch of Caudoviricetes distinct to other known siphovirus, contributing to the current knowledge on the diversity of phages infecting Escherichia coli.},
}
@article {pmid40065594,
year = {2025},
author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB},
title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70272},
doi = {10.1002/vms3.70272},
pmid = {40065594},
issn = {2053-1095},
support = {//Harry M. Zweig Memorial Fund for Equine Research/ ; 1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; W81XWH-22-1-0891//Department of Defense/ ; },
mesh = {Horses ; Animals ; *Horse Diseases/microbiology/virology/blood/epidemiology ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/etiology ; Microbiota ; Male ; Female ; },
abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.<br><br>OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.<br><br>STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5&#xb0;F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.<br><br>METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.<br><br>RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.<br><br>MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.<br><br>CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.},
}
@article {pmid40064809,
year = {2025},
author = {Ouarabi, L and Taminiau, B and Daube, G and Barache, N and Bendali, F and Drider, D and Lucau-Danila, A},
title = {Insights into fungal diversity and dynamics of vaginal mycobiota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40064809},
issn = {1678-4405},
support = {Alibiotech CPER/FEDER 2016-2021//R&#xe9;gion Hauts-de-France/ ; },
abstract = {Although less studied than its bacterial counterpart, the fungal component of the vaginal microbiota plays a critical role in maintaining vaginal homeostasis. Most research on the composition of the vaginal mycobiota has focused on pathological conditions, with relatively few studies involving healthy women. To gain comprehensive insights into the vaginal mycobiota of Algerian women in two different age groups, we performed a targeted metagenomic analysis using ITS2 region sequencing data from 14 vaginal samples collected from healthy women in reproductive and postmenopausal stages. A single dominant fungal species per individual was observed in both young and postmenopausal women, with differences in fungal community composition between the two groups being related to hormone levels. Our results show that Candida and Saccharomyces were the dominant genera in both young and postmenopausal women. Notably, the postmenopausal group had twice as many species, along with the presence of uncommon taxa such as Dipodascus and Fusarium, indicating greater taxonomic diversity. These findings suggest that menopause is associated with increased microbial variability, likely due to hormonal changes that disrupt the vaginal environment. This study paves the way for more extensive analyses involving diverse age groups and ethnic backgrounds.},
}
@article {pmid40064789,
year = {2025},
author = {Wang, H and Ma, H and Yan, H and Pei, Z and Zhao, J and Zhang, H and Zhang, Z and Lu, W},
title = {Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40064789},
issn = {1867-1314},
support = {32172212, 32394052//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; WMCC202403//Cohort and Clinical Research Program of Wuxi Medical Center, Nanjing Medical University/ ; },
abstract = {Prolonged high-intensity exercise consumes significant energy, leading to fatigue and decreased performance. This study explores the effects of Bifidobacterium adolescentis CCFM1066 on exercise performance, gut microbiota, and its metabolites in mice. The results of the mouse experiments showed the mice which were intervened by Bifidobacterium adolescentis CCFM1066 have a significant increase in exercise performance, including forceful swimming time, fatigue baton turning time, and forelimb grip strength. Through metagenomic sequencing and differential metabolites, analysis indicated that the intervention of CCFM1066 increased Lachnospiraceae bacterium, Parabacteroides goldsteinii, Bacteroides xylanisolvens, and Bifidobacterium adolescentis and altered the key metabolic pathways including protein digestion and absorption and biosynthesis of amino acids. Supplementation with CCFM1066 modulates the production of short-chain fatty acids (SCFAs) and fatty acid amides (FAAs) by gut microbiota, decreasing levels of lactic acid (LA), blood urea nitrogen (BUN), lactate dehydrogenase (LDH), and creatine kinase (CK) while increasing muscle and hepatic glycogen content, thus reducing central nervous system fatigue and thereby improving exercise endurance and performance. These findings provide new insights into nutritional interventions for sports performance.},
}
@article {pmid40064739,
year = {2025},
author = {Thakur, SS and González, SS and Suravajhala, P and Jain, SK and Yadav, S and Narayan, KS and Esack, E and Kuzyakov, Y and Ratnasari, A},
title = {Metagenomic insights of microbial functions under conventional and conservation agriculture.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {3},
pages = {100},
pmid = {40064739},
issn = {1573-0972},
support = {Grant ID: 3203/SKMCCC/EPCO/2021//Environmental Planning &amp; Coordination Organisation (EPCO), Ministry of Environment, Government of Madhya Pradesh, India/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Agriculture ; *Archaea/genetics/classification ; *Soil/chemistry ; Metagenome ; Phylogeny ; Biodiversity ; Carbon/metabolism ; Nitrogen/metabolism ; },
abstract = {Agricultural practices such as conventional (CN) and conservation agriculture (CA) influence the composition and structure of soil microorganisms. We used short reads and genome-resolved metagenomic-based dual sequencing approaches to create a profile of bacterial and archaeal communities in hyperthermic Typic Haplustepts soil after seven years of CA and CN. The most differences in the physico-chemical and biological properties of soil were higher pH, organics carbon, available nitrogen and microbial biomass contents, activities of dehydrogenase, β-glucosidase, and arylsulfatase, found in CA soil. The dominant bacterial taxa under both management types were Pseudomonadota (46-48%), Acidobacteriota (12-13%), Planctomycetota (8-10%), Bacteroidota (7-8%), and Actinomycetota (6-7%). Nitrososphaerota (1.1-1.5%) was the predominant archaeal phyla in CA and CN soils. The alpha diversity was 1.5 times higher in CA compared to CN soils. Fourteen high-quality (HQ) metagenomic-assembled genomes (MAGs) were recovered from both groups. Four HQ metagenome-assembled genomes (MAGs) from the Pseudomonadota phylum were exclusively recovered from the CA soil. The dominance of this phylum in the CA soil might be correlated with its nutrient richness, as certain classes of Pseudomonadota, such as Alpha, Beta-, Gamma-, and Deltaproteobacteria, are known to be copiotrophic. Copiotrophic organisms thrive in nutrient-rich environments, which could explain their prevalence in the CA soil. CAZyme gene analysis showed that Glycoside Hydrolases (GH) and GlycosylTransferases (GT) classes are dominant in the CA group, possibly due to higher substrate availability from the application of crop residues, which provide a rich source of complex carbohydrates. Several biogeochemical gene families related to C1 compounds, hydrogen, oxygen, and sulfur metabolism were enriched in CA soils, suggesting these practices may contribute to a soil environment with increased organic matter content, microbial diversity, and nutrient availability. Overall, CA practices seemed to improve soil health by supporting soil microbial communities abundance.},
}
@article {pmid40064231,
year = {2025},
author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y},
title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126028},
doi = {10.1016/j.envpol.2025.126028},
pmid = {40064231},
issn = {1873-6424},
abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.},
}
@article {pmid40064141,
year = {2025},
author = {She, Y and Wu, L and Qi, X and Sun, S and Li, Z},
title = {Aging behaviors intensify the impacts of microplastics on nitrate bioreduction-driven nitrogen cycling in freshwater sediments.},
journal = {Water research},
volume = {279},
number = {},
pages = {123448},
doi = {10.1016/j.watres.2025.123448},
pmid = {40064141},
issn = {1879-2448},
abstract = {Microplastics (MPs) inevitably undergo aging processes in natural environments; however, how aging behaviors influence the interactions between MPs exposures and nitrate bioreduction in freshwater sediments remains poorly understood. Here, we explored the distinct impacts of virgin and aged MPs (polystyrene (PS) and polylactic acid (PLA)) on nitrate bioreduction processes in lake sediments through a long-term microcosm experiment utilizing the [15]N isotope tracing technique and molecular analysis. Compared to virgin MPs, aged PLA significantly increased the rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) (p < 0.05), facilitating sediment nitrogen loss, while aged PS only significantly improved the rates of DNRA by 272-297 % and contributed to nitrogen retention in sediments. Metagenomic sequencing demonstrated that a more significant enrichment of functional genes responsible for nitrate bioreduction pathways occurred with aged MPs exposures than with virgin MPs. By combining analyses of MPs aging traits and the key drivers of nitrate bioreduction, we revealed that aging behaviors directly regulated sediment nutrient status (e.g., DOC/NOx[-] ratio) and microbiological properties (from genes to bacteria), thereby further determining the activity of nitrate bioreduction. This work provides new insights into the impacts of aged MPs on sediment nitrate reduction and highlights the role of MPs aging in future assessments of long-term MPs pollution in freshwater ecosystems.},
}
@article {pmid40063888,
year = {2025},
author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J},
title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319461},
pmid = {40063888},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; },
abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.},
}
@article {pmid40063675,
year = {2025},
author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001365},
pmid = {40063675},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; },
abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.},
}
@article {pmid40063348,
year = {2025},
author = {Koul, M and Kaushik, S and Singh, K and Sharma, D},
title = {VITALdb: to select the best viroinformatics tools for a desired virus or application.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf084},
pmid = {40063348},
issn = {1477-4054},
support = {BT/2014-15/Plan/P-955//MHRD/ ; R.11013/51/2021-GIA/HR//DHR/ ; },
mesh = {Humans ; *Computational Biology/methods ; Antiviral Agents/therapeutic use ; COVID-19/virology/epidemiology ; SARS-CoV-2/genetics ; Viruses/genetics/classification ; Virus Diseases/virology ; Algorithms ; Software ; },
abstract = {The recent pandemics of viral diseases, COVID-19/mpox (humans) and lumpy skin disease (cattle), have kept us glued to viral research. These pandemics along with the recent human metapneumovirus outbreak have exposed the urgency for early diagnosis of viral infections, vaccine development, and discovery of novel antiviral drugs and therapeutics. To support this, there is an armamentarium of virus-specific computational tools that are currently available. VITALdb (VIroinformatics Tools and ALgorithms database) is a resource of ~360 viroinformatics tools encompassing all major viruses (SARS-CoV-2, influenza virus, human immunodeficiency virus, papillomavirus, herpes simplex virus, hepatitis virus, dengue virus, Ebola virus, Zika virus, etc.) and several diverse applications [structural and functional annotation, antiviral peptides development, subspecies characterization, recognition of viral recombination, inhibitors identification, phylogenetic analysis, virus-host prediction, viral metagenomics, detection of mutation(s), primer designing, etc.]. Resources, tools, and other utilities mentioned in this article will not only facilitate further developments in the realm of viroinformatics but also provide tremendous fillip to translate fundamental knowledge into applied research. Most importantly, VITALdb is an inevitable tool for selecting the best tool(s) to carry out a desired task and hence will prove to be a vital database (VITALdb) for the scientific community. Database URL: https://compbio.iitr.ac.in/vitaldb.},
}
@article {pmid40062866,
year = {2025},
author = {Ingle, DJ and Walsh, CJ and Samuel, GR and Wick, RR and Davidovich, N and Fiocchi, E and Judd, LM and Elliman, J and Owens, L and Stinear, TP and Basso, A and Pretto, T and Newton, HJ},
title = {The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0100224},
doi = {10.1128/msphere.01002-24},
pmid = {40062866},
issn = {2379-5042},
abstract = {The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever, Coxiella burnetii, represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus Coxiella cheraxi represents a novel genus within this family, herein denoted Candidatus Paracoxiella cheracis. Interestingly, we demonstrate that Candidatus P. cheracis encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important C. burnetii effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in C. burnetii.IMPORTANCEUsing long-read sequencing technology, we have uncovered the full genome sequence of Candidatus Paracoxiella cheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus P. cheracis also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus P. cheracis possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.},
}
@article {pmid40062856,
year = {2025},
author = {Kralj, JG and Servetas, SL and Forry, SP and Hunter, ME and Dootz, JN and Jackson, SA},
title = {Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0280624},
doi = {10.1128/spectrum.02806-24},
pmid = {40062856},
issn = {2165-0497},
abstract = {We assessed the analytical performance of metagenomic workflows using NIST Reference Material (RM) 8376 DNA from bacterial pathogens spiked into two simulated clinical samples: cerebrospinal fluid (CSF) and stool. Sequencing and taxonomic classification were used to generate signals for each sample and taxa of interest and to estimate the limit of detection (LOD), the linearity of response, and linear dynamic range. We found that the LODs for taxa spiked into CSF ranged from approximately 100 to 300 copy/mL, with a linearity of 0.96 to 0.99. For stool, the LODs ranged from 10 to 221 kcopy/mL, with a linearity of 0.99 to 1.01. Furthermore, discriminating different E. coli strains proved to be workflow-dependent as only one classifier:database combination of the three tested showed the ability to differentiate the two pathogenic and commensal strains. Surprisingly, when we compared the linear response of the same taxa in the two different sample types, we found those functions to be the same, despite large differences in LODs. This suggests that the "agnostic diagnostic" theory for metagenomics (i.e., any organism can be identified because DNA is the measurand) may apply to different target organisms and different sample types. Because we are using RMs, we were able to generate quantitative analytical performance metrics for each workflow and sample set, enabling relatively rapid workflow screening before employing clinical samples. This makes these RMs a useful tool that will generate data needed to support the translation of metagenomics into regulated use.IMPORTANCEAssessing the analytical performance of metagenomic workflows, especially when developing clinical diagnostics, is foundational for ensuring that the measurements underlying a diagnosis are supported by rigorous characterization. To facilitate the translation of metagenomics into clinical practice, workflows must be tested using control samples designed to probe the analytical limitations (e.g., limit of detection). Spike-ins allow developers to generate fit-for-purpose control samples for initial workflow assessments and inform decisions about further development. However, clinical sample types include a wide range of compositions and concentrations, each presenting different detection challenges. In this work, we demonstrate how spike-ins elucidate workflow performance in two highly dissimilar sample types (stool and CSF), and we provide evidence that detection of individual organisms is unaffected by background sample composition, making detection sample-agnostic within a workflow. These demonstrations and performance insights will facilitate the translation of the technology to the clinic.},
}
@article {pmid40062854,
year = {2025},
author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B},
title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0263924},
doi = {10.1128/spectrum.02639-24},
pmid = {40062854},
issn = {2165-0497},
abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.<br><br>IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.},
}
@article {pmid40062772,
year = {2025},
author = {Connolly, JP and Kelly, L},
title = {The physical biogeography of Fusobacterium nucleatum in health and disease.},
journal = {mBio},
volume = {},
number = {},
pages = {e0298924},
doi = {10.1128/mbio.02989-24},
pmid = {40062772},
issn = {2150-7511},
abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.},
}
@article {pmid40062294,
year = {2025},
author = {Kuzudisli, C and Bakir-Gungor, B and Qaqish, B and Yousef, M},
title = {RCE-IFE: recursive cluster elimination with intra-cluster feature elimination.},
journal = {PeerJ. Computer science},
volume = {11},
number = {},
pages = {e2528},
pmid = {40062294},
issn = {2376-5992},
abstract = {The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, microRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency.},
}
@article {pmid40061332,
year = {2025},
author = {Moore, CM and Secor, EA and Fairbanks-Mahnke, A and Everman, JL and Elhawary, JR and Witonsky, JI and Pruesse, E and Chang, CH and Contreras, MG and Eng, C and Canales, K and Rosado, T and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Lopez, N and Valentin, AM and Medina, V and Montanez-Lopez, CA and Morin, A and Nieves, NA and Oh, SS and Otero, RA and Colon, R and Rodriguez, L and Sajuthi, SP and Salazar, S and Serrano, G and Morales, EV and Vazquez, G and Morales, NV and Williams, BJM and Zhang, P and Sheppard, D and Rodriguez Santana, JR and Seibold, MA},
title = {Independent and interactive effects of viral species on risk for lower respiratory tract illnesses in early life.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.25.25322678},
pmid = {40061332},
abstract = {IMPORTANCE: All children experience upper respiratory tract illnesses (URI) caused by viral infections. However, some of these illnesses progress to the lower airways. Although studies have found infection with certain viral species are more likely to trigger lower respiratory illnesses (LRIs), a comprehensive analysis of viruses underlying early-life LRIs is lacking.<br><br>OBJECTIVE: Determine the incidence of URIs, mild and severe LRIs (mLRI, sLRI) during the first 2 years of life and the association between viral respiratory pathogens and odds of LRIs versus URIs in Puerto Rican children, a population at high risk for respiratory disease.<br><br>Healthy mother-infant pairs were enrolled in the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes birth cohort, in Caguas, Puerto Rico. Infants (n=2,061) were surveilled for respiratory illnesses during the first two years of life (March 2020 to April 2024). Nasal swabs from a subset of 1,363 illnesses from 774 participants were screened for 21 pathogens.<br><br>EXPOSURES: Infection with respiratory pathogens.<br><br>MAIN OUTCOMES AND MEASURES: URI, mLRI, and sLRI in the first two years of life.<br><br>RESULTS: RSV infections occurred in 23% of sLRIs and were associated with dramatically increased odds of sLRI vs URI (OR=9.28; 95% CI, 5.43-15.85). Metapneumovirus, parainfluenza, and non-SARS-CoV-2 coronavirus infections also increased odds of sLRIs. SARS-CoV-2 was associated with lower risk of sLRIs vs. URIs (OR=0.33; 95% CI, 0.16-0.68). Though rhinovirus (43%) and bocavirus (16.1%) were commonly detected in sLRIs, neither was associated with increased sLRI risk. Infection with multiple viral species (i.e. co-infection) occurred in one-third of sLRIs and was associated with 2.92-fold greater odds of sLRI (95% CI, 2.05-4.16) compared to single viral species infections. Rhinovirus-bocavirus was the most common co-infection (32.4%), and interaction between these viral infections was associated with increased sLRI risk (OR=2.21; 95% CI, 1.20-4.09) relative to illnesses that were negative for rhinovirus and bocavirus.<br><br>CONCLUSIONS AND RELEVANCE: A diversity of viral pathogens drive early-life sLRIs. Some viral pathogens (e.g. RSV and metapneumovirus) have intrinsic propensity to cause sLRIs, whereas many sLRIs are caused by viruses whose lower airway pathogenicity is dependent on other factors, including co-infection.<br><br>KEY POINTS: Question: How do common respiratory viruses differ in their prevalence and risk of causing severe lower respiratory illnesses (LRIs) during early childhood?Findings: RSV, metapneumovirus, and parainfluenza are independent risk factors for early childhood severe LRIs. While rhinovirus and bocavirus infections alone do not increase the risk of severe LRIs, these two viruses significantly elevate risk when they occur as co-infections.Meaning: Our findings highlight significant variability in viruses that drive severe early-life LRIs. Some viral species appear to inherently predispose individuals to lower airway disease, while for others, the development of disease likely depends on co-infections and/or host susceptibility.},
}
@article {pmid40060957,
year = {2025},
author = {Zhao, JH and Li, WJ and Jiao, J and Wang, MX and Zhang, XM and Yin, JY and Hu, WZ and Song, Q and Liu, J},
title = {Treatment of a rare and severe infection of central nervous system by Angiostrongylus cantonensis: A case report.},
journal = {World journal of radiology},
volume = {17},
number = {2},
pages = {105059},
pmid = {40060957},
issn = {1949-8470},
abstract = {BACKGROUND: Angiostrongylus cantonensis-induced acute parasitic infection is a rare food-borne disease in clinical practice. Lack of its specific laboratory markers and subsequent difficulty in detecting pathogens cause high misdiagnosis and missed diagnosis rates.<br><br>CASE SUMMARY: A 20-year-old male developed persistent neck and back pain after consuming raw snail meat, followed by urinary retention and low fever. After admission, the patient was misdiagnosed as viral infection and Mycobacterium tuberculosis in central nervous system. After detection of Angiostrongylus cantonensis in blood and cerebrospinal fluid by metagenomics next generation sequencing, albendazole was administered with ceftriaxone and methylprednisolone treatment simultaneously. With effective antiparasitic treatment, the patient weaned from mechanical ventilation successfully and transferred out of intensive care unit for hyperbaric oxygen and rehabilitation treatment.<br><br>CONCLUSION: This case highlights the diagnostic challenges of Angiostrongylus cantonensis infection and the importance of advanced sequencing techniques in identifying rare pathogens.},
}
@article {pmid40060808,
year = {2025},
author = {Gao, B and Shi, X and Zhao, M and Ren, F and Xu, W and Gao, N and Shan, J and Shen, W},
title = {Mixture Effects of Polystyrene Microplastics on the Gut Microbiota in C57BL/6 Mice.},
journal = {ACS omega},
volume = {10},
number = {8},
pages = {7597-7608},
pmid = {40060808},
issn = {2470-1343},
abstract = {Microplastics are plastic particles with sizes of less than 5 mm. The ubiquity of microplastics in the environment has raised serious public health concerns. Microplastics could disturb the composition of the gut microbiota due to both chemical composition and physical interactions, which might further influence the metabolism and immune function of the host. However, most of the exposure studies chose microplastics of specific sizes. In the natural environment, living organisms are exposed to a mixture of microplastics of various sizes. In this study, male C57BL/6 mice were exposed to polystyrene (PS) microplastics with different sizes, including microplastics with diameters of 0.05-0.1 μm (PS0.1 group, 100 ppb), 9-10 μm (PS10 group, 100 ppb), and microplastic mixtures of both 0.05-0.1 and 9-10 μm (PSMix group) at a total concentration of 100 ppb (50 ppb for each size). Mixture effects of microplastics were investigated on the composition of bacteria and fungi as well as functional metagenome and microbial genes encoding antibiotic resistance and virulence factors. We found that some bacteria, fungi, and microbial metabolic pathways were only altered in the PSMix group, not in the PS0.1 or PS10 group, suggesting the toxic effects of the microplastic mixture on the composition of fungi and bacteria, and the functional metagenome is different from the effects of microplastics at specific sizes. Meanwhile, altered genes encoding antibiotic resistance and virulence factors in the PSMix group were shared with the PS0.1 and PS10 groups, possibly due to functional redundancy. Our findings help improve the understanding of the toxic effects of the microplastic mixture on the gut microbiome.},
}
@article {pmid40060671,
year = {2025},
author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A},
title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.28.640732},
pmid = {40060671},
issn = {2692-8205},
abstract = {UNLABELLED: Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with HIV (PWH) yet poorly understood. HIV infection alters the human virome, and virome perturbations have been linked to neurocognitive issues in people without HIV. Once thought to be sterile, the cerebrospinal fluid (CSF) hosts a recently discovered virome, presenting an unexplored avenue for understanding brain and mental health in PWH. This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA/RNA viruses. Taxonomic composition (reads and contigs), α and β diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV infection, markers of neuroinflammation and neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of viral groups and blood-brain barrier permeability were also performed. Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. Alpha diversity was lower in PWH versus CWH, although p>0.05. At β diversity analysis, HIV status explained 3.3% of the variation in viral composition (p=0.016). Contigs retained 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (p=0.002) and β-Amyloid 1-42 fragment (βA-42, p=0.026), while higher RA of nhEV with poorer cognitive performance (p=0.022). Conversely, higher RA of hEV correlated with better cognition (p=0.003) and lower βA-42 (p=0.012). Sensitivity analyses in virome-positive samples only confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and nhEV-enriched CSF (models'p<0.05). This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.<br><br>AUTHOR SUMMARY: HIV can affect brain health and mental well-being, even in people on successful antiretroviral therapy. The reasons behind this are still unclear. HIV also influences the communities of microbes and viruses living in the human body, and recent research suggests that the human virome, the collection of all viruses within the body, may play a role in cognitive functions, mood, and brain health. For a long time, scientists believed that the cerebrospinal fluid (CSF), which surrounds the brain, was sterile, while robust evidence has shown that the CSF hosts its own unique virome. Via advanced genetic sequencing (shotgun metagenomics), we analyzed the CSF virome in people with and without HIV looking for possible links to neuroinflammation, cognitive performance, and depression. We found that while HIV infection does affect the composition of CSF viral communities, there were no remarkable differences in the CSF virome of individuals with and without HIV. Most viral sequences appeared to come outside the brain. A higher abundance of non-human viral sequences, such as viruses of bacteria, plants, fungi, and animals, was associated with neuroinflammation and poorer cognitive performance. On the other hand, a higher abundance of human viruses correlated with better cognitive function and healthier signature of neuromarkers. These findings provide new insights into the presence and characteristics of the human CSF virome and how it might influence brain health. They also suggest new potential mechanisms of HIV-associated neuropathology.},
}
@article {pmid40060627,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.28.640651},
pmid = {40060627},
issn = {2692-8205},
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defense systems. Using functional metagenomic selections, we identified new examples of these systems from human fecal, human oral, and grassland soil microbiomes. Our antiphage selections in Escherichia coli revealed over 200 putative defenses from 14 diverse bacterial phyla, highlighting the broad phylogenetic interoperability of these systems. Many defense systems were unrecognizable based on sequence or predicted structure, so could only be identified via functional assays. In mechanistic studies, we show that some defense systems encode nucleases that only degrade covalently modified phage DNA, but which accommodate diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of previously unknown defense systems with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed among non-model bacteria.},
}
@article {pmid40060500,
year = {2025},
author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T},
title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.25.640119},
pmid = {40060500},
issn = {2692-8205},
abstract = {Metagenomic read classification is a fundamental task in computational biology, yet it remains challenging due to the scale, diversity, and complexity of sequencing datasets. We propose a novel, lossless, run-length compressed index that enables efficient multi-class metagenomic classification in O (r) space, based on the move structure. Our method identifies all super-maximal exact matches (SMEMs) of length at least L between a read and the reference dataset and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs with their class identifier into a single classification per read. We are the first to perform run-length compressed read classification based on full SMEMs instead of semi-SMEMs. We evaluate our approach on both long and short reads in two conceptually distinct datasets: a large bacterial pan-genome with few metagenomic classes and a smaller 16S rRNA gene database spanning thousands of genera or classes. Our method consistently outperforms SPUMONI 2 in accuracy and runtime, with only a modest memory overhead. Compared to Cliffy, we demonstrate better memory efficiency while achieving superior accuracy on the simpler dataset and comparable performance on the more complex one. Overall, our implementation carefully balances accuracy, runtime, and memory usage, offering a versatile solution for metagenomic classification across diverse datasets. The open-source C++11 implementation is available at https://github.com/biointec/tagger under the AGPL-3.0 license.},
}
@article {pmid40060387,
year = {2025},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.03.592475},
pmid = {40060387},
issn = {2692-8205},
abstract = {Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g . osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}
@article {pmid40060187,
year = {2025},
author = {Cao, J and Ma, Y and Fu, J and Wang, Z and Zhao, Y and Zhong, N and Zhao, P},
title = {Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome.},
journal = {aBIOTECH},
volume = {6},
number = {1},
pages = {33-49},
pmid = {40060187},
issn = {2662-1738},
abstract = {UNLABELLED: Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS. These studies revealed that DX-9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8-dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00199-3.},
}
@article {pmid40060112,
year = {2024},
author = {Wei, B and Xu, Q and Kong, J and Su, X and Chen, K and Wang, H},
title = {Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1518637},
pmid = {40060112},
issn = {1664-462X},
abstract = {INTRODUCTION: Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays a critical role in livestock production and grassland restoration. This study investigates the rhizospheric and non-rhizospheric soil microorganisms of Poa alpigena L. in the Ganzi River area of the Qinghai Lake basin using metagenomic sequencing to understand their diversity and potential ecological functions.<br><br>METHODS: Soil samples were collected from rhizospheric and non-rhizospheric areas of Poa alpigena L. using the S-type five-point sampling method. DNA was extracted, and metagenomic sequencing was performed using the BGISEQ-500 platform. Alpha and Beta diversity analyses were conducted, and LEfSe analysis was used to identify differentially abundant microbial taxa and metabolic pathways.<br><br>RESULTS: A total of 5,681 microbial species across 1,606 genera, 521 families, 61 phyla, and 246 orders were identified. Non-rhizospheric soils exhibited higher species richness than rhizospheric soils. Proteobacteria was the most abundant phylum in both soil types. Rhizospheric soils showed significant enrichment in pathways related to antibiotic biosynthesis, carbon metabolism, and methane metabolism, while non-rhizospheric soils were enriched in quorum sensing and drug-metabolizing pathways.<br><br>DISCUSSION: The findings highlight the selective influence of Poa alpigena L. on soil microbial communities and their potential role in mitigating methane emissions. The study provides a foundation for understanding the ecological functions of soil microorganisms in alpine meadows and supports sustainable grassland management practices.},
}
@article {pmid40059905,
year = {2025},
author = {Su, Z and Gu, AZ and Wen, D and Li, F and Huang, B and Mu, Q and Chen, L},
title = {Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads.},
journal = {Environmental science and ecotechnology},
volume = {23},
number = {},
pages = {100502},
pmid = {40059905},
issn = {2666-4984},
abstract = {Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44-96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future.},
}
@article {pmid40059755,
year = {2025},
author = {Munk, P and Brinch, C and Aarestrup, FM},
title = {Resistance genes are not like chemical pollutants and surveillance of them should reflect that.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1080/17460913.2025.2476880},
pmid = {40059755},
issn = {1746-0921},
}
@article {pmid40059174,
year = {2025},
author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS},
title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {71},
pmid = {40059174},
issn = {2049-2618},
support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; },
abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.<br><br>RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.<br><br>CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.},
}
@article {pmid40058902,
year = {2025},
author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF},
title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.},
journal = {Food research international (Ottawa, Ont.)},
volume = {206},
number = {},
pages = {116035},
doi = {10.1016/j.foodres.2025.116035},
pmid = {40058902},
issn = {1873-7145},
mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; },
abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.},
}
@article {pmid40058900,
year = {2025},
author = {Wang, X and Li, Q and Li, W and Cai, G and Wu, D and Xie, G and Lu, J},
title = {Metagenomics unveils the roles of microbes in the metabolic network of purine formation during Huangjiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {206},
number = {},
pages = {116031},
doi = {10.1016/j.foodres.2025.116031},
pmid = {40058900},
issn = {1873-7145},
mesh = {*Fermentation ; *Purines/metabolism ; *Metagenomics ; Metabolic Networks and Pathways ; Bacteria/metabolism/genetics/classification ; Microbiota/physiology ; Fermented Foods/microbiology ; },
abstract = {Purine is a major factor contributing to the development of hyperuricemia and gout, and it is found in large quantities in Huangjiu as free bases. Purine production in Huangjiu is strongly associated with microbial metabolism. However, to the best of our knowledge the microorganisms responsible for and the mechanisms of purine formation during Huangjiu fermentation are yet to be evaluated. Herein, changes in purine levels during Huangjiu fermentation were analyzed. Further, the microbes responsible for purine production were identified and their gene abundance was studied. Results revealed that adenine, guanine, hypoxanthine, and xanthine are produced during Huangjiu fermentation. The total purines content on day 0 (27.99 mg/L) was found to be considerably lower than that produced on day 24 (122.15 mg/L) during Huangjiu fermentation. Metagenomics showed that the composition of the microbial community fluctuates sharply during five fermentation periods of Huangjiu, with the microbial community richness and diversity being the most prominent on day 3. At the genus level, Klebsiella, Lactobacillus, Staphylococcus, Saccharopolyspora, and Saccharomyces were abundant during Huangjiu fermentation and were involved in purine metabolism. Relationships between the dominant microorganisms and key enzyme genes of the purine pathways were also established based on the Kyoto Encyclopedia of Genes and Genomes database. Correlation analysis showed that Lactobacillus and Saccharomyces were the main genera involved in purine formation. Saccharomyces cerevisiae, Lactobacillus paralimentarius, and Lactiplantibacillus plantarum were involved in purine formation during Huangjiu fermentation. Overall, this study improves our understanding of the purine formation mechanism during Huangjiu fermentation and provides valuable insights into the regulation of purine formation by microorganisms.},
}
@article {pmid40058503,
year = {2025},
author = {Chang, Z and Deng, J and Zhang, J and Wu, H and Wu, Y and Bin, L and Li, D and Liu, J and Yu, R and Lin, H and An, L and Sun, B},
title = {Rapid and Accurate Diagnosis of Urinary Tract Infections Using Targeted Next-Generation Sequencing: A Multicenter Comparative Study with Metagenomic Sequencing and Traditional Culture Methods.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106459},
doi = {10.1016/j.jinf.2025.106459},
pmid = {40058503},
issn = {1532-2742},
abstract = {BACKGROUND: Urinary tract infections (UTIs) rank among the most prevalent bacterial infections globally. Traditional urine culture methods have significant limitations in detection time and sensitivity, prompting the need to evaluate targeted next-generation sequencing (tNGS) as a potential diagnostic tool.<br><br>METHODS: The study included a discovery cohort of 400 suspected UTI patients (202 analyzed) and a validation cohort of 200 patients (110 analyzed). The study assessed detection time, concordance rates, ability to identify polymicrobial infections, and antibiotic resistance genes (ARGs). Both clear and turbid urine samples were evaluated across different clinical settings.<br><br>RESULTS: In the discovery cohort, tNGS demonstrated 96.5% concordance with culture-positive samples, while showing superior specificity in culture-negative specimens (53.1% vs 28.1% for mNGS). Detection time for tNGS (12.89h) was notably shorter than mNGS (17.38h) and traditional culture (61.48h). tNGS exhibited remarkable capability in identifying polymicrobial infections (55.4% of samples), significantly outperforming both mNGS (27.7%) and traditional culture methods, which failed to detect any co-infections. The method showed particular strength in detecting fastidious organisms like Ureaplasma parvum and fungal species such as Candida tropicalis. For antibiotic resistance prediction, tNGS detected more ARGs (52.67% vs 41.22% for mNGS) and achieved 100% sensitivity for vancomycin and methicillin resistance in Gram-positive pathogens. The validation cohort confirmed tNGS's robust performance, maintaining high concordance rates for both culture-positive (90.00%) and culture-negative samples (55.00%), demonstrating consistent reliability across different clinical settings CONCLUSIONS: tNGS demonstrates advantages in rapid and accurate UTI diagnosis, particularly in detecting polymicrobial infections and analyzing antibiotic resistance genes. It shows promise as an effective complementary tool for UTI diagnostics.},
}
@article {pmid40058443,
year = {2025},
author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D},
title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141858},
doi = {10.1016/j.ijbiomac.2025.141858},
pmid = {40058443},
issn = {1879-0003},
abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.},
}
@article {pmid40058279,
year = {2025},
author = {Chen, H and Zeng, Z and Lal, R and Wu, J and Chen, J and Li, M and Cao, L and Liu, X and Zhang, R and Gong, C},
title = {Acetic acid production from corn straw via enzymatic degradation using putative acetyl esterase from the metagenome assembled genome.},
journal = {Enzyme and microbial technology},
volume = {187},
number = {},
pages = {110619},
doi = {10.1016/j.enzmictec.2025.110619},
pmid = {40058279},
issn = {1879-0909},
abstract = {Acetic acid production from corn straw by enzyme catalysis shows its application value in food industry. In this study, a gene encoding for a putative acetyl esterase derived from Sphingobacterium soilsilvae Em02 was discovered in metagenome assembled genome. The gene was expressed in Escherichia coli BL21 to obtain enzyme with a molecular mass of 38.8 kDa. P-Nitrophenyl acetate was used as a substrate to determine the enzyme activity. The enzyme demonstrated optimal activity under conditions of 40 °C and a neutral pH of 7.0. Under optimal conditions, 17.58 mg of acetic acid was obtained using the enzyme from 50 mg corn straw pretreated with amylase. The acetyl esterase derived from Sphingobacterium soilsilvae Em02, demonstrates significant potential for biotechnological applications, particularly in biomass degradation.},
}
@article {pmid40058278,
year = {2025},
author = {Neri, LCM and Guðmundsson, H and Meurrens, G and Robert, A and Fridjonsson, OH and Hreggvidsson, GO and Adalsteinsson, BT},
title = {Identification and characterization of endo-xylanases from families GH10 and GH11 sourced from marine thermal environments.},
journal = {Enzyme and microbial technology},
volume = {187},
number = {},
pages = {110592},
doi = {10.1016/j.enzmictec.2025.110592},
pmid = {40058278},
issn = {1879-0909},
abstract = {Seaweed biomass is an underutilized resource that is rich in polysaccharides, including xylan. Seaweed polysaccharides could be used as a feedstock in industrial microbiology and and for production of prebiotic oligosaccharides and rare monosaccharides - processes that would benefit from the availability of robust enzymes that break down the seaweed polysaccharides. The present study aimed to identify genes encoding endo-xylanases in bacterial genomes and metagenomes sourced from marine thermal environments, and to characterize the respective enzymes. Twelve endo-xylanases were studied which displayed 59 % median maximal sequence similarity to characterized GH10 or GH11 enzymes. Overall, most of the enzymes functioned optimally at high temperatures, in the presence of salt, and at circumneutral pH. Eight enzymes functioned optimally at temperatures of 50°C or higher, and in the most extreme cases at 85°C to 95°C. Six enzymes retained activity after three-hour incubation at 60°C or higher. Ten enzymes displayed improved catalytic function in the presence of salt, and several retained high catalytic function at 10 % NaCl concentration. All the enzymes hydrolyzed xylan from diverse sources, including crude biomass. The study contributes to an increased understanding of the structural diversity of xylanases; it expands the availability of thermostable xylanases of marine origin; and contributes to increased valorization of seaweed biomass.},
}
@article {pmid40058228,
year = {2025},
author = {Tromas, N and Simon, DF and Fortin, N and Hernández-Zamora, M and Pereira, A and Mazza, A and Pacheco, SM and Levesque, MJ and Martínez-Jerónimo, L and Antuna-González, P and Munoz, G and Shapiro, BJ and Sauvé, S and Martínez-Jerónimo, F},
title = {Metagenomic insights into cyanotoxin dynamics in a Mexican subtropical lake.},
journal = {Chemosphere},
volume = {376},
number = {},
pages = {144285},
doi = {10.1016/j.chemosphere.2025.144285},
pmid = {40058228},
issn = {1879-1298},
abstract = {Valle de Bravo is a vital water supply for part of the metropolitan area of the Valle de Mexico megacity, providing 30% of Mexico City's water demand. This water body has experienced an acceleration in its trophic status, going from oligotrophic to eutrophic in just a few years. This temperate lake (at a tropical latitude) is in a persistent bloom dominated by a variety of co-occurring cyanobacteria, many of which have toxigenic potential based on microscopic identification, that makes it difficult or even impractical to identify the cyanotoxin producers. To unravel this complexity and directly identify the toxigenic genera, we showed that integrating classical approaches with metagenomic is required. We first characterized, from genes to metagenomes assembled genomes, the toxigenic Cyanobacteria. We found that Microcystis was the most dominant cyanobacterial genus and the sole carrier of the mcy operon, making it the only microcystin producer. We then quantified twenty-one different cyanopeptides, including twelve microcystin congeners using a high-performance liquid chromatography-high-resolution. Nine microcystins (MCs) and the emerging cyanotoxin anabaenopeptin-A and -B were found at varying concentrations throughout the year, with MC-LA being the most common and abundant. Our findings, constrained by our sampling strategy, indicate that conventional cyanotoxin biomarkers (e.g., toxin mcy genes) were not consistently reliable indicators of cyanotoxin concentrations in this freshwater system. In this study, we followed the dynamics of the cyanobacterial community and the associated cyanopeptides with unprecedented resolution. Our results have implications for better management of toxic blooms in this freshwater system, which supplies drinking water to more than 7 million people in the megalopolis of Valle de México.},
}
@article {pmid40058051,
year = {2025},
author = {Castellano-Hinojosa, A and Gallardo-Altamirano, MJ and Pozo, C and González-Martínez, A and González-López, J and Marshall, IPG},
title = {Salinity levels influence treatment performance and the activity of electroactive microorganisms in a microbial fuel cell system for wastewater treatment.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124858},
doi = {10.1016/j.jenvman.2025.124858},
pmid = {40058051},
issn = {1095-8630},
abstract = {There is growing interest in developing effective treatment technologies to mitigate the environmental impact of saline wastewater while also potentially recovering valuable resources from it. However, it remains largely unknown how different salinity levels impact treatment performance, energy generation, and the diversity and composition of electroactive microorganisms in MFCs treating real effluents such as urban wastewater. This study explores the impact of three salinity levels (3.5, 7, and 15 g/L NaCl) on current production, organic removal rates, and bacterial community dynamics in a continuous-flow microbial fuel cell (MFC) fed with urban wastewater. Using metagenomics and metatranscriptomics, we explored variations in the abundance and expression of extracellular electron transfer (EET) genes and those involved in other general metabolisms. We found that low salinity (3.5 g/L NaCl) enhanced both current production and organic removal efficiency compared to higher salinity levels. This improvement was linked to an increased abundance and activity of electroactive microorganisms, particularly taxa within the Ignavibacteria class, which possess genes coding for outer membrane cytochromes and porin cytochromes. Additionally, salinity influenced general metabolic genes and microbial community composition, with higher salinity levels limiting bacterial growth and diversity. This research provides valuable insights into the interplay between salinity stress and microbial adaptation, contributing to the optimization of MFC technologies for enhanced environmental and bioengineering applications.},
}
@article {pmid40057978,
year = {2025},
author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S},
title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf046},
pmid = {40057978},
issn = {1751-7370},
abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.},
}
@article {pmid40057571,
year = {2025},
author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD},
title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8136},
pmid = {40057571},
issn = {2045-2322},
mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration &amp; dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; },
abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.},
}
@article {pmid40057258,
year = {2025},
author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP},
title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107577},
doi = {10.1016/j.actatropica.2025.107577},
pmid = {40057258},
issn = {1873-6254},
abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.},
}
@article {pmid40057163,
year = {2025},
author = {Leonard, AFC and Higgins, SL and Hui, M and Gaze, WH},
title = {Investigating landscape-scale variables impacting human exposure to antibiotic resistant bacteria using a targeted metagenome approach.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126015},
doi = {10.1016/j.envpol.2025.126015},
pmid = {40057163},
issn = {1873-6424},
abstract = {Research has shown that exposure to coastal waters containing antibiotic resistant bacteria (ARB) is associated with higher likelihood of gut colonisation by ARB. The aim was to identify landscape-scale processes contributing to the spread of ARB in Hong Kong's coastal waters and to estimate the scale of bathers' exposure to ARB. Twelve recreational water locations were sampled in 2017 for Escherichia coli. A targeted metagenomic approach was used to quantify the abundance and diversity of antibiotic resistance genes (ARGs) harboured by viable E. coli. Data on environmental variables related to ARB distribution in the environment were modelled to identify processes driving the abundance and diversity of ARG-bearing E. coli in coastal waters. These data were combined with data about Hong Kong residents' use of blue space to quantify human exposure to E. coli borne ARG. Several meteorological variables, like rainfall and temperature, were associated with E. coli-borne ARG profiles. Yet when rigorous statistical methods were applied, these relationships were not significant. Meropenem-resistant bacteria were also isolated from samples, most of which were taken from western beaches. Additionally, there was some evidence of elevated abundances of several ARGs, including blaCTX-M, in western beaches. The average E. coli harboured 6.09 ARGs. Over 1.16 million exposure events occurred in 2017 that involved ingestion of E. coli harbouring at least one ARG. This study used robust methods to quantify and explain the abundance and diversity of ARB in Hong Kong's coastal waters. We detected elevated levels of several E. coli-borne ARGs and meropenem-resistant pathogens at western beaches, indicating an influence of the Pearl River on Hong Kong's water quality. Despite updates to wastewater treatment in Hong Kong, recreational use of natural surface waters remains a significant risk of exposure to ARB capable of human gut colonisation.},
}
@article {pmid40056814,
year = {2025},
author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M},
title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.},
journal = {Chemosphere},
volume = {376},
number = {},
pages = {144296},
doi = {10.1016/j.chemosphere.2025.144296},
pmid = {40056814},
issn = {1879-1298},
abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.},
}
@article {pmid40056517,
year = {2025},
author = {Choonut, A and Wongfaed, N and Wongthong, L and Poolpol, A and Chaikitkaew, S and Sittijunda, S and Reungsang, A},
title = {Microbial degradation of polypropylene microplastics and concomitant polyhydroxybutyrate production: An integrated bioremediation approach with metagenomic insights.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137806},
doi = {10.1016/j.jhazmat.2025.137806},
pmid = {40056517},
issn = {1873-3336},
abstract = {The persistence of plastics, particularly polypropylene (PP), and their conversion into microplastics (MPs), specifically PP-MPs, have emerged as serious ecological threats to soil and aquatic environments. In the present study, we aimed to isolate a microbial consortium capable of degrading PP-MPs. The results revealed that three microbial consortia (CPP-KKU1, CPP-KKU2, and CPP-KKU3) exhibited the ability to degrade PP-MPs, achieving weight losses ranging from 11.6 ± 0.2 % to 17.8 ± 0.5 % after 30 days. Fourier transform infrared (FTIR) spectroscopy analysis confirmed the degradation through oxidation, as evidenced by the presence of new functional groups (-OH and -C=O). In particular, CPP-KKU3 showed the highest degradation efficiency, with scanning electron microscopy (SEM) analysis revealing surface cracking after treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis identified various intermediate compounds, including heterocyclic aromatic compounds, phenyl groups, methylthio derivatives, and ethoxycarbonyl derivatives, indicating complex biochemical processes that were likely mediated by microbial enzymes. Furthermore, polyhydroxybutyrate (PHB) production by these consortia was also investigated. The result showed that both CPP-KKU2 and CPP-KKU3 successfully produced PHB, with CPP-KKU3 demonstrating superior performance in terms of PP-MP degradation and PHB production. Metagenomic analysis of CPP-KKU3 revealed abundant carbohydrate-active enzymes (CAZymes), particularly glycosyl transferases and glycoside hydrolases, which are associated with MP digestion. This study presents a promising bioremediation approach that addresses plastic waste degradation and sustainable bioplastic production, offering a potential solution for environmental plastic pollution.},
}
@article {pmid40056474,
year = {2025},
author = {Wang, H and Zhong, Y and Yang, Q and Li, J and Li, D and Wu, J and Yang, S and Liu, J and Deng, Y and Song, J and Peng, P},
title = {Coupling of sulfate reduction and dissolved organic carbon degradation accelerated by microplastics in blue carbon ecosystems.},
journal = {Water research},
volume = {279},
number = {},
pages = {123414},
doi = {10.1016/j.watres.2025.123414},
pmid = {40056474},
issn = {1879-2448},
abstract = {Microplastics have increasingly accumulated in sulfate- and organic matter-rich mangrove ecosystems, yet their effects on microbially mediated carbon and sulfur cycling in sediments remains poorly understood. In this study, we performed a 70-day anaerobic microcosm experiment to examine the effects of polylactic acid (PLA) microplastics with different sizes on sulfate reduction and dissolved organic carbon (DOC) degradation in mangrove sediments. Our results demonstrated that millimeter-scale PLA (mm-PLA) more effectively enhanced sulfate reduction, sulfur isotope fractionation, reduced sulfide production, and carbon dioxide (CO2) emission compared to micrometer-scale PLA (m-PLA). These results suggested that mm-PLA had a more pronounced impact on the carbon and sulfur cycles. Integrated 16S rRNA gene amplicon sequencing and metagenomic analyses revealed that mm-PLA preferentially enriched key functional microorganisms, including acetate-producing bacteria (e.g., Acetobacteroides), completely oxidizing sulfate-reducing bacteria (e.g., Desulfobacter), and incompletely oxidizing sulfate-reducing bacteria (e.g., Desulfobulbus). These microorganisms exhibited higher abundances and greater genetic potential for carbon metabolism and sulfate reduction under mm-PLA treatment. Their relative abundances showed positive correlations with sulfate reduction rates, sulfur isotope fractionation, and CO2 emission, identifying them as crucial drivers of coupled carbon-sulfur cycling. Furthermore, the synergistic interactions among Acetobacteroides, Desulfobacter, and Desulfobulbus facilitated the oxidation of sediment-derived DOC, highlighting significant implications for carbon sequestration in blue carbon ecosystems.},
}
@article {pmid40056186,
year = {2025},
author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J},
title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {4},
pages = {140},
pmid = {40056186},
issn = {1432-0851},
support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; },
abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.},
}
@article {pmid40055840,
year = {2025},
author = {Rannon, E and Shaashua, S and Burstein, D},
title = {DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {67},
pmid = {40055840},
issn = {2049-2618},
mesh = {*Machine Learning ; *Metagenomics/methods ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Computational Biology/methods ; Metagenome ; },
abstract = {BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefits of antibiotics. Therefore, early detection of antimicrobial resistance genes (ARGs), especially in pathogens, is crucial for human health. Most computational methods for ARG detection rely on homology to a predefined gene database and therefore are limited in their ability to discover novel genes.<br><br>RESULTS: We introduce DRAMMA, a machine learning method for predicting new ARGs with no sequence similarity to known ARGs or any annotated gene. DRAMMA utilizes various features, including protein properties, genomic context, and evolutionary patterns. The model demonstrated robust predictive performance both in cross-validation and an external validation set annotated by an empirical ARG database. Analyses of the high-ranking model-generated candidates revealed a significant enrichment of candidates within the Bacteroidetes/Chlorobi and Betaproteobacteria taxonomic groups.<br><br>CONCLUSIONS: DRAMMA enables rapid ARG identification for global-scale genomic and metagenomic samples, thus holding promise for the discovery of novel ARGs that lack sequence similarity to any known resistance genes. Further, our model has the potential to facilitate early detection of specific ARGs, potentially influencing the selection of antibiotics administered to patients. Video Abstract.},
}
@article {pmid40055835,
year = {2025},
author = {Yin, CF and Pan, P and Li, T and Song, X and Xu, Y and Zhou, NY},
title = {The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {68},
pmid = {40055835},
issn = {2049-2618},
support = {32400079//the National Natural Science Foundation of China/ ; 2024YFA0919000//the National Key R&amp;D Program of China/ ; 2024YFA0919000//the National Key R&amp;D Program of China/ ; },
mesh = {*Acetaminophen/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Aminophenols/metabolism ; *Antipyretics ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; China ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Humans ; Microbiota ; Analgesics ; Metagenome ; },
abstract = {BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.<br><br>RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20&#xa0;nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68&#xa0;nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.<br><br>CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.},
}
@article {pmid40055808,
year = {2025},
author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB},
title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {66},
pmid = {40055808},
issn = {2049-2618},
support = {2022067//Helse S&#xf8;r-&#xd8;st RHF/ ; },
mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation &amp; purification ; Basidiomycota/genetics/isolation &amp; purification/classification ; Databases, Genetic ; },
abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.<br><br>RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.<br><br>CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.},
}
@article {pmid40054447,
year = {2025},
author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S},
title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.},
journal = {Cell},
volume = {188},
number = {5},
pages = {1363-1377.e9},
doi = {10.1016/j.cell.2024.12.036},
pmid = {40054447},
issn = {1097-4172},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.},
}
@article {pmid40054445,
year = {2025},
author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O},
title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.},
journal = {Cell},
volume = {188},
number = {5},
pages = {1178-1197},
doi = {10.1016/j.cell.2025.01.038},
pmid = {40054445},
issn = {1097-4172},
mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; },
abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.},
}
@article {pmid40054329,
year = {2025},
author = {Saticioglu, IB and Ajmi, N and Coskuner-Weber, O and Alpsoy, S and Ay, H and Aydin, F and Abay, S and Karakaya, E and Kayman, T and Dalyan, C and Koca, FD and Tasci, G and Yarim, D and Morick, D and Yibar, A and Erdogan, S and Altun, S and Duman, M},
title = {Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {3},
pages = {126600},
doi = {10.1016/j.syapm.2025.126600},
pmid = {40054329},
issn = {1618-0984},
abstract = {Three bacterial strains, Mu-43[T], Mu-80[T], and Mu-86[T], were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus Microbacterium. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. M. istanbulense Mu-43[T] showed 99.0 % 16S rRNA similarity to M. bandirmense Mu-80[T], with digital DNA-DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. M. bandirmense Mu-80[T] exhibited 99.2 % similarity to M. esteraromaticum DSM 8609[T], with dDDH and ANIb values of 23.6 % and 80 %. M. marmarense Mu-86[T] showed 97.4 % similarity to M. arthrosphaerae JCM 30492[T], with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: M. istanbulense sp. nov. Mu-43[T] (LMG 33297[T] = DSM 117065[T]), M. bandirmense sp. nov. Mu-80[T] (LMG 33295[T] = DSM 117210[T]), and M. marmarense sp. nov. Mu-86[T] (LMG 33293[T] = DSM 117066[T]).},
}
@article {pmid40054170,
year = {2025},
author = {Aalam, J and Ahmad Shah, SN and Parveen, R},
title = {An extensive review on infectious disease diagnosis using machine learning techniques and next generation sequencing: State-of-the-art and perspectives.},
journal = {Computers in biology and medicine},
volume = {189},
number = {},
pages = {109962},
doi = {10.1016/j.compbiomed.2025.109962},
pmid = {40054170},
issn = {1879-0534},
abstract = {UNLABELLED: Infectious diseases, including tuberculosis (TB), HIV/AIDS, and emerging pathogens like COVID-19 pose severe global health challenges due to their rapid spread and significant morbidity and mortality rates. Next-generation sequencing (NGS) and machine learning (ML) have emerged as transformative technologies for enhancing disease diagnosis and management.<br><br>OBJECTIVE: This review aims to explore integrating ML techniques with NGS for diagnosing infectious diseases, highlighting their effectiveness and identifying existing challenges.<br><br>METHODS: A comprehensive literature review spanning the past decade was conducted using reputable databases, including IEEE Xplore, PubMed, Scopus, SpringerLink, and Science Direct. Research papers, articles, and conference proceedings meeting stringent quality criteria were analysed to assess the performance of ML algorithms applied to NGS and metagenomic NGS (mNGS) data.<br><br>RESULTS: The findings reveal that ML algorithms, such as deep neural networks (DNNs), support vector machines (SVM), and K-nearest neighbours (KNN), achieve high accuracy rates, often exceeding 95&#xa0;%, in diagnosing infectious diseases. Deep learning methods excel in genomic and metagenomic data analysis, while traditional algorithms like Gaussian mixture models (GMM) also demonstrate robust classification capabilities. Challenges include reliance on single data types and difficulty distinguishing closely related pathogens.<br><br>CONCLUSION: The integration of ML and NGS significantly advances infectious disease diagnosis, offering rapid and precise detection capabilities. Addressing current limitations can further enhance the effectiveness of these technologies, ultimately improving global public health outcomes.},
}
@article {pmid40056781,
year = {2025},
author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X},
title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.},
journal = {Poultry science},
volume = {104},
number = {4},
pages = {104930},
doi = {10.1016/j.psj.2025.104930},
pmid = {40056781},
issn = {1525-3171},
abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.},
}
@article {pmid40056745,
year = {2025},
author = {Zhu, S and Mao, H and Yang, X and Zhao, W and Sheng, L and Sun, S and Du, X},
title = {Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance.},
journal = {Ecotoxicology and environmental safety},
volume = {292},
number = {},
pages = {117956},
doi = {10.1016/j.ecoenv.2025.117956},
pmid = {40056745},
issn = {1090-2414},
abstract = {This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.},
}
@article {pmid40056594,
year = {2025},
author = {Zhang, H and Zhang, Y and Li, L and Huang, S and Ma, W and Xu, B and Ng, HY and Kim, DH and Kang, S and Shi, X},
title = {An innovative high-rate biofilm-based process: Biopolymer production and recovery from wastewater organic pollutants.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124800},
doi = {10.1016/j.jenvman.2025.124800},
pmid = {40056594},
issn = {1095-8630},
abstract = {In this study, a novel high-rate moving bed biofilm reactor (MBBR) was constructed to enhance wastewater COD bio-conversion and biopolymer recovery with a hydraulic retention time (HRT) of 1.0 h and an organic loading rate (OLR) of 4.8 kg COD·m[-3]·d[-1]. A superior specific COD reduction rate of 4.1 kg COD·m[-3]·d[-1] was obtained. The settleability analyses showed that within a settling time of 30 min, a low effluent suspended solids (SS) concentration (40.6 mg/L) with a high biomass recovery rate (83.3%) was achieved. From the recovered biomass, a remarkably higher alginate-like exopolymer (ALE) yield (274.2-385.1 mg/g VSS) was extracted as compared with seeding sludge (148.3 mg/g VSS). In addition, high protein/polysaccharide ratios of 8.5-12.4 were revealed owing to the short HRT condition. Moreover, key functional genes involving classic ALE synthesis were fully detected in such mixed-cultured bioprocess through metagenomic sequencing. Overall, this study offers a proof of concept that bio-refinery of organics into value-added biopolymers could provide a promising direction for the transformation of wastewater treatment plants from energy/resource-consuming factories to resource-recovery factories.},
}
@article {pmid40056581,
year = {2025},
author = {Wu, Y and Xu, L and He, F and Song, X and Ding, J and Ma, J},
title = {Effects of micro-magnetite on anaerobic co-digestion of waste activated sludge and slaughterhouse waste: Microbial community and metabolism analyses.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124896},
doi = {10.1016/j.jenvman.2025.124896},
pmid = {40056581},
issn = {1095-8630},
abstract = {Micro-magnetite has been widely applied to improve anaerobic digestion (AD) performance, while comprehensive investigation of microbial community succession, metabolic pathway and magnetite fate remains unclear. In the current study, the effects of micro-magnetite (Fe3O4) on anaerobic co-digestion (AcD) of waste activated sludge and slaughterhouse waste were investigated. Experimental results indicated that the cumulative methane production was significantly increased from 484.6 mL/g VS to 524.4 mL/g VS with 0.8 g/L Fe3O4 addition. Recycled magnetite remained the initial physicochemical properties, including morphology, particle size and crystal structure, as evidenced by various characterization methods. Microbial community analysis indicated that magnetite addition enriched syntrophic bacteria (Armatimonadota, Syntrophomonas and Petrimonas) and methanogens (Methanosarcina). Metagenomic sequencing analysis demonstrated that hydrolysis and acidogenesis metabolic pathways were reinforced by magnetite addition. Meanwhile, the magnetite stimulated the direct interspecies electron transfer via enriching syntrophic microbes (Syntrophomonas and Methanosarcina) and conductive pili functional genes (pilA, mshA and mshC), finally achieving higher cumulative methane yield. This study provided in-depth investigation of the methane production facilitated by micro-magnetite addition and the magnetite fate during the AcD process.},
}
@article {pmid40056523,
year = {2025},
author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y},
title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137804},
doi = {10.1016/j.jhazmat.2025.137804},
pmid = {40056523},
issn = {1873-3336},
abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.},
}
@article {pmid40056518,
year = {2025},
author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S},
title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137870},
doi = {10.1016/j.jhazmat.2025.137870},
pmid = {40056518},
issn = {1873-3336},
abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.},
}
@article {pmid40054748,
year = {2025},
author = {Wine, E},
title = {Metagenome-informed metaproteomics: a new frontier in gut host-microbe-diet analysis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.02.024},
pmid = {40054748},
issn = {1528-0012},
}
@article {pmid40054424,
year = {2025},
author = {Ding, C and Sun, J},
title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.},
journal = {Marine environmental research},
volume = {207},
number = {},
pages = {107056},
doi = {10.1016/j.marenvres.2025.107056},
pmid = {40054424},
issn = {1879-0291},
abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.},
}
@article {pmid40054356,
year = {2025},
author = {Yu, Y and Wu, J and Tang, Z and Wan, S and Hu, J and Li, B and Wang, J and Li, F},
title = {Unveiling the nitrogen metabolism mechanism for nitrogen retention in compost via in-situ ammonia recycling strategy.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124863},
doi = {10.1016/j.jenvman.2025.124863},
pmid = {40054356},
issn = {1095-8630},
abstract = {A large amount of ammonia volatilization in compost causes environmental pollution and reduces the quality of compost. Ammonia recycling composting strategy (ARCS) is new strategy for reducing ammonia volatilization by absorbing with backfilling ammonia into the compost. This study revealed the mechanism of ARCS on ammonia volatilization and nitrogen retention during chicken manure composting. The results showed that the adsorption layer containing wood vinegar had an obvious inhibition effect on ammonia volatilization. Compared to CK, ARCS treatment could reduce ammonia emissions and nitrogen loss by 20.65% and 39.6% with T3 (12d), respectively. Different adsorption time would affect the occurrence of various nitrogen components in the adsorption layer, especially the change of inorganic nitrogen content. Metagenomic analysis showed that ARCS treatment resulted in significant changes in bacterial communities, and different backfilling times had significant effects on nitrogen metabolism pathways in compost. Glutamate dehydrogenase and glutamate synthase were the key nitrogen metabolism processes during composting, which played an important role in ammonia volatilization and nitrogen retention. The suitable backfilling time (12d) promoted the acceleration of ammonia nitrogen metabolism in the early stage of composting and enhanced the ammonia assimilation and dissimilatory nitrate reduction function in the maturation stage to achieve nitrogen retention. This study provided valuable insights into the effects of in-situ ammonia absorption and backfilling on nitrogen metabolism pathways during composting.},
}
@article {pmid40054196,
year = {2025},
author = {Wang, S and Li, T and Yuan, X and Yu, J and Luan, Z and Guo, Z and Yu, Y and Liu, C and Duan, C},
title = {Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137818},
doi = {10.1016/j.jhazmat.2025.137818},
pmid = {40054196},
issn = {1873-3336},
abstract = {The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes.},
}
@article {pmid40053579,
year = {2025},
author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R},
title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.},
journal = {Science advances},
volume = {11},
number = {10},
pages = {eads5631},
pmid = {40053579},
issn = {2375-2548},
support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; },
mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics ; *Carbon Cycle ; Sulfur/metabolism ; Gene Regulatory Networks ; Phylogeny ; Metagenome ; Carbon/metabolism ; Proteome/metabolism ; Oxidation-Reduction ; Metabolic Networks and Pathways ; },
abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.},
}
@article {pmid40053318,
year = {2025},
author = {Nihalani, R and Zola, J and Aluru, S},
title = {Disambiguating a Soft Metagenomic Clustering.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0825},
pmid = {40053318},
issn = {1557-8666},
abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.},
}
@article {pmid40053297,
year = {2025},
author = {Scholand, KK and Schaefer, L and Govindarajan, G and Yu, Z and Galletti, JG and de Paiva, CS},
title = {Aged regulatory T cells fail to control autoimmune lacrimal gland pathogenic CD4[+] T cells.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40053297},
issn = {2509-2723},
support = {R01EY030447/EY/NEI NIH HHS/United States ; EY-002520/EY/NEI NIH HHS/United States ; EY021725/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01EY035333/EY/NEI NIH HHS/United States ; P30CA125123/CA/NCI NIH HHS/United States ; CPRIT-RP180672//CPRIT/ ; CA125123//National Institutes of Health (US)/ ; RR024574//National Institutes of Health (US)/ ; 221859/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; PICT 2020-00138//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2021-00109//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; },
abstract = {CD25KO mice are a model of Sjögren disease. CD25KO mice have severe inflammation and infiltrating lymphocytes to the lacrimal glands (LG). Whether the pathogenicity of CD25KO CD4[+] T cells can be controlled in vivo by Tregs is unknown. Eight-week-old B6 and CD25KO mice LGs were submitted for RNA bulk sequencing. A total of 3481 genes were differentially expressed in CD25KO LG compared to B6. Tear washing analysis identified CD25KO mice had elevated protein levels of TNF, IFN-γ, and CCL5 and decreased protein levels of IL-12p40 and VEGF-A. Co-adoptive transfer of CD25KO CD4[+] T cells with either young or aged B6 Tregs was performed in RAG1KO mice. Recipients of CD25KO CD4[+] T cells alone had higher LG inflammation than naive mice. However, in recipients of young B6 Tregs plus CD25KO CD4[+] T cells, LGs had significantly reduced inflammation. Recipients of CD25KO CD4[+] T cells with aged B6 Tregs had more inflamed LGs than young Tregs, suggesting aged Tregs have less suppressive capacity in vivo. Altogether, CD25KO mice have phenotypic and genetic changes resulting in increased inflammation and severe lymphocytic infiltration in the LGs. However, this autoimmunity can be controlled by the addition of young, but not aged, Tregs, suggesting that aging Tregs have dysfunctional suppression.},
}
@article {pmid40052570,
year = {2025},
author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L},
title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.},
journal = {Journal of Crohn's &amp; colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf039},
pmid = {40052570},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.<br><br>METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.<br><br>RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.<br><br>CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.},
}
@article {pmid40052474,
year = {2025},
author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M},
title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {2},
pages = {e70156},
doi = {10.1111/1541-4337.70156},
pmid = {40052474},
issn = {1541-4337},
support = {//United Arab Emirates University/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; },
abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.},
}
@article {pmid40052450,
year = {2025},
author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S},
title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2474730},
doi = {10.1080/07853890.2025.2474730},
pmid = {40052450},
issn = {1365-2060},
mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation &amp; purification ; Overweight/microbiology/complications ; },
abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.<br><br>METHODS: A total of 103 PLWHIV were followed for 48&#x2009;weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238&#x2009;dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.<br><br>RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48&#x2009;weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.<br><br>CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48&#x2009;weeks of ART.},
}
@article {pmid40052378,
year = {2025},
author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H},
title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf055},
pmid = {40052378},
issn = {1365-2672},
abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.<br><br>METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied&#xa0;>&#xa0;50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.<br><br>CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.},
}
@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}
@article {pmid40052063,
year = {2025},
author = {Zheng, H and Peng, P and Wang, S and Zhang, B and Yang, L and Wang, Y and Li, L and Pang, G},
title = {Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1223-1236},
pmid = {40052063},
issn = {1178-6973},
abstract = {OBJECTIVE: Community-acquired pneumonia (CAP) presents a significant public health concern, necessitating timely and precise diagnosis. Metagenomic next-generation sequencing (mNGS) has shown promise as a powerful tool for pathogen identification in infectious diseases. This study aimed to evaluate the diagnostic efficacy and clinical applicability of mNGS for immunocompromised patients with CAP compared to the culture method.<br><br>METHODS: This study included 168 patients. We used both mNGS and conventional culture methods to identify the pathogen spectrum and evaluate diagnostic performance. Treatment regimens and clinical outcomes were meticulously documented.<br><br>RESULTS: The sensitivity of mNGS was greater than that of the culture method across all samples (79.05% vs 16.03%; p < 0.001). mNGS identified pathogens missed by culture in 59.52% of patients and detected polymicrobial infections that were not detected by culture in 47.62% of patients. Streptococcus pneumoniae, Candida albicans, and Human herpesvirus 4 at classification level emerged as the predominant pathogens identified in CAP patients through mNGS. When examining the mNGS results between groups, the proportions of immunocompromised patients with bacterial (p < 0.001), fungal (p < 0.001), viral (p < 0.05), and mixed infections (p < 0.001) were all significantly higher than those in immunocompetent patients. Treatment adjustments guided by mNGS were observed in 73.21% of patients. Specifically, a beneficial clinical effect was observed in 50.60% (85/168) of patients, treatment confirmation in 22.62% (38/168) of patients, and no clinical benefit in 26.80% (45/168) of patients based on mNGS-guided antibiotic treatment adjustments.<br><br>CONCLUSION: These findings highlight the diagnostic performance of mNGS for identifying pathogens, particularly in immunocompromised patients vulnerable to infections, offering valuable insights for clinical decision-making.},
}
@article {pmid40051621,
year = {2025},
author = {Chen, Y and Liang, S and Lu, Y and Zhou, X and Zheng, R and Chen, Y},
title = {Case Report: First report of Legionella micdadei pneumonia and organizing pneumonia in a patient with myelodysplastic and Sweet syndromes.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1510948},
pmid = {40051621},
issn = {1664-3224},
mesh = {Humans ; *Myelodysplastic Syndromes/complications ; *Sweet Syndrome/diagnosis/drug therapy ; Male ; Legionella ; Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology ; Immunocompromised Host ; Legionellosis/diagnosis/drug therapy/microbiology ; Aged ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Glucocorticoids/therapeutic use ; Female ; Legionnaires' Disease/diagnosis/drug therapy/complications/immunology ; Organizing Pneumonia ; },
abstract = {The immunocompromised population is susceptible to Legionella pneumonia. The diagnosis and treatment of Legionella pneumonia in immunocompromised individuals are challenging clinical endeavors. Previous studies have identified Legionella pneumonia as a potential cause of organizing pneumonia (OP), however, the association between Legionella pneumonia and OP has not received enough clinical attention. We retrospectively evaluated a case involving Legionella micdadei infection and OP in a patient with myelodysplastic syndrome and concurrent Sweet syndrome. The diagnosis of Legionella micdadei pneumonia was confirmed through various methods: metagenomic next generation sequencing (mNGS), Giemsa-staining and fluorescence in situ hybridization of lung tissue, as well as serum immunofluorescence antibody testing. Histopathological analysis of lung tissue revealed OP. The patient was successfully treated with a combination of antibiotics and low-dose glucocorticoids. In immunocompromised individuals, mNGS was capable of detection non-Legionella pneumophila serogroup 1. The pathological examination is important for identifying secondary OP and provides the evidence for treatment with glucocorticoids.},
}
@article {pmid40051412,
year = {2025},
author = {Houttu, V and Boulund, U and Troelstra, M and Csader, S and Stols-Gonçalves, D and Mak, AL and Dijk, AV and Bouts, J and Winkelmeijer, M and Verdoes, X and van den Berg-Faay, S and Lek, D and Ronteltap, T and de Haan, F and Jorstad, H and Männistö, V and Savonen, K and Pentikäinen, H and Hanhineva, K and Babu, AF and Panagiotou, G and van Delden, O and Verheij, J and Doukas, M and Nederveen, A and Schwab, U and Grefhorst, A and Nieuwdorp, M and Holleboom, AG},
title = {Deep phenotyping of patients with MASLD upon high-intensity interval training.},
journal = {JHEP reports : innovation in hepatology},
volume = {7},
number = {3},
pages = {101289},
pmid = {40051412},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: Exercise is a key component of lifestyle management in patients with metabolic dysfunction-associated steatotic liver disease (MASLD), but neither its therapeutic effect on the active stage of the disease, that is metabolic dysfunction-associated steatohepatitis (MASH) nor the mediating mechanisms have been characterized. Therefore, we performed multi-omic phenotyping of patients with MASLD-MASH on an exercise program.<br><br>METHODS: Fifteen patients with MASLD conducted high-intensity interval training (HIIT) combined with home-based training for 12 weeks. MASLD was evaluated using histology, transient elastography, and multiparametric magnetic resonance imaging (MRI) before and after the intervention. Change in maximal oxygen consumption (VO2max) and MRI-determined liver fat were compared with a control group of patients with MASLD (n&#xa0;= 22). RNA sequencing was performed on liver, muscle, and fat biopsies of patients in the exercise group. Stool was analyzed by shotgun metagenomics and untargeted metabolomics was performed on plasma, urine, adipose, and stool.<br><br>RESULTS: HIIT increased VO2max by 10.1% and improved mitochondrial metabolism in skeletal muscle, indicating improved cardiorespiratory fitness and adherence. VO2max increased significantly in the exercise group compared with controls. Histologically, no reduction in steatosis, MASH, or liver fibrosis was observed; however, transient elastography tended to improve. MRI-determined liver fat did not change in the exercise group compared with controls. HIIT induced changes in mRNA expression of genes related to beiging of adipose tissue and fibrogenesis in liver. In addition, specific gut microbial taxa and metabolites changed.<br><br>CONCLUSIONS: HIIT increased cardiorespiratory fitness and induced beneficial gene expression changes in muscle, adipose tissue, and liver, but without translation into histological improvement of MASLD. Longer exercise intervention trials are warranted to validate or refute current recommendations for exercise as a cornerstone treatment for MASLD-MASH.<br><br>IMPACT AND IMPLICATIONS: Despite exercise being considered as a key component of lifestyle management for steatotic liver disease, neither the clinical effects nor the mechanisms involved are completely understood. We show that a high-intensity interval training (HIIT) program in 15 patients with metabolic dysfunction-associated steatotic liver disease (MASLD) improved cardiorespiratory fitness, compared with 22 control patients with MASLD who did not participate in an exercise program, however, it did not improve MASLD. HIIT induced a positive effect on fat tissue and muscle metabolism which was accompanied with changes in certain gut bacteria and metabolites in blood and urine. These findings improve our understanding of the effects of exercise on the whole-body metabolism in relation to steatotic liver disease. As such, this study provides a basis for future exercise interventions in patients with MASLD, required to thoroughly test current guideline advice for exercise as a cornerstone treatment for MASLD of all stages.<br><br>CLINICAL TRIAL REGISTRY: Dutch Trial Register (registration number NL7932).},
}
@article {pmid40050994,
year = {2025},
author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU},
title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {27},
pmid = {40050994},
issn = {2524-6372},
support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.<br><br>RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.<br><br>CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.},
}
@article {pmid40050500,
year = {2025},
author = {Dave, M and Tattar, R},
title = {Antimicrobial resistance genes in the oral microbiome.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40050500},
issn = {1476-5446},
abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .<br><br>DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.<br><br>DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.<br><br>STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics&#xa0;for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.<br><br>DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.<br><br>RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n&#x2009;=&#x2009;10) or NGS metagenomics (n&#x2009;=&#x2009;5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.<br><br>CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.},
}
@article {pmid39726137,
year = {2025},
author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N},
title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14060},
doi = {10.1111/1755-0998.14060},
pmid = {39726137},
issn = {1755-0998},
support = {01UT2101C//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01UT2101B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; },
abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.},
}
@article {pmid40050382,
year = {2025},
author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q},
title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7910},
pmid = {40050382},
issn = {2045-2322},
support = {32230071//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; },
abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.},
}
@article {pmid40050078,
year = {2025},
author = {Zheng, YJ and Hou, JY and Zhong, J and Ye, XW},
title = {[A case of COVID-19-associated pulmonary aspergillosis combined with COVID-19-associated pulmonary mucormycosis].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {3},
pages = {267-271},
doi = {10.3760/cma.j.cn112147-20240809-00476},
pmid = {40050078},
issn = {1001-0939},
support = {82460015//National Natural Science Foundation of China/ ; 2019PT320003//Special Fund for Basic Scientific Research Operations of the Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; *Mucormycosis/diagnosis/complications ; *COVID-19/complications ; *Pulmonary Aspergillosis/complications/diagnosis ; Male ; Tomography, X-Ray Computed ; SARS-CoV-2/isolation &amp; purification ; Lung Diseases, Fungal/diagnosis/complications ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/pathology/diagnostic imaging/microbiology ; Antifungal Agents/therapeutic use ; },
abstract = {COVID-19-associated invasive fungal infections are fungal infections that develop during COVID-19, including pulmonary aspergillosis (CAPA) and pulmonary mucormycosis (CAPM). This report presents a case of a patient with recurrent COVID-19 infections who showed pulmonary cavities and pleural effusion on chest CT. A mixed diagnosis of CAPA and CAPM was confirmed by histopathological analysis of bronchoalveolar lavage fluid and metagenomic next-generation sequencing. This study highlights the importance of suspecting CAPA and CAPM in diabetic COVID-19 patients with unexplained radiological findings that cannot be attributed to common infections or pulmonary tumors. Prompt and thorough diagnostic investigations, including histopathology, microbiology, and molecular techniques, are essential for accurate diagnosis. Early and effective antifungal treatment can significantly improve patient outcomes.},
}
@article {pmid40049907,
year = {2025},
author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J},
title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {678-690},
doi = {10.1016/j.jes.2024.10.002},
pmid = {40049907},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; },
abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.},
}
@article {pmid40049896,
year = {2025},
author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H},
title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {550-562},
doi = {10.1016/j.jes.2024.08.026},
pmid = {40049896},
issn = {1001-0742},
mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; },
abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.},
}
@article {pmid40049874,
year = {2025},
author = {Yao, W and Chang, R and Chen, K and Yang, C and Lu, Y and Wang, S and Dong, K and Huang, B and Jin, R},
title = {Performance and mechanism of enhanced phosphorus release and volatile fatty acid production from Fe-P sludge via co-fermenting with agricultural wastes.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {290-299},
doi = {10.1016/j.jes.2024.07.019},
pmid = {40049874},
issn = {1001-0742},
mesh = {*Phosphorus/metabolism ; *Fatty Acids, Volatile/metabolism ; *Sewage ; *Fermentation ; *Agriculture/methods ; *Waste Disposal, Fluid/methods ; Iron/metabolism ; },
abstract = {Anaerobic fermentation is an efficient method to extract phosphorus from excess sludge, thereby facilitating its recovery and mitigating the phosphorus resource shortage. However, the prevalent metal-bound phosphorus species within sludge was difficult to release into the fermentation liquor. To address this, this study evaluated the enhanced phosphorus release performance from sludge containing iron-phosphorus compounds (Fe-P) via co-fermenting it with agriculture wastes. Specifically, protein-rich feather (Feather Group) and polysaccharide-rich tea residue (Tea Group) was respectively dosed into batch-scale fermentation jar. Results showed that the Feather Group exhibited significantly higher levels of released soluble phosphorus (2.1 folds) and volatile fatty acids (41.4 folds) compared to the Control Group, with concentrations reaching up to 280 mg/L and 9366 mg chemical oxygen demand /L, respectively. The activities of α-glucosidase, neutral protease and acetate kinase in the Feather group were increased by 11.1 %, 92.3 % and 37.6 %, respectively, compared with the Control group. Methanogen abundance decreased while hydrolytic acid-producing bacteria and iron-reducing bacteria increased significantly after supplying agricultural wastes. Metagenomic analysis demonstrated a significant increase in genes related to acetic acid synthesis. Mechanism elucidation suggested that increased iron-reducing bacteria abundance promoted Fe[3+] reduction into Fe[2+], thus enhancing phosphorus release from Fe-P compounds. This work may provide valuable information for developing effective strategy to extract phosphorus resource from complex environmental wastes.},
}
@article {pmid40049354,
year = {2025},
author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J},
title = {Metabolic and Ecological Responses of Denitrifying Consortia to Different Carbon Source Strategies Under Fluctuating C/N Conditions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121292},
doi = {10.1016/j.envres.2025.121292},
pmid = {40049354},
issn = {1096-0953},
abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.},
}
@article {pmid40049094,
year = {2025},
author = {Yu, C and He, Q and Nie, WB and Zhang, T and Wu, H and Yang, Y and Fu, S and Tan, X and Chen, Y},
title = {Effluent organic matter facilitates anaerobic methane oxidation coupled with nitrous oxide reduction in river sediments.},
journal = {Water research},
volume = {278},
number = {},
pages = {123415},
doi = {10.1016/j.watres.2025.123415},
pmid = {40049094},
issn = {1879-2448},
abstract = {Effluent organic matter (EfOM) from wastewater treatment plants (WWTPs) contains humic-like substances that function as electron shuttles, thereby facilitating microbially-mediated redox reactions. However, the mechanisms governing the coupled processes of anaerobic oxidation of methane (CH4) (AOM) and nitrous oxide (N2O) reduction in river sediments, which receive WWTPs effluents, remain poorly understood. In this study, an incubation experiment with anoxic river sediments was conducted to assess the impacts of EfOM on AOM and nitrous oxide reduction using different effluent dilution ratios. The results showed that EfOM significantly enhanced both processes. Specifically, the AOM rate increased from 8.1 to 14.3 μg gdw[-1] d[-1], while the N2O reduction rate increased from 29.2 to 56.5 μg gdw[-1] d[-1]. The results of batch tests demonstrated that AOM process enhanced N2O reduction in the presence of EfOM, highlighting the critical role of EfOM in linking these processes. Nitrate-dependent anaerobic methane oxidation (n-DAMO) archaea and denitrifying bacteria dominated the sediment incubated with EfOM. Metagenomic and metatranscriptomic analyses revealed that the denitrifying bacteria exclusively reduce N2O, confirming the role of EfOM in facilitating electron transfer between n-DAMO archaea and N2O reducers. This indicates that effluent discharge could be a potential factor driving the concurrent sinks of methane and nitrous oxide, offering a perspective for investigating the impacts of WWTPs effluent on greenhouse gas sinks in freshwater ecosystems.},
}
@article {pmid40048953,
year = {2025},
author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y},
title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178989},
doi = {10.1016/j.scitotenv.2025.178989},
pmid = {40048953},
issn = {1879-1026},
abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.},
}
@article {pmid40048849,
year = {2025},
author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK},
title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105630},
doi = {10.1016/j.ebiom.2025.105630},
pmid = {40048849},
issn = {2352-3964},
abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.<br><br>METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.<br><br>FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E.&#xa0;coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.<br><br>INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.<br><br>FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Troms&#xf8; Research Foundation, Norway.},
}
@article {pmid40048707,
year = {2025},
author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A},
title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.},
journal = {Neuro-oncology},
volume = {},
number = {},
pages = {},
doi = {10.1093/neuonc/noaf059},
pmid = {40048707},
issn = {1523-5866},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.<br><br>METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.<br><br>RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.<br><br>CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.},
}
@article {pmid40047424,
year = {2025},
author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D},
title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0247724},
doi = {10.1128/aem.02477-24},
pmid = {40047424},
issn = {1098-5336},
abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.<br><br>IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.},
}
@article {pmid40047330,
year = {2025},
author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L},
title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.},
journal = {Journal of food science},
volume = {90},
number = {3},
pages = {e70106},
doi = {10.1111/1750-3841.70106},
pmid = {40047330},
issn = {1750-3841},
support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; },
abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.},
}
@article {pmid40047235,
year = {2025},
author = {Garg, RK},
title = {Tuberculosis of the central nervous system: current concepts in diagnosis and treatment.},
journal = {Current opinion in neurology},
volume = {},
number = {},
pages = {},
pmid = {40047235},
issn = {1473-6551},
abstract = {PURPOSE OF REVIEW: The outcome of central nervous system (CNS) tuberculosis has shown little improvement over several decades, with diagnosis remaining unconfirmed in nearly half of the cases. This review highlights current insights and advancements in the diagnosis and treatment of CNS tuberculosis.<br><br>RECENT FINDINGS: Miliary pulmonary tuberculosis is often linked to CNS tuberculosis and is associated with a worse prognosis. Complications, such as, optochiasmatic arachnoiditis, strokes, and transverse myelitis severely affect prognosis and quality of life. Nearly half of tuberculous meningitis patients exhibited impaired cognition. Diagnosing CNS tuberculosis is challenging because of the low accuracy of standard tests. Advanced techniques like metagenomic and nanopore sequencing enhance detection but are hindered by high costs and limited access. Treatment outcomes remain suboptimal but approaches such as higher drug doses, novel medications, and host-directed therapies are being explored. Drug-resistant tuberculous meningitis is increasingly recognized, posing significant challenges to both diagnosis and treatment. Artificial intelligence (AI) enhances care by enabling early diagnosis, disease monitoring, and personalized treatments, improving outcomes.<br><br>SUMMARY: CNS tuberculosis diagnosis faces challenges due to limited sensitivity and delayed results of available tests. Treatments remain suboptimal, with multidrug-resistant cases posing high mortality risks. AI aids in early diagnosis and personalized care.},
}
@article {pmid40046986,
year = {2025},
author = {Zhang, D and Deng, M and Li, F and Shen, R},
title = {A Report of Primary Pyogenic Ventriculitis Caused by Streptococcus Constellatus Diagnosed by Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1209-1214},
pmid = {40046986},
issn = {1178-6973},
abstract = {BACKGROUND: Primary ventriculitis is a rare but serious brain infection characterized by inflammation of the ependyma and purulence within the ventricular system. Due to the challenges in early diagnosis and the potential for suboptimal treatment, this condition carries a significant risk of complications such as recurrence, hydrocephalus, and death. Metagenomic next-generation sequencing (mNGS) enables the rapid and broad-spectrum identification of pathogens, facilitating timely and precise diagnosis.<br><br>CASE REPORT: This study presents the first reported case of primary ventriculitis caused by Streptococcus constellatus. An 81-year-old female patient with hydrocephalus and clinical signs of central nervous system infection was diagnosed with primary ventriculitis based on brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) analysis using mNGS. The patient underwent external ventricular drainage (EVD) and received a five-week course of ceftriaxone and linezolid. Following timely and targeted therapy, she demonstrated significant clinical improvement and was discharged without residual symptoms.<br><br>CONCLUSION: Key insights from this case include: 1) mNGS is an invaluable tool for the early and accurate diagnosis of primary ventriculitis; 2) MRI is indispensable for identifying characteristic radiological features of the condition; 3) prompt initiation and completion of appropriate antibiotic regimens significantly improve clinical outcomes.},
}
@article {pmid40046887,
year = {2025},
author = {Kim, M and Damronglerd, P and Molina Garcia, S and Yetmar, ZA and Razi, S and Ranganath, N and Mahmood, M and Abu Saleh, OM},
title = {Illuminating the Challenges and Diagnostic Utility of Plasma Microbial Cell-Free DNA Sequencing in Suspected Infective Endocarditis: A Retrospective Observational Cohort Study.},
journal = {Open forum infectious diseases},
volume = {12},
number = {3},
pages = {ofaf099},
pmid = {40046887},
issn = {2328-8957},
abstract = {BACKGROUND: Infective endocarditis (IE) is a life-threatening infection often challenging to diagnose, particularly in culture-negative cases. Plasma microbial cell-free DNA (mcfDNA) sequencing has shown potential for detecting pathogens in IE. However, its clinical utility, diagnostic impact, and limitations remain debated. This study evaluates its use in diagnosing and managing IE in a tertiary care setting.<br><br>METHODS: This single-center retrospective cohort study included adult patients (&#x2265;18 years) who underwent mcfDNA sequencing via the Karius test for suspected IE at Mayo Clinic Rochester between December 2019 and February 2024. Diagnostic classification followed the 2023 Duke-International Society of Cardiovascular Infectious Diseases criteria. Data on demographics, clinical features, routine microbiologic workup, and mcfDNA sequencing results were collected. Statistical analysis was conducted to evaluate diagnostic utility and treatment impact.<br><br>RESULTS: Among 141 patients, 66 had a diagnosis of IE, with mcfDNA sequencing identifying pathogens in 60.6% of them, compared with 39.4% with routine workup. mcfDNA sequencing was the sole microbiologic test with positive results in 33.3% of patients, leading to antimicrobial adjustments in 50.0% of that group. Clinically insignificant mcfDNA sequence detection occurred in 28.6% of patients without a diagnosis of IE.<br><br>CONCLUSIONS: mcfDNA sequencing is a valuable adjunctive tool for diagnosing culture-negative IE and guiding antimicrobial therapy when clinical suspicion is high. However, its utility depends on appropriate clinical context, highlighting the need for careful test interpretation and further prospective studies to assess patient-centered outcomes and cost-effectiveness.},
}
@article {pmid40046856,
year = {2025},
author = {Tan, L and He, Z and Liang, Y and Wang, K and Chen, X},
title = {Correlation analysis between the severity of respiratory syncytial virus pneumonia and the expression levels of inflammatory cytokines in bronchoalveolar lavage fluid among infants and young children.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1482029},
pmid = {40046856},
issn = {2296-2360},
abstract = {PURPOSE: RSV is the primary cause of lower respiratory tract infections in infants and young children. Current study aims to investigate the correlation between the severity of respiratory syncytial virus pneumonia (RSVP) in infants and young children and the number of RSV infection sequences as well as the levels of cytokines in bronchoalveolar lavage fluid (BALF).<br><br>METHODS: Metagenomics next-generation sequencing (mNGS) and enzyme-linked immunosorbent assay (ELISA) were used to detect the number of RSV infection sequences and the levels of related inflammatory cytokines in BALF samples. Comparisons between groups and Logistic regression analysis were performed to examine the differences in RSV infection sequences and inflammatory cytokine levels between the sRSVP and nsRSVP groups. Spearman's correlation coefficient was used to analyze the correlations among PCIS, RSV infection sequences, and inflammatory cytokines. Finally, ROC curve analysis was conducted to assess the diagnostic performance of inflammatory cytokines as biomarkers in determining the severity of RSVP.<br><br>RESULTS: A total of 49 infants and young children diagnosed with RSV infection were enrolled and divided into severe RSVP (sRSVP) and non-severe RSVP (nsRSVP) groups based on the pediatric critical illness score (PCIS) scale. The levels of Interleukin (IL)-6, IL-8, IL-10, tumor necrosis factor &#x3b1; (TNF-&#x3b1;), IL-17A, and monocyte chemotactic protein 1 (MCP-1) as well as the number of RSV sequences in BALF were significantly higher in the sRSVP group than in the nsRSVP group. Additionally, elevated levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and the number of RSV sequences were identified as risk factors for the severity of RSVP. Spearman's correlation analysis revealed significant negative correlations between the levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and MCP-1 in BALF with PCIS, and significant positive correlations with the number of RSV sequences. Furthermore, a significant negative correlation was observed between RSV sequence count and PCIS. ROC curve analysis showed that the levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and MCP-1, as well as their combined diagnostic approach, exhibited high diagnostic performance in determining the severity of RSVP.<br><br>CONCLUSION: The levels of inflammatory cytokines and RSV sequences in BALF are significantly correlated with the severity of RSVP in infants and young children. The levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and MCP-1 can serve as potential biomarkers for diagnosing the severity of RSVP.},
}
@article {pmid40046438,
year = {2025},
author = {Lin, K and Lin, W and Guo, Z and Chen, C and Chen, L and Cai, X},
title = {Plasma exosomal miRNA expression and gut microbiota dysbiosis are associated with cognitive impairment in Alzheimer's disease.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1545690},
pmid = {40046438},
issn = {1662-4548},
abstract = {INTRODUCTION: The gut microbiota composition and the expression profiles of microRNAs (miRNAs) in the brain tissue, cerebrospinal fluid, and blood of patients with Alzheimer's disease (AD) differ significantly from those with normal cognition function. The study aimed to initially explore the relationship between plasma exosomal microRNAs, gut microbiota, and cognitive impairment, providing insights into the pathogenesis and treatment of AD.<br><br>METHODS: The study enrolled 8 participants with AD and 8 participants with normal cognition. The Mini-Mental State Examination (MMSE) was utilized to evaluate cognitive function. High-throughput sequencing was used to identify differentially expressed miRNAs in plasma exosomes, while metagenomic sequencing was employed to detect differences in the abundance of gut microbiota. Furthermore, the associations among them were analyzed.<br><br>RESULTS: Four exosomal miRNAs and 14 microbiota taxa, which exhibited differential expression and abundance, respectively, in comparison between AD group and normal cognition group, were identified to be significantly associated with MMSE scores. Notably, the abundance of potential probiotics, including Faecalibacterium prausnitzii, Roseburia intestinalis and Roseburia inulinivorans, which was decreased in AD patients, exhibited positive correlations with specific exosomal miRNAs: Roseburia intestinalis correlated with miR-3120-3p and miR-6529-5p; Roseburia inulinivorans correlated with miR-3120-3p, miR-6529-5p and miR-124-3p; Faecalibacterium prausnitzii correlated with miR-3120-3p.<br><br>DISCUSSION: The study revealed a close association among gut microbiota, plasma exosomal miRNAs, and cognitive impairment in AD, and suggested that specific components of gut microbiota and exosomal miRNAs may serve as potential biomarkers and therapeutic targets for AD on the microbiota-gut-brain axis.},
}
@article {pmid40046298,
year = {2025},
author = {Sun, W and Li, M and Zhu, X},
title = {Bordetella pertussis bacteremia in infants co-infected with cytomegalovirus and respiratory syncytial virus.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1544935},
pmid = {40046298},
issn = {1664-302X},
abstract = {INTRODUCTION: Hematogenous infections caused by Bordetella pertussis are rare. This study aimed to increase clinicians' knowledge of B. pertussis bacteremia.<br><br>METHODS: We described a case of an infant with B. pertussis bacteremia, searched and reviewed for B. pertussis bacteremia-related literatures published in the PubMed database between 1946 to 2022.<br><br>RESULTS: A 3-month-old male infant was admitted to the hospital with a respiratory tract infection. Respiratory pathogen testing indicated the presence of B. pertussis, cytomegalovirus, and respiratory syncytial viruses. Blood metagenomic next-generation sequencing (mNGS) confirmed B. pertussis bacteremia. After 32&#x202f;days of anti-infective treatment and supportive therapy, the patient's condition improved, and he was discharged. The literature review found that B. pertussis bacteremia is rare, often with fever as the first symptom, and is most common in individuals with underlying diseases or prolonged immunosuppressive therapy.<br><br>DISCUSSION: In infants lacking specific protective antibodies against B. pertussis, B. pertussis bacteremia should be considered when bacteremia-associated clinical manifestations are present and the causative organism remains undetected. Timely refinement of mNGS can help clarify the diagnosis.},
}
@article {pmid40046038,
year = {2025},
author = {Bird, E and Pickens, V and Molik, D and Silver, K and Nayduch, D},
title = {BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40046038},
issn = {2578-9430},
abstract = {BALROG-MON is a Nextflow pipeline for automated analysis of metagenomic long-read data to detect pathogens, annotate antimicrobial resistance genes (ARGs), link ARGs to specific pathogens, predict ARG origin (e.g., plasmid, chromosomal) and optionally perform steps like community analysis. With both assembly-based and assembly-free workflows, BALROG-MON is applicable to a wide range of sample types with low or high coverage, varying complexities and origins. Optional genome binning provides a comprehensive overview of ARGs within the dataset. BALROG-MON additionally presents results in summarized reports, overall serving as a flexible analysis tool for exploring diverse metagenomic samples for pathogens and antibiotic resistance.},
}
@article {pmid40045326,
year = {2025},
author = {Zhang, R and Yu, J and Shang, X and Wang, Z and Li, H and Cao, B},
title = {Heterogeneity in clinical patterns of adult lung abscess patients: an 8-year retrospective study in a tertiary hospital.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {101},
pmid = {40045326},
issn = {1471-2466},
support = {NO. 82030002/H0102//National Natural Science Foundation of China/ ; NO.20220484049//Beijing Nova Program of Science and Technology under grant/ ; No. ZRJY2021-QM09//National High Level Hospital Clinical Research Funding, the Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; },
mesh = {Humans ; *Lung Abscess/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; China/epidemiology ; *Tertiary Care Centers ; Aged ; *Tomography, X-Ray Computed ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Hospital Mortality ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: The widespread use of broad-spectrum antibiotics has led to changes in both the microbiological and clinical characteristics of lung abscesses. It is necessary to re-evaluate the bacterial spectrum associated with these infections. As a novel method for pathogen detection, metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical practice. There is limited research evaluating the use of mNGS in patients with lung abscesses.<br><br>METHODS: A retrospective analysis was conducted on patients with lung abscess who were hospitalized between July 2015 and July 2023 at a teaching hospital in China. Patients who underwent both computerized tomography (CT) imaging and conventional pathogen testing were included in the study. The efficacy of pathogen detection using conventional methods was compared with that of mNGS. Additionally, the clinical and radiological features were analyzed to provide a comprehensive understanding of the disease patterns.<br><br>RESULTS: A total of 782 patients with lung abscess were included in the study and hematogenous abscess accounting for 7.16% (56/782) of cases. The overall hospital mortality rate was 1.53%. The mean age of the patients with lung abscess was 60 years, with a male predominance (80.2%). A significant proportion of patients had comorbid conditions, including diabetes (29.7%) and cardiovascular disease (18.2%). Lung abscesses were predominantly located in the right lung, and pleural effusion was more commonly observed in the deceased group. The detection rate of pathogen via conventional test was lower at 41.8% (327/782). Among patients with positive mNGS results, only 51.9% had pathogens identified through conventional testing methods. Klebsiella pneumoniae was the most frequently detected pathogen by conventional culture, while mNGS identified was Parvimonas micra. Infections caused solely by anaerobic bacteria or facultative anaerobes were associated with shorter hospital stays. Patient infected with Gram-negative bacilli (GNB) had a higher proportion of liver abscesses (11.8%).<br><br>CONCLUSION: Compared to conventional testing methods, mNGS demonstrates superior performance in detecting anaerobic and facultative anaerobic bacteria. The low detection rate of conventional tests may result in an underestimation of the clinical significance of anaerobic bacteria infections. In patients with lung abscess caused by GNB, hematogenous dissemination, liver abscess and diabetes were more commonly observed and these patients tended to have longer hospital stays.},
}
@article {pmid40045185,
year = {2025},
author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL},
title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {120},
pmid = {40045185},
issn = {1471-2180},
support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; },
mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; },
abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.<br><br>RESULTS: We observed that the water column microbiome significantly varied by season (R[2]&#x2009;=&#x2009;0.59, P&#x2009;=&#x2009;0.003). Temperature (R[2]&#x2009;=&#x2009;0.27, P&#x2009;=&#x2009;0.004), dissolved organic matter (R[2]&#x2009;=&#x2009;0.13, P&#x2009;=&#x2009;0.004), and dissolved oxygen (R[2]&#x2009;=&#x2009;0.089, P&#x2009;=&#x2009;0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.<br><br>CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.},
}
@article {pmid40045177,
year = {2025},
author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S},
title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkaf026},
pmid = {40045177},
issn = {2515-5091},
abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.},
}
@article {pmid40044917,
year = {2025},
author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A},
title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.},
journal = {Mycorrhiza},
volume = {35},
number = {2},
pages = {17},
pmid = {40044917},
issn = {1432-1890},
support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; },
mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.},
}
@article {pmid40044690,
year = {2025},
author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M},
title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2226},
pmid = {40044690},
issn = {2041-1723},
support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; },
abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .},
}
@article {pmid40044673,
year = {2025},
author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G},
title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1798},
pmid = {40044673},
issn = {2041-1723},
mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; },
abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.},
}
@article {pmid40043990,
year = {2025},
author = {Lou, D and Xiao, S and Cui, J and Duan, J and Duan, H and Cao, Y and Wang, D and Zhou, B and Tan, J},
title = {Discovery and characterization of the first hyperthermophilic 3-quinuclidinone reductase from hot-spring metagenomes.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141706},
doi = {10.1016/j.ijbiomac.2025.141706},
pmid = {40043990},
issn = {1879-0003},
abstract = {Extremozymes play an essential part in the biosynthesis of pharmaceuticals (intermediates). In this study, a mixed assembly was performed for five metagenomes from hot springs. Via a series of procedures, including homology analysis, heterologous expression, and catalytic property characterization, the first hyperthermophilic 3-quinuclidinone reductase (SbQR) was successfully identified. The SbQR exhibits an optimal temperature of ≥95 °C and demonstrates remarkable thermal stability, with over 80 % of its activity retained following a 48-hour incubation at 50 °C. At particular concentrations, Mg[2+], Na[+], and Mn[2+] can substantially enhance the enzymatic activity. However, no significant influence of K[+] on the activity of SbQR was detected within the concentration range of 0-400 mM. Employing AlphaFold2, the three-dimensional structure of SbQR was predicted, which presents the typical traits of the Rossmann fold and is classified as a member of the short-chain dehydrogenases/reductases (SDR) superfamily. Molecular dynamics simulations were carried out and the results showed that when the temperature was increased to 390 K, the flexibility of residues 90-104 and the C-terminal increased significantly. This increase might lead to the destruction of the three-dimensional structure of the enzyme. In conclusion, this study identified the first hyperthermophilic 3-quinuclidinone reductase, providing a potential biocatalyst for the biopreparation of (R)-3-quinuclidinol.},
}
@article {pmid40043973,
year = {2025},
author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X},
title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.},
journal = {International journal of biological macromolecules},
volume = {306},
number = {Pt 4},
pages = {141714},
doi = {10.1016/j.ijbiomac.2025.141714},
pmid = {40043973},
issn = {1879-0003},
abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.},
}
@article {pmid40043931,
year = {2025},
author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ},
title = {Mangrove Plastisphere as a Hotspot for High-Risk Antibiotic Resistance Genes and Pathogens.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121282},
doi = {10.1016/j.envres.2025.121282},
pmid = {40043931},
issn = {1096-0953},
abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.},
}
@article {pmid40043916,
year = {2025},
author = {Yang, H and Zhu, X and Zhan, Z and Wu, X and Mou, S and Zhou, P and Peng, Q and Wang, W and Teng, H and Tang, H},
title = {Metagenomic Analysis of Pathogenic Microorganisms in Bloodstream Infections Following Venomous Snakebites.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {108304},
doi = {10.1016/j.toxicon.2025.108304},
pmid = {40043916},
issn = {1879-3150},
abstract = {PURPOSE: This study aimed to investigate the biometric characterization of pathogenic microorganisms associated with bloodstream infections in patients bitten by venomous snakes, and to determine whether the composition of these microorganisms influences the effects of snake venom.<br><br>METHODS: The composition and relative abundance of microorganisms were statistically analyzed using metagenomic next-generation sequencing (mNGS) on blood samples from patients with varying degrees of snakebite injuries. These patients were admitted to the our study.<br><br>RESULTS: In the light injury group (group L), the dominant phylum and genus were Pseudomonadota (73.31%) and Pseudomonas (35.32%). In the moderate injury group (group M), the predominant phylum was Bacillota (56.74%) and Aerococcus (45.45%). There was no statistically significant difference in the microbial composition between group L and group M based on &#x3b1;- and &#x3b2;- diversity analyses. LEfSe differential analysis revealed that the absolute abundances of Actinomycetota and Actinomycetes were higher in group L, while Pseudomonas aeruginosa emerged as a significantly differential species in Group M.<br><br>CONCLUSION: The study found that differences in bacterial bloodstream infections due to venomous snakebite may enhance the effects of snake venom, leading to more severe injuries. The mNGS technique can rapidly detect pathogens related to venomous snakebites and has the potential for broader clinical use.},
}
@article {pmid40043765,
year = {2025},
author = {Yang, Y and Wu, X and Xu, Y and Shuang, Q and Xia, YN},
title = {Influence of Feeding Systems on the Microbial Community and Flavor Characteristics of Raw Milk: A Comparative Analysis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25959},
pmid = {40043765},
issn = {1525-3198},
abstract = {This study analyzed the composition of the microbial community in raw milk and its effects on flavor compounds by comparing samples from cows raised on pasture (PXN) and in housing (HXN). In August 2023, 9 raw milk samples from Holstein cows were collected from a pasture in the Xilin Gol League, Inner Mongolia, China, and labeled as the PXN group. Simultaneously, 9 raw milk samples were collected from Holstein cows raised by individual farmers in the region and labeled as the HXN group. Metagenomic sequencing technology was used to detect and analyze the dynamics of microbial community in milk samples. At the same time, headspace solid phase microextraction, electronic nose and electronic tongue technology were used to monitor the flavor characteristics of raw milk under the 2 feeding conditions and to analyze the correlations between them. The results showed that raw milk protein (PXN 3.43%; HXN 3.36%) and fat (PXN 4.01%; HXN 3.79%) content in pasture group were higher than that in the housed group, while lactose content (PXN 4.98%; HXN 5.12%) and total solid content (PXN 4.98%; HXN 5.12%) were lower than that under the housed system. However, there was no significant difference between non-milk fat solid contents of the 2 groups. W1C, W5C, W5S, W2S sensors of electronic nose played an important role in distinguishing the 2 groups of samples. The sour taste of raw milk in pasture group was different from that in house feeding group. There were significant differences in the microbial communities of the 2 groups, with Macrococcus caseolyticus (39.85%) in PXN group and Lactococcus lactis (49.59%) in HXN group being the dominant bacteria. The volatile compounds of raw milk in PXN and HXN groups were detected by headspace solid phase microextraction method. A total of 62 and 53 flavor compounds were detected in PXN and HXN groups, respectively. Terpenoids, esters and aldehydes were dominant in PXN group, while acids were dominant in HXN group. The saturated fatty acid (SFA) content in HXN group (76.13%) was higher than that in PXN group (72.47%). The gamma-linolenic acid (GLA) content in PXN group (3.56 g/100g) was higher than that in HXN group (1.32 g/100g). The dominant strains, i.e., Macrococcus caseolyticus, Lactococcus lactis and Lactococcus cremoris, in both PXN and HXN groups exhibited positive effects on the formation of alcohols, esters, phenols and unsaturated fatty acids. In addition, Macrococcus caseolyticus in PXN group showed significant positive correlation with calcium lactate (CAL). This study comprehensively elaborates the microbial community structure and flavor quality of raw milk under different feeding methods, which may serve as a reference to control the quality of raw milk.},
}
@article {pmid40043731,
year = {2025},
author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q},
title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14147},
pmid = {40043731},
issn = {1600-051X},
support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; },
abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.<br><br>MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.<br><br>RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.<br><br>CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.},
}
@article {pmid40043574,
year = {2025},
author = {Wang, B and Chen, X and Wen, G and Duan, Z and Xue, P and Gao, H},
title = {Treating nitrobenzene (NB) wastewater via an enhanced iron‒manganese oxides electron transfer strategy: Methods and mechanisms.},
journal = {Water research},
volume = {278},
number = {},
pages = {123407},
doi = {10.1016/j.watres.2025.123407},
pmid = {40043574},
issn = {1879-2448},
abstract = {Nitrobenzene (NB) is widely used in the fine chemical, pharmaceutical, and textile industries, but its toxicity and resistance to degradation present challenges, and traditional treatment methods are limited due to costs and a lack of efficiency. In this study, using a three-dimensional biofilm electrode reactor (3D-BER) enhanced with iron-manganese oxide catalysts was explored for the treatment of NB wastewater. Modifying polyurethane (PU) sponge fillers with Fe3O4 and Mn3O4 improved the conductivity and microbial electron transfer of the 3D-BER, significantly enhancing organic compound degradation, nitrogen and phosphorus removal. At the optimal voltage of 6 V and hydraulic retention time (HRT) of 24 h, the reactor achieved CODCr and ammonia nitrogen removal rates of 93.04 % and 86.25 %, respectively, which were more than 20 % higher than those in the control group. The iron and manganese present facilitated increased microbial activity and electron transfer efficiency, and metagenomic sequencing revealed shifts in the microbial communities and the enrichment of specific functional genes related to NB degradation. This integrated bioelectrochemical approach offers an effective and low-cost solution for treating NB wastewater, with broader implications for organic chemical wastewater management.},
}
@article {pmid40043404,
year = {2025},
author = {Pang, L and Chen, J and Li, W and Chatzisymeon, E and Xu, K and Yang, P},
title = {Particle size of zero-valent iron affects the risks from antibiotic resistance genes in waste activated sludge during anaerobic digestion.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137785},
doi = {10.1016/j.jhazmat.2025.137785},
pmid = {40043404},
issn = {1873-3336},
abstract = {Zero-valent iron (ZVI) is the promising enhancer for sludge anaerobic digestion (AD) performance and for mitigating the proliferation of antibiotic resistance genes (ARGs). However, concerns about its size effects in shifting the behavior and risk of ARGs in sludge, during the AD process. Here, the metagenomics-based profile of ARGs, along with their potential (pathogenic) hosts in sludge were investigated, during mesophilic AD enhanced by ZVI with three different sizes. Results showed that the size of ZVI affected the profiles of ARGs, with nano-ZVI (nZVI, 50 nm) demonstrating the most significant reduction in abundance (by 45.0 %) and diversity (by 8.6 %) of total ARGs, followed by micron-ZVI (150 μm) and iron scrap (1 mm). Similar trends were also observed for high-risk ARGs, pathogens, and potential pathogenic hosts for ARGs. Notably, nZVI achieved the greatest reductions in the abundance of risk ARGs and potential pathogenic hosts (superbugs) by 58.8 % and 53.9 %, respectively. Correlation and redundancy analyses revealed that, the size of ZVI induced concentration differences in ammonium nitrogen, pH, carbonaceous matters, iron, and potential microbial hosts were the main reasons for the variation in the risk of ARGs. Moreover, the down-regulation of genes involved in oxidative stress contributed to the lower risk of ARGs in the three ZVI groups, especially in nZVI. This study provides insights into AD processes of solid wastes using ZVI enhancers.},
}
@article {pmid40043390,
year = {2025},
author = {Li, F and Zeng, Z and Wu, Y and Wang, Y and Shen, L and Huang, X and Wang, X and Sun, Y},
title = {Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137808},
doi = {10.1016/j.jhazmat.2025.137808},
pmid = {40043390},
issn = {1873-3336},
abstract = {Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.},
}
@article {pmid40043057,
year = {2025},
author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI},
title = {What defines a photosynthetic microbial mat in western Antarctica?.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0315919},
pmid = {40043057},
issn = {1932-6203},
mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation &amp; purification ; Photosynthesis ; Archaea/genetics/classification/isolation &amp; purification ; Biodiversity ; Phylogeny ; Microbiota ; },
abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.},
}
@article {pmid40042766,
year = {2025},
author = {Kumar, A and Saini, S and Anvikar, A and Mishra, N and Misra, G},
title = {Evolving Landscape of Emerging Virus Diagnosis: Challenges and Innovations.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40042766},
issn = {1559-0305},
abstract = {Emerging and re-emerging viruses (like Spanish flu, SARS-CoV-2, etc.) have substantially impacted global public health since the early twentieth century. These outbreaks are unpredictable and novel viruses are difficult to understand due to emerging variations. Advanced virology and diagnostic technologies have revolutionized viral diagnostics, enabling accurate early identification and successful treatment and containment. Next-generation sequencing (NGS) technologies, such as metagenomics and whole-genome sequencing, have played a crucial role in the detection and monitoring of emerging viruses, such as SARS-CoV-2 and its variants. Advanced diagnostic methods, such as digital PCR, CRISPR-based tools, and serological techniques like ELISA, enhance viral detection's sensitivity, specificity, and speed. Research has shown that innovations such as lateral flow immunoassays, biosensors, and aptamers have the potential to significantly enhance diagnostic accuracy in various fields. The integration of AI in diagnostics aids researchers in understanding viral evolution and outbreak management, offering new avenues for rapid response. This review aims to examine the latest advancements in virus diagnosis technologies, identify unresolved accuracy and detection issues, and discuss emerging ideas that are transforming the future of viral diagnostics. It is important to improve early identification, rendering the system more cost-effective and adaptable to new viral threats.},
}
@article {pmid39902625,
year = {2025},
author = {Pelosi, JA and Sorojsrisom, ES and Barbazuk, WB and Sessa, EB},
title = {Population genomics of the gametophyte-only fern Vittaria appalachiana provides insights into clonal plant evolution.},
journal = {The New phytologist},
volume = {246},
number = {1},
pages = {349-364},
doi = {10.1111/nph.20433},
pmid = {39902625},
issn = {1469-8137},
support = {2024-67012-43394//National Institute of Food and Agriculture/ ; 1701708//Division of Environmental Biology/ ; 1754911/2310485//Division of Integrative Organismal Systems/ ; //Department of Biology, University of Florida/ ; //Southern Appalachian Botanical Society/ ; },
mesh = {*Germ Cells, Plant/physiology ; *Ferns/genetics/physiology ; *Genetic Variation ; *Biological Evolution ; Reproduction, Asexual/genetics ; Genome, Plant ; Metagenomics ; Genetics, Population ; Mutation/genetics ; Clone Cells ; },
abstract = {How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time. The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history. We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum. Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.},
}
@article {pmid40042720,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y},
title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {14},
pmid = {40042720},
issn = {2197-4365},
abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.},
}
@article {pmid40042334,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM},
title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156124},
doi = {10.1128/spectrum.01561-24},
pmid = {40042334},
issn = {2165-0497},
abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.},
}
@article {pmid40042126,
year = {2025},
author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB},
title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.},
journal = {Pediatric pulmonology},
volume = {60},
number = {3},
pages = {e71024},
doi = {10.1002/ppul.71024},
pmid = {40042126},
issn = {1099-0496},
support = {//This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; },
mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Feces/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Infant ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; beta-Lactams/pharmacology/therapeutic use ; Bacterial Load/drug effects ; Longitudinal Studies ; },
abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).<br><br>OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.<br><br>DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") &#x3b2;-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.<br><br>RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). &#x3b1;-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. &#x3b2;-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample &#x3b2;-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.<br><br>CONCLUSIONS: &#x3b2;-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.},
}
@article {pmid40041876,
year = {2025},
author = {Zhang, Y and Peng, J and Wang, Z and Zhou, F and Yu, J and Chi, R and Xiao, C},
title = {Metagenomic analysis revealed the bioremediation mechanism of lead and cadmium contamination by modified biochar synergized with Bacillus cereus PSB-2 in phosphate mining wasteland.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1529784},
pmid = {40041876},
issn = {1664-302X},
abstract = {INTRODUCTION: Phosphate mining wasteland is contaminated with heavy metals, such as lead (Pb) and cadmium (Cd), which pose significant environmental risks. Ecological restoration of these lands is crucial, but limited research has focused on the remediation of heavy metal-contaminated soils using modified biochar and functional microorganisms.<br><br>METHODS: In this study, we investigated the bioremediation of phosphate mining wasteland soil using modified biochar in combination with the phosphate-solubilizing bacterium Bacillus cereus. The effects of this synergistic approach on soil nutrient content, heavy metal immobilization, and microbial community structure were assessed.<br><br>RESULTS AND DISCUSSION: The results indicated that the available phosphate content in the soil increased by 59.32%. The content of extractable state Pb[2 +] and Cd[2 +] decreased by 65.06 and 71.26%, respectively. And the soil nutrient conditions were significantly improved. Synergistic remediation can significantly increase the diversity and abundance of soil microbial communities (p < 0.05). Janibacter, Lysobacter, Ornithinimicrobium, Bacillus, and Salinimicrobium were the main functional flora during soil remediation, with significant correlations for the promotion of Pb[2 +] and Cd[2 +] immobilization and the increase of available phosphate and organic matter. ZitB, czcD, zntA, and cmtR are the major heavy metal resistance genes and regulate metabolic pathways to make microbial community function more stable after soil remediation in phosphate mining wasteland.},
}
@article {pmid40041864,
year = {2025},
author = {Brick, S and Niggemann, J and Reckhardt, A and Könneke, M and Engelen, B},
title = {Interstitial microbial communities of coastal sediments are dominated by Nanoarchaeota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1532193},
pmid = {40041864},
issn = {1664-302X},
abstract = {Microbial communities in subsurface coastal sediments are highly diverse and play an important role in nutrient cycling. While the major fraction of microorganisms in sandy sediments lives as epipsammon (attached to sand grains), only a small fraction thrives in the interstitial porewaters. So far, little is known about the composition of these free-living microbial communities. In the subsurface of the sandy beach, investigated in this study, we compared the archaeal and bacterial community structures within sediments and corresponding porewaters applying 16S rRNA gene sequencing. We found that the free-living prokaryotes only had a proportion of about 0.2-2.3% of the bulk communities, depending on the pore space. The interstitial microbial communities showed a small overlap with the attached fraction of 4-7% ASVs, and comprised a unique composition of 75-81% ASVs found exclusively in the porewaters. They were more diverse than the respective sediment-attached fraction and showed a much higher archaea-to-bacteria ratio. The archaea were mainly affiliated to Nanoarchaeota of the DPANN superphylum, with a relative abundance up to 50% of the interstitial communities. The bacterial fraction included several species related to the Candidate Phyla Radiation (CPR). Both prokaryotic lineages are known to have small cell sizes, comprising not-yet cultured species with unidentified metabolic functions. Our findings were supported by the investigation of an adjacent tidal flat, showing a similar trend. Thus, our results indicate the presence of distinct interstitial microbial communities in the subsurface of coastal sediments. This natural enrichment of not-yet cultured Nanoarchaeota and members of the CPR provides the opportunity for targeted metagenomic analyses or even isolating members of these groups for further metabolic characterization.},
}
@article {pmid40041703,
year = {2025},
author = {Sato, Y},
title = {Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf021},
pmid = {40041703},
issn = {2730-6151},
abstract = {Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.},
}
@article {pmid40041700,
year = {2025},
author = {Wang, X and Cao, D and Zhang, H and Chen, W and Sun, J and Hu, H},
title = {Utilizing metagenomic profiling and machine learning model to identify bacterial biomarkers for major depressive disorder.},
journal = {Frontiers in psychiatry},
volume = {16},
number = {},
pages = {1539596},
pmid = {40041700},
issn = {1664-0640},
abstract = {BACKGROUND: Major depressive disorder (MDD) is highly heterogeneous, which provides a significant challenge in the management of this disorder. However, the pathogenesis of major depressive disorder is not fully understood. Studies have shown that depression is highly correlated with gut flora. The objective of this study was to explore the potential of microbial biomarkers in the diagnosis of major depressive disorder.<br><br>METHODS: In this study, we used a metagenomic approach to analyze the composition and differences of gut bacterial communities in 36 patients with major depressive disorder and 36 healthy individuals. We then applied a Support Vector Machine Recursive Feature Elimination (SVM-RFE) machine learning model to find potential microbial markers.<br><br>RESULTS: Our results showed that the alpha diversity of the intestinal flora did not differ significantly in major depressive disorder compared to healthy populations. However, the beta diversity was significantly altered. Machine learning identified 8 MDD-specific bacterial biomarkers, with Alistipes, Dysosmobacter, Actinomyces, Ruthenibacterium, and Thomasclavelia being significantly enriched, while Faecalibacterium, Pseudobutyrivibrio, and Roseburia were significantly reduced, demonstrating superior diagnostic accuracy (area under the curve, AUC = 0.919). In addition, the gut bacteria performed satisfactorily in the validation cohort with an AUC of 0.800 (95% CI: 0.6334-0.9143).<br><br>CONCLUSION: This study reveals the complex relationship between gut microbiota and major depressive disorder and provides a scientific basis for the development of a microbiota-based diagnostic tool for depression.},
}
@article {pmid40041441,
year = {2025},
author = {Xu, C and Shen, Y and Chen, S and Liu, T and Chen, X and Yu, Y and Liu, L and Ma, R and Zhang, L and Liu, X and Zhou, L and Zhu, G and Feng, S},
title = {Effect of Interpretation of Positive Metagenomic Next-Generation Sequencing Reports on the Infection Diagnosis in Patients With Hematological Disorders.},
journal = {Open forum infectious diseases},
volume = {12},
number = {2},
pages = {ofaf076},
pmid = {40041441},
issn = {2328-8957},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a crucial diagnostic tool for infectious diseases in patients with hematological disorders. However, despite the abundant microbial information provided by positive mNGS reports, interpreting these results remains challenging due to the lack of standardized criteria.<br><br>METHODS: We surveyed 92 clinicians to identify common challenges in understanding mNGS reports. Microbiologists then provided additional "report interpretation cards" (RICs) for positive mNGS results alongside original reports. The aim of using RICs was to determine whether each detected microorganism was likely cause of infection. After a 3-month period, a panel of clinical experts retrospectively reviewed 281 cases, involving 728 detected microorganisms, to assess RIC accuracy.<br><br>RESULTS: In total, 82.6% of clinicians (76 of 92) experienced difficulties in interpreting mNGS reports. After receiving RICs, 97.8% of clinicians (90 of 92) reported satisfaction. The overall concordance rates between interpretation and adjudication in the 281 cases was 79.0% (222 of 281). In 203 cases in which multiple microorganisms were detected, 37.9% (77 of 203) and 37.4% (76 of 203) were interpreted and adjudicated as mixed infections. Among the 728 microorganisms, interpretation and adjudication revealed concordance rates of 93.9% (154 of 164), 95.7% (88 of 92), and 72.3% (339 of 469) for bacterial, fungal, and viral infections, respectively. In 68.7% of the cases (193 of 281), mNGS positively influenced pathogen diagnosis.<br><br>CONCLUSIONS: Not all microorganisms detected by mNGS are responsible for infection, and appropriate interpretation is essential. The provision of interpretations by microbiologists aids clinicians in accurately using mNGS for infection diagnosis.},
}
@article {pmid40040800,
year = {2025},
author = {He, J and Ye, L and Xu, H and Yang, H and Shen, J and Li, M and Weng, S and Jiao, D and Chu, C and Liao, Q and Zou, H and Zhu, J and Wang, C and Xu, X},
title = {Multi-omics analysis reveals a novel NFE2L3 variant impairing choroidal vasculature development in high myopia and myopic maculopathy.},
journal = {National science review},
volume = {12},
number = {2},
pages = {nwae291},
pmid = {40040800},
issn = {2053-714X},
}
@article {pmid40040609,
year = {2025},
author = {Liu, FQ and An, ZY and Cui, LJ and Xiao, MY and Wu, YJ and Li, W and Zhang, BS and Yu, L and Feng, J and Liu, ZG and Feng, R and Jiang, ZX and Huang, RB and Jing, HM and Ren, JH and Zhu, XY and Cheng, YF and Li, YH and Zhou, HB and Gao, D and Liu, Y and Yu, F and Wang, X and Qiao, JL and Hu, DH and Wang, LL and Zang, MT and Chen, Q and Qu, QY and Zhou, JY and Li, ML and Chen, YX and Huang, QS and Fu, HX and Li, YY and Wang, QF and Huang, XJ and Zhang, XH and , },
title = {Correlation Between Fecal Microbiota and Corticosteroid Responsiveness in Primary Immune Thrombocytopenia: an Exploratory Study.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2410417},
doi = {10.1002/advs.202410417},
pmid = {40040609},
issn = {2198-3844},
support = {2023YFC2507803//Key Technologies Research and Development Program/ ; 82300149//National Natural Science Foundation of China/ ; 82130008//National Natural Science Foundation of China/ ; 82230004//National Natural Science Foundation of China/ ; 82350004//National Natural Science Foundation of China/ ; 82430006//National Natural Science Foundation of China/ ; 2024M761208//China Postdoctoral Science Foundation/ ; 2023ZB182//Department of Human Resources and Social Security of Jiangsu Province/ ; 2022-1-4082//Capital Health Research and Development of Special Fund/ ; 7242154//Natural Science Foundation of Beijing Municipality/ ; 7232188//Natural Science Foundation of Beijing Municipality/ ; 71003Y3035//Peking University Medicine/ ; },
abstract = {Corticosteroids (CSs) are the initial therapy for immune thrombocytopenia (ITP); however, their efficacy is not adequately predicted. As a novel biomarker, the composition of the gut microbiota is non-invasively tested and altered in patients with ITP. This study aims to develop a predictive model that leverages gut microbiome data to predict the CS response in patients with ITP within the initial four weeks of treatment. Metagenomic sequencing is performed on fecal samples from 212 patients with ITP, 152 of whom underwent CS treatment and follow-up. Predictive models are trained using six machine-learning algorithms, integrating clinical indices and gut microbiome data. The support vector machine (SVM) algorithm-based model has the highest accuracy (AUC = 0.80). This model utilized a comprehensive feature set that combined clinical data (including sex, age, duration, platelet count, and bleeding scales) with selected microbial species (including Bacteroides ovatus, Bacteroides xylanisolvens, and Parabacteroides gordonii), alpha diversities, KEGG pathways, and microbial modules. This study will provide new ideas for the prediction of clinical CS efficacy, enabling informed decision-making regarding the initiation of CS or personalized treatment in patients with ITP.},
}
@article {pmid40040342,
year = {2025},
author = {Ren, M and Hu, A and Zhao, Z and Yao, X and Kimirei, IA and Zhang, L and Wang, J},
title = {Trait-environmental relationships reveal microbial strategies of environmental adaptation.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70047},
doi = {10.1002/ecy.70047},
pmid = {40040342},
issn = {1939-9170},
support = {BK20240111//Basic Research Program of Jiangsu/ ; 067GJHZ2023034MI//the International Collaboration Program of Chinese Academy of Sciences/ ; 151542KYSB20210007//the International Collaboration Program of Chinese Academy of Sciences/ ; SAJC202403//the International Collaboration Program of Chinese Academy of Sciences/ ; 42002304//National Natural Science Foundation of China/ ; 42107445//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; 92251304//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.},
}
@article {pmid40038896,
year = {2025},
author = {Zhang, H and Ruan, Y and Kuzyakov, Y and Sun, H and Huang, Q and Guo, S and Shen, Q and Ling, N},
title = {Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15458},
pmid = {40038896},
issn = {1365-3040},
support = {//This study was supported by the National Nature Science Foundation of China (32302670) and Nanjing Agricultural University (XUEKEN2023039)./ ; },
abstract = {Viruses alter the ecological and evolutionary trajectories of bacterial host communities. Plant grafting is a technique that integrates two species or varietiies and have consequences on the rhizosphere functioning. The grafting effects on the taxonomic and functional assembly of viruses and their bacterial host in the plant rhizosphere remain largely elusive. Using shotgun metagenome sequencing, we recover a total of 1441 viral operational taxonomic units from the rhizosphere of grafted and ungrafted plants after 8-year continuous monoculture. In the grafted and ungrafted rhizosphere, the Myoviridae, Zobellviridae and Kyanoviridae emerged as the predominant viral families, collectively representing around 40% of the viral community in each respective environment. Grafting enriched the members in viral family Kyanoviridae, Tectiviridae, Peduoviridae and Suoliviridae, and auxiliary metabolic genes related to pyruvate metabolism and energy acquisition (e.g., gloB, DNMT1 and dcyD). The virus-bacterial interactions increased the rapid growth potential of bacteria, which explains the strong increase in abundance of specific bacterial hosts (i.e., Chitinophagaceae, Cyclobacteriaceae and Spirosomaceae) in the grafted-plant rhizosphere. Overall, these results deepen our understanding of microbial community assembly and ecological services from the perspective of virus-host interactions.},
}
@article {pmid40038838,
year = {2025},
author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K},
title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {65},
pmid = {40038838},
issn = {2049-2618},
support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; },
mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; },
abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.<br><br>RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live&#x2009;+&#x2009;dead) sequencing.<br><br>CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.},
}
@article {pmid40038823,
year = {2025},
author = {Liu, F and Yang, J and Shen, W and Fu, J and Meng, J and Zhang, Y and Li, J and Yuan, Z},
title = {Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {26},
pmid = {40038823},
issn = {2524-6372},
support = {No. ES202308//Open Project of State Key Laboratory of Urban Water Resource and Environment/ ; No. 2024M763244//China Postdoctoral Science Foundation/ ; No. 242300421652//Natural Science Foundation of Henan Province/ ; No. 30501300//Top Talent Foundation of Henan Agricultural University/ ; },
abstract = {BACKGROUND: The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as "Wetland") and a drained wetland that used as farmland (referred to as "Dryland").<br><br>RESULTS: The results demonstrated that annual cumulative N2O and CO2 fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH4 annual cumulative fluxes decreased from 12,669.45&#x2009;&#xb1;&#x2009;564.69&#xa0;kg&#xb7;ha[-&#x2009;1] to 8,238.40&#x2009;&#xb1;&#x2009;207.72&#xa0;kg&#xb7;ha[-&#x2009;1] in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50&#x2009;&#xb1;&#x2009;48.83 and 422.21&#x2009;&#xb1;&#x2009;73.59&#xa0;mg&#xb7;CO2-eq&#xb7;m[-&#x2009;2]&#xb7;h[-&#x2009;1], respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH4 production. Functional genes related to CH4 oxidation (pmoA) and gene related to N2O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p&#x2009;<&#x2009;0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH4 serving as an electron donor. This suggests that Dryland may act as a CH4 sink, despite the significant enhancement in CO2 and N2O fluxes.<br><br>CONCLUSIONS: In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.},
}
@article {pmid40038809,
year = {2025},
author = {Reyes, G and Betancourt, I and Andrade, B and Pozo, Y and Sorroza, L and Trujillo, LE and Bayot, B},
title = {Genomic sequence data of Thiohalocapsa marina: a sulfur-oxidizing bacterium prevalent in treated municipal wastewater and commercial shrimp hatchery effluents.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {97},
pmid = {40038809},
issn = {1756-0500},
mesh = {*Wastewater/microbiology ; Animals ; *Genome, Bacterial ; *Sulfur/metabolism ; Oxidation-Reduction ; Biodegradation, Environmental ; Chlorobi/genetics/metabolism ; Aquaculture ; Penaeidae/microbiology ; Phylogeny ; },
abstract = {OBJECTIVES: This study highlighted the gap in the genetic characterization of marine bacteria, specifically within the genus Thiohalocapsa. This genus thrives in contaminated environments with high concentrations of sulfide, such as treated municipal wastewater. Thc. marina is a phototrophic purple bacterium known for its role in sulfur oxidation and bioremediation in marine aquaculture systems. To date, only one Thc. marina genome has been published in the GenBank database. This study enhances the understanding of the ecological adaptation and bioremediation capabilities of Thc. marina in treated municipal wastewater effluents.<br><br>DATA DESCRIPTION: We present a draft genome of Thc. marina LNA26 recovered from treated municipal wastewater effluents using shotgun metagenomic sequencing. The genome of Thc. marina LNA26 harbors 4,356,720 bp and contains 4,032 genes (3,936 CDSs, 50 RNA genes, and 46 pseudogenes), some of them involved in sporulation, siderophores biosynthesis, arsenate bioremediation, sulfide metabolism, capacity for nitrogen fixation, the biosynthesis of PHA, and NHPL bacteriocins. Thc. marina LNA26 exhibits 3 CRISPR Arrays and a high abundance of COGs in signal transduction, energy production, and cell wall biogenesis, indicating advanced environmental responsiveness, energy efficiency, and cellular robustness.},
}
@article {pmid40038603,
year = {2025},
author = {Gao, M and Zhong, S and Han, G and Kuang, D and Yun, C and Fu, C},
title = {Atypical rat bite fever associated with knee joint infection in a Chinese patient: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {312},
pmid = {40038603},
issn = {1471-2334},
mesh = {*Rat-Bite Fever/microbiology/diagnosis/drug therapy ; Humans ; *Streptobacillus/isolation &amp; purification/genetics ; *Knee Joint/microbiology/pathology ; Animals ; Male ; *Anti-Bacterial Agents/therapeutic use ; *RNA, Ribosomal, 16S/genetics ; Synovial Fluid/microbiology ; Arthroscopy ; China ; Middle Aged ; Rats ; East Asian People ; },
abstract = {BACKGROUND: Rat bite fever (RBF) is a rare zoonosis transmitted from rodents to humans through bites and scratches. However, diagnosis and treatment of atypical clinical cases can be challenging.<br><br>CASE PRESENTATION: Herein, we report an atypical case of RBF with unilateral knee joint infection caused by Streptobacillus moniliformis. Streptobacillus moniliformis was isolated from the knee synovial fluid of the patient via microbiological culture and metagenomic next-generation sequencing (mNGS). After treatment with antibiotics and arthroscopic surgery, the patient reported symptom alleviation and was subsequently discharged home. This is the first reported detection of intraarticular histopathological changes caused by Streptobacillus moniliformis during knee arthroscopy.<br><br>CONCLUSIONS: In atypical cases, importantly, clinical healthcare professionals should promptly obtain microbiological culture results. When culture is negative, 16S ribosomal RNA gene polymerase chain reaction (16S rRNA PCR) or mNGS can be considered for identification, with inquiring about the patient's disease history, including any contact with rodents. Surgical interventions, such as arthroscopy, may be included in treatment. Streptobacillus moniliformis infection should be considered when considerable fibrous connective tissue and capillary proliferation are observed under arthroscopic guidance.},
}
@article {pmid40038315,
year = {2025},
author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C},
title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {378},
pmid = {40038315},
issn = {2052-4463},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; },
mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; },
abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.},
}
@article {pmid38892504,
year = {2024},
author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M},
title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.},
journal = {Nutrients},
volume = {16},
number = {11},
pages = {},
pmid = {38892504},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; },
abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).},
}
@article {pmid40038282,
year = {2025},
author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and , and Brodie, EL},
title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2186},
pmid = {40038282},
issn = {2041-1723},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; },
mesh = {*Ecosystem ; *Methane/metabolism ; *Genomics/methods ; *Microbiota/genetics ; Arctic Regions ; Metagenomics/methods ; Wetlands ; Greenhouse Gases/metabolism ; Climate Change ; Bacteria/genetics/metabolism/classification ; },
abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.},
}
@article {pmid40038255,
year = {2025},
author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F},
title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {79},
pmid = {40038255},
issn = {2059-3635},
support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/genetics/microbiology/metabolism ; Female ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/genetics/microbiology/metabolism ; Neoplastic Stem Cells/metabolism/pathology ; Wnt Signaling Pathway/genetics ; Breast Neoplasms/genetics/metabolism/pathology/microbiology ; },
abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.},
}
@article {pmid40038232,
year = {2025},
author = {Gohar, M and Shaheen, N and Goyal, SM and Mor, SK and Rodriguez-R, LM and Imran, M},
title = {Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40038232},
issn = {1867-1314},
support = {No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; MPC-2022-02167//OeAD-GmbH, Austria &#x301;s Agency for Education and Internationalization/ ; MPC-2022-02167//OeAD-GmbH, Austria &#x301;s Agency for Education and Internationalization/ ; No. PSF/CRP/C-QU/T-Helix (70)//Pakistan Science Foundation (PSF) Research/ ; },
abstract = {Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.},
}
@article {pmid40038088,
year = {2025},
author = {Leung, MBW and Chan, DYL and Fok, EKL and Yim, HCH and Jiang, X and Li, TC},
title = {Semen metagenomics and spent culture media in patients undergoing conventional in vitro fertilisation: abridged secondary publication.},
journal = {Hong Kong medical journal = Xianggang yi xue za zhi},
volume = {31 Suppl 1},
number = {1},
pages = {45-47},
pmid = {40038088},
issn = {1024-2708},
}
@article {pmid40037896,
year = {2025},
author = {Chen, N and Kishida, K and Stari, L and Moriuchi, R and Ohtsubo, Y and Damborsky, J and Nagata, Y},
title = {Haloalkane dehalogenases other than LinB can contribute to the γ-hexachlorocyclohexane utilization.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf022},
pmid = {40037896},
issn = {1347-6947},
abstract = {Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols by a simple hydrolytic mechanism. Although many bacterial strains possess HLDs or HLD homologues, LinB is the only HLD known to be involved in the utilization of γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide. In this study, to gain insight into the functional evolution of HLDs toward the γ-HCH utilization, the linB gene in γ-HCH-degrading Sphingobium japonicum strain UT26 was replaced by 7 other HLD or HLD homologous genes, including 3 putative ancestral enzymes. Interestingly, strains carrying genes for DmmA from marine metagenome or Rluc_anc, an ancestor of Renilla-luciferin 2-monooxygenase (Rluc) and LinB, produced 2,5-dichlorophenol and 2,5-dichlorohydroquinone from γ-HCH, which are indicators of LinB activity, and grew in minimal medium supplied with γ-HCH as a sole carbon source. These results indicated that other HLDs in addition to LinB can play roles in the γ-HCH utilization.},
}
@article {pmid40037607,
year = {2025},
author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R},
title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf030},
pmid = {40037607},
issn = {1472-765X},
abstract = {This study investigates the role of microbial dynamics during the fermentation of Buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after eight days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the 8th-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.},
}
@article {pmid40037564,
year = {2025},
author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB},
title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.},
journal = {Age and ageing},
volume = {54},
number = {3},
pages = {},
doi = {10.1093/ageing/afaf042},
pmid = {40037564},
issn = {1468-2834},
support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; },
mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation &amp; purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics &amp; numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics &amp; numerical data ; Age Factors ; Long-Term Care/statistics &amp; numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification ; },
abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.<br><br>OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.<br><br>METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.<br><br>RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P&#x2009;<&#x2009;.0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P&#x2009;<&#x2009;.0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P&#x2009;=&#x2009;.03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P&#x2009;=&#x2009;.04).<br><br>CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.},
}
@article {pmid40037293,
year = {2025},
author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG},
title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf026},
pmid = {40037293},
issn = {1751-7370},
abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 to 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.},
}
@article {pmid40037072,
year = {2025},
author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX},
title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.},
journal = {Ecotoxicology and environmental safety},
volume = {292},
number = {},
pages = {117976},
doi = {10.1016/j.ecoenv.2025.117976},
pmid = {40037072},
issn = {1090-2414},
abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.},
}
@article {pmid40036691,
year = {2025},
author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX},
title = {Benchmarking short-read metagenomics tools for removing host contamination.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf004},
pmid = {40036691},
issn = {2047-217X},
support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; },
abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.<br><br>RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.<br><br>CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.},
}
@article {pmid40036505,
year = {2025},
author = {Langenfeld, K and Hegarty, B and Vidaurri, S and Crossette, E and Duhaime, MB and Wigginton, KR},
title = {Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
doi = {10.1093/nar/gkaf118},
pmid = {40036505},
issn = {1362-4962},
support = {1&#xa0;545&#xa0;756//NSF/ ; //University of Michigan Integrated Training in Microbial Systems (ITiMS)/ ; //University of Michigan/ ; //NSF/ ; //ITiMS/ ; //Burroughs Wellcome Fund/ ; },
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Humans ; Wastewater/virology/microbiology ; DNA Viruses/genetics ; DNA, Viral/genetics ; Bacteriophages/genetics ; Genome, Viral/genetics ; Viruses/genetics ; },
abstract = {Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (i) entropy-based detection thresholds to confidently determine the presence of targets, and (ii) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome-assembled genomes. We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriophages. Concentrations of total DNA viruses in wastewater influent and effluent were >108 copies/ml using QuantMeta. Human-associated DNA viruses were detected and quantifiable with QuantMeta thresholds, including polyomavirus, papillomavirus, and crAss-like phages, at concentrations similar to previous reports that utilized quantitative polymerase chain reaction (PCR)-based assays. Our results highlight the higher detection thresholds of quantitative metagenomics (approximately 500 copies/μl) as compared to PCR-based quantification (approximately 10 copies/μl) despite a sequencing depth of 200 million reads per sample. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target absolute abundances.},
}
@article {pmid40036345,
year = {2025},
author = {Hemeda, AA and Zahran, SA and Tammam, MA and Ewida, MA and Kashef, MT and Yassin, AS and Mitra, A and Youssef, NH and Elshahed, MS},
title = {Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuaf006},
pmid = {40036345},
issn = {1476-5535},
abstract = {The equine gut harbours a diverse microbial community and represents a rich source of carbohydrate-active enzymes (CAZymes). To identify and characterize potentially novel CAZymes from a horse's hindgut metagenome, shotgun metagenomic sequencing was performed on DNA extracted from a stool sample of a male horse followed by CAZyme annotation. Here, we report on the characterization of a novel enzyme (AH2) that was identified, synthesized, cloned and characterized from the obtained CAZyme dataset. AH2 was identified as a GH130 family member and displayed an exclusive xylanase activity, a trait hitherto unreported in prior characterization of GH130 CAZymes. AH2 displayed an optimal activity at a pH of 5.6 and a temperature of 50°C. AH2 maintained significant activity across a pH range of 4 to 10 (62 -72%) and temperatures of 30 to 70°C (77-86%). The enzyme had remarkable stability, with minimal reductions in activity across a temperature range of 4 to 70°C and pH levels of 3, 7, and 9. Docking studies identified AH2's amino acids (Glu90 and Glu149) to be involved in substrate binding. Molecular dynamics simulation confirmed the structural stability of AH2 at pH 5.6 and 50°C, further supporting its resilience under these conditions. Our results expand on the known activities associated with the GH130 CAZyme family and demonstrate that the horse gut metagenome represents an unexplored source of novel CAZymes.},
}
@article {pmid40035787,
year = {2025},
author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG},
title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.2742},
pmid = {40035787},
issn = {1941-2444},
support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; },
abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.<br><br>METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for &#x2264;1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.<br><br>RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.<br><br>CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.},
}
@article {pmid40034816,
year = {2024},
author = {Liu, Z and Jiang, A and Ma, D and Liu, D and Han, X and Zhao, M and Zhou, C and Tan, Z},
title = {The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1463209},
pmid = {40034816},
issn = {2297-1769},
abstract = {Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus <glomeromycetes>, Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP-binding cassette transporters pathways. Additionally, CAZymes such as GH84 and GH37 were significantly associated with differential physiological indicators and milk traits. In conclusion, this study reveals the complex relationship between rumen microbiota and metabolic characteristics in Sanhe and Holstein cows of different parities, indicating that changes in the structure of the rumen microbiome may be key factors affecting lactation performance and metabolic differences in dairy cows.},
}
@article {pmid40034572,
year = {2025},
author = {Phillips, R and Fisher, BT and Ladas, EJ and Patel, P and Robinson, PD and Dupuis, LL and Ammann, RA and Beauchemin, MP and Carlesse, F and Castagnola, E and Davis, BL and Efremov, K and Elgarten, CW and Groll, AH and Haeusler, GM and Koenig, C and Morris, A and Santolaya, ME and Spinelli, D and Tissing, WJE and Wolf, J and Sung, L and Lehrnbecher, T},
title = {Use of food restrictions to prevent infections in paediatric patients with cancer and haematopoietic cell transplantation recipients: a systematic review and clinical practice guideline.},
journal = {EClinicalMedicine},
volume = {81},
number = {},
pages = {103093},
pmid = {40034572},
issn = {2589-5370},
abstract = {BACKGROUND: Food restrictions during periods of neutropenia have been widely used in oncology settings to prevent infections. As there is a lack of clearly demonstrated effectiveness, this strategy is being increasingly questioned.<br><br>METHODS: A multi-national panel of 23 individuals was convened to develop a clinical practice guideline (CPG) on the use of food restrictions to prevent infections in paediatric patients with cancer and haematopoietic cell transplantation (HCT) recipients. It included representation from persons with lived experience and physicians, dieticians, nurses, pharmacists and guideline methodologists working in paediatric oncology/HCT or infectious diseases. Panel members (female n&#xa0;=&#xa0;15; 65%) were from North America (12, 52%), Europe (8, 35%), South America (2, 9%) and Australia (1, 4%). The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to formulate the CPG recommendations based on a systematic review of randomised controlled trials (RCTs). MEDLINE, MEDLINE in-Process and Embase databases were searched from January 1, 1980, to May 7, 2024, with a broad strategy which combined subject headings and text words relating to neutropenia, infection and diet.<br><br>FINDINGS: The systematic review, which provided the evidence base for the CPG recommendations, identified 4312 unique citations, of which 52 were retrieved for full-text evaluation. Eight RCTs met the eligibility criteria and informed panel deliberations. Although there was clinical heterogeneity in the food restrictions evaluated, data were consistent in suggesting that food restrictions lack clinically significant benefit in preventing infections. The panel made two conditional recommendations against the use of food restrictions in a) paediatric patients with cancer receiving chemotherapy and b) in the setting of allogeneic and autologous HCT. The panel developed a good practice statement to emphasise the importance of health care organisations and families adhering to local food safety practices.<br><br>INTERPRETATION: This CPG provides the first evidence-based recommendations on use of food restrictions to prevent infections in children and adolescents undergoing chemotherapy and paediatric haematopoietic cell transplant recipients.<br><br>FUNDING: This CPG was funded and developed through the POGO Guidelines Program.},
}
@article {pmid40034495,
year = {2025},
author = {Zhao, SY and Meng, YL and Yang, ZH and Li, BL and Li, YY and Han, H and Liu, L and Duan, PF and Chen, ZJ},
title = {Rhizosphere microbiome metagenomics in PGPR-mediated alleviation of combined stress from polypropylene microplastics and Cd in hybrid Pennisetum.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549043},
pmid = {40034495},
issn = {1664-302X},
abstract = {The simultaneous presence of microplastics (MPs) and heavy metals in soil may result in heightened toxicity, causing more significant adverse effects on plant growth. Plant growth-promoting rhizobacteria (PGPR) have demonstrated significant capacities in alleviating the toxic stress caused by the combined pollution of heavy metals and other contaminants. However, research on the impacts and processes of PGPR in alleviating stress induced by the combined pollution from MPs and heavy metals is still insufficient. This study involved a pot experiment to evaluate the ability of PGPR to mitigate stress induced by the combined pollution from polypropylene microplastic (PP MPs) particles of different sizes (6.5 μm and 830 μm) and the heavy metal cadmium (Cd) in the bioenergy plant hybrid Pennisetum. Moreover, metagenomic analysis was used to examine the effects of PGPR on the rhizospheric microbial community and function. The cocontamination of PP and Cd affected the growth of the hybrid Pennisetum differently depending on the size of the MPs particles, with the aboveground and underground lengths of the 6.5 μm PP + Cd experimental group being smaller than those of the 830 μm PP + Cd group. The PGPRs (Bacillus sp. Y-35, Bacillus sp. Y-62, Bacillus sp. Y-S, and Enterobacter sp. Y-V) successfully alleviated the stress caused by the combined pollution of PP and Cd, resulting in increases of 8.24 and 42.21% in the plant height and dry weight, respectively. The metagenomic studies indicated that the cocontamination of PP and Cd, along with PGPR inoculation, altered the composition of the rhizospheric bacterial community, leading to changes in microbial diversity indices and the composition of dominant groups such as Pseudomonadota, Actinomycetota, and Acidobacteriota. The functional analysis revealed that the main functional groups involved glucose metabolism, energy metabolism, signal transduction, and nucleotide metabolism. The MPs particle size and different PGPR significantly affected functions such as the pentose phosphate pathway, benzoate degradation, and amide biosynthesis. This study provides essential data and scientific evidence on the ecotoxicological effects of simultaneous contamination by MPs and heavy metals, as well as insights into potential bioremediation methods.},
}
@article {pmid40033444,
year = {2025},
author = {Dias, BDC and Lamarca, AP and Machado, DT and Kloh, VP and de Carvalho, FM and Vasconcelos, ATR},
title = {Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {20},
pmid = {40033444},
issn = {2524-4671},
support = {88887.508687/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 88887.677436/2022-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; E-26/200.200/2024//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.},
}
@article {pmid40032396,
year = {2025},
author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA},
title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e092938},
doi = {10.1136/bmjopen-2024-092938},
pmid = {40032396},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome ; Switzerland ; Infant ; Infant, Newborn ; *Sleep/physiology ; Double-Blind Method ; Child Development ; Infant, Premature ; Child, Preschool ; Brain-Gut Axis ; Female ; Randomized Controlled Trials as Topic ; Male ; Probiotics/therapeutic use ; Multicenter Studies as Topic ; },
abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.<br><br>METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3&#x2009;months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.<br><br>ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.<br><br>TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.},
}
@article {pmid40032028,
year = {2025},
author = {Ismaiah, MJ and Kwan Lo, EK and Chen, C and Shing-Jie Tsui, J and Johnson-Hill, WA and Felicianna, and Zhang, F and Matthew Leung, HK and Oger, C and Durand, T and Chung-Yung Lee, J and El-Nezami, H},
title = {Alpha-aminobutyric acid administration suppressed visceral obesity and modulated hepatic oxidized PUFA metabolism via gut microbiota modulation.},
journal = {Free radical biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.02.029},
pmid = {40032028},
issn = {1873-4596},
abstract = {BACKGROUND: High-fat diet (HFD) is associated with visceral obesity due to disruption in the lipid metabolism and gut dysbiosis. These symptoms may contribute to hepatic steatosis and the formation of oxidized polyunsaturated fatty acids (PUFAs). Alpha-aminobutyric acid (ABA) is an amino-acid derived metabolite, and its concentration has been correlated with several metabolic conditions and gut microbiome diversity while its direct effects on visceral obesity, lipid metabolism and the gut microbiota are not well understood. This study was designed to investigate the effect of physiological dose of ABA on diet-induced visceral obesity and lipid metabolism dysregulation by examining the fatty acids and oxidized PUFAs profile in the liver as well as the gut microbiota.<br><br>RESULTS: ABA administration reduced visceral obesity by 28% and lessened adipocyte hypertrophy. The expression of liver Cd36 was lowered by more than 50% as well as the saturated and monounsaturated FA concentration. Notably, the desaturation index for C16 and C18 FAs that are correlated with adiposity were reduced. The concentration of several DHA-derived oxidized PUFAs were also enhanced. Faecal metagenomics sequencing revealed enriched abundance of Leptogranulimonas caecicola and Bacteroides sp. ZJ-18 and were positively correlated with several DHA- and ALA-derived oxidized PUFAs in ABA group.<br><br>CONCLUSION: Our study revealed the modulatory effect of physiological dose of ABA on attenuating visceral obesity, reducing hepatic steatosis, and promoting the production of anti-inflammatory oxidized PUFAs that were potentially mediated by the gut microbiota.},
}
@article {pmid40030240,
year = {2024},
author = {Xiao, Z and Sun, H and Wei, A and Zhao, W and Jiang, X},
title = {A Novel Framework for Predicting Phage-Host Interactions Via Host Specificity-Aware Graph Autoencoder.},
journal = {IEEE journal of biomedical and health informatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/JBHI.2024.3500137},
pmid = {40030240},
issn = {2168-2208},
abstract = {Due to the abuse of antibiotics, some pathogenic bacteria have developed resistance to most antibiotics, leading to the emergence of antibiotic-resistant superbugs. Therefore, researchers resort to phage therapy for bacterial infections. For phage therapy, the fundamental step is to accurately identify phage-host interactions. Although various methods have been proposed, the existing methods suffer from the following two shortcomings: 1) they fail to make full use of genetic information including both genome and protein sequence of phages; 2) host specificity of phages is not explicitly utilized when learning representations of phages and bacteria. In this paper, we present an efficient computational method called PHISGAE for predicting phage-host interactions, in which the host specificity is explicitly employed. Firstly, initial phage-phage connections are efficiently constructed via utilizing phage genome and protein sequence. Then, the refined heterogeneous network is derived by applying K-nearest neighbor strategy, keeping relatively more meaningful local semantics among phages and bacteria. Finally, a host specificity-aware graph autoencoder is proposed to learn high-quality representations of phages and bacteria for predicting phage-host interactions. Experimental results show that PHISGAE outperforms the state-of-the-art methods on predicting phage-host interactions at both species level and genus level (AUC values of 94.73% and 96.32%, respectively). Moreover, results of case study demonstrate that PHISGAE is able to identify candidate hosts with high probability for previously unseen phages identified from metagenomics, effectively predicting potential phage-host interactions in real-world applications.},
}
@article {pmid40030030,
year = {2025},
author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK},
title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2413953122},
doi = {10.1073/pnas.2413953122},
pmid = {40030030},
issn = {1091-6490},
support = {R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Gastrointestinal Microbiome ; *Multiple Sclerosis/microbiology ; Animals ; Humans ; Mice ; Female ; *Dysbiosis/microbiology ; *Feces/microbiology ; Male ; Akkermansia ; Adult ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Middle Aged ; Bifidobacterium ; Prevotella/isolation &amp; purification ; Mice, Inbred C57BL ; Case-Control Studies ; },
abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.},
}
@article {pmid39882942,
year = {2025},
author = {Tran Lu Y, A and Ruault, S and Daguin-Thiebaut, C and Le Port, AS and Ballenghien, M and Castel, J and Gagnaire, PA and Bierne, N and Arnaud-Haond, S and Poitrimol, C and Thiebaut, E and Lallier, F and Broquet, T and Jollivet, D and Bonhomme, F and Hourdez, S},
title = {Comparative Population Genomics Unveils Congruent Secondary Suture Zone in Southwest Pacific Hydrothermal Vents.},
journal = {Molecular biology and evolution},
volume = {42},
number = {2},
pages = {},
doi = {10.1093/molbev/msaf024},
pmid = {39882942},
issn = {1537-1719},
support = {ANR-17-CE02-0003//ANR CERBERUS project/ ; },
mesh = {*Hydrothermal Vents ; *Phylogeography ; Pacific Ocean ; Gene Flow ; Genetic Variation ; Metagenomics ; },
abstract = {How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs. Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach-especially in addressing knowledge gaps on the life history traits of deep-sea species.},
}
@article {pmid40028749,
year = {2025},
author = {Salahi, A and Abd El-Ghany, WA},
title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70263},
doi = {10.1002/vms3.70263},
pmid = {40028749},
issn = {2053-1095},
mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; },
abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.},
}
@article {pmid40028600,
year = {2025},
author = {Lu, K and Wang, Y and Wang, Y and Zhang, Q and Zhu, Y and Yu, X and Niu, G},
title = {Chijiahe virus, a novel mosquito-associated virus of the Iflaviridae family found in Shandong Province, China.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42532},
pmid = {40028600},
issn = {2405-8440},
abstract = {Climate change is increasing the threat of arboviruses globally, amplifying their geographic distribution and virulence. This poses a grave risk to public health as mosquito-transmitted viral infections resurge and spread. Unbiased metagenomics plays a crucial role in identifying unknown pathogens and monitoring significant ones. Using this approach, a novel mosquito-associated virus, named Chijiahe virus, was discovered. We collected 2910 mosquitoes and divided them into 65 pools based on species and collection site. To ascertain the existence of Chijiahe virus, we utilized nested PCR alongside real-time quantitative reverse transcription PCR (RT-qPCR). Further analysis of the virus's genomic characteristics and phylogenetic relationships revealed its detection in 10 out of 65 mosquito pools, yielding a minimum infection rate (MIR) of 0.34 %. The virus genome consists of a 9654-nucleotide single-stranded RNA, containing an open reading frame (ORF) that encodes essential proteins, including the capsid protein, RNA helicase, and RNA-dependent RNA polymerase (RdRp). Pairwise distance analysis revealed high nucleotide identity among all obtained sequences. Phylogenetic analysis demonstrated Chijiahe virus's close relationship to Arthropod iflavirus, a member of the family Iflaviridae. Additional analyses confirmed Chijiahe virus as a novel member of Iflaviridae.},
}
@article {pmid40028274,
year = {2025},
author = {Veluz, JT and Mallari, LAN and Gloria, PCT and Siringan, MAT},
title = {Exploring the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1522253},
pmid = {40028274},
issn = {1664-8021},
}
@article {pmid40027914,
year = {2025},
author = {Huang, M and Wang, Y and Lu, Y and Qu, W and Zou, Q and Zhang, D and Shen, Y and Han, D and Yu, F and Zheng, S},
title = {Clinical Characteristics and Predicting Disease Severity in Chlamydia psittaci Infection Based on Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1171-1181},
pmid = {40027914},
issn = {1178-6973},
abstract = {INTRODUCTION: Psittacosis pneumonia, as a zoonotic infection, is induced by the pathogen Chlamydia psittaci. In the present study, we sought to characterize the clinical manifestations and prognosticate the severity of psittacosis pneumonia.<br><br>METHODS: We retrospectively verified instances of psittacosis pneumonia in Zhejiang province, China, from January 2021 to April 2024. Relevant data pertaining to epidemiological, clinical, and laboratory aspects were compiled and evaluated.<br><br>RESULTS: Among a total of 110 individuals enrolled who were diagnosed with psittacosis pneumonia, the median age being 62.0 years (IQR, 53-69 years). The most common comorbidities were hypertension (36.4%) and diabetes mellitus (17.3%). Patients categorized as having severe disease (n=68) were significantly older than those with mild disease (n=42). Most patients had notable elevations in aspartate aminotransferase (AST), creatine kinase (CK), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), D-dimer, C-reactive protein (CRP), procalcitonin, total bilirubin (TBil), and interleukin-6, as along with significant reductions in lymphocytes, monocytes, albumin, and interleukin-4. Chest CT scans showed bilateral lung involvement in 70 cases. In the cohort of patients having received empirical antibiotic therapy, 57.3% had their antibacterial medication adjusted in light of the mNGS findings. mNGS results indicated that 31.8% (35/110) had suspected coinfections. The random forest classifiers based upon the clinical and laboratory characteristics attained AUC values of 0.822.<br><br>DISCUSSION: The study underscores the efficacy of mNGS as a robust diagnostic tool for detecting Chlamydia psittaci, which can simultaneously detect other pathogens and guide clinical treatment. Severe patients exhibit significant inflammatory imbalances and lymphocyte depletion. A predictive model based on clinical and laboratory data at admission can effectively guide early clinical intervention.},
}
@article {pmid40027489,
year = {2025},
author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX},
title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70001},
pmid = {40027489},
issn = {2770-596X},
abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.},
}
@article {pmid40027486,
year = {2025},
author = {Zhao, Y and Hu, J and Wang, J and Yao, X and Zhang, T and Hu, B},
title = {Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e271},
pmid = {40027486},
issn = {2770-596X},
abstract = {The discovery of comammox Nitrospira in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox Nitrospira to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox Nitrospira perform under different pH conditions. Results showed that comammox Nitrospira dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox Nitrospira may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox Nitrospira uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox Nitrospira became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox Nitrospira will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox Nitrospira perform in weakly acidic soil and its response to pH changes.},
}
@article {pmid40027485,
year = {2025},
author = {Liu, Y and Li, H and Sun, T and Sun, G and Jiang, B and Liu, M and Wang, Q and Li, T and Cao, J and Zhao, L and Xiao, F and Zhao, F and Cui, H},
title = {Gut microbiome and metabolome characteristics of patients with cholesterol gallstones suggest the preventive potential of prebiotics.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70000},
pmid = {40027485},
issn = {2770-596X},
abstract = {Cholesterol gallstones (CGS) still lack effective noninvasive treatment. The etiology of experimentally proven cholesterol stones remains underexplored. This cross-sectional study aims to comprehensively evaluate potential biomarkers in patients with gallstones and assess the effects of microbiome-targeted interventions in mice. Microbiome taxonomic profiling was conducted on 191 samples via V3-V4 16S rRNA sequencing. Next, 60 samples (30 age- and sex-matched CGS patients and 30 controls) were selected for metagenomic sequencing and fecal metabolite profiling via liquid chromatography-mass spectrometry. Microbiome and metabolite characterizations were performed to identify potential biomarkers for CGS. Eight-week-old male C57BL/6J mice were given a lithogenic diet for 8 weeks to promote gallstone development. The causal relationship was examined through monocolonization in antibiotics-treated mice. The effects of short-chain fatty acids such as sodium butyrate, sodium acetate (NaA), sodium propionate, and fructooligosaccharides (FOS) on lithogenic diet-induced gallstones were investigated in mice. Gut microbiota and metabolites exhibited distinct characteristics, and selected biomarkers demonstrated good diagnostic performance in distinguishing CGS patients from healthy controls. Multi-omics data indicated associations between CGS and pathways involving butanoate and propanoate metabolism, fatty acid biosynthesis and degradation pathways, taurine and hypotaurine metabolism, and glyoxylate and dicarboxylate metabolism. The incidence of gallstones was significantly higher in the Clostridium glycyrrhizinilyticum group compared to the control group in mice. The grade of experimental gallstones in control mice was significantly higher than in mice treated with NaA and FOS. FOS could completely inhibit the formation of gallstones in mice. This study characterized gut microbiome and metabolome alterations in CGS. C. glycyrrhizinilyticum contributed to gallstone formation in mice. Supplementing with FOS could serve as a potential approach for managing CGS by altering the composition and functionality of gut microbiota.},
}
@article {pmid40026814,
year = {2025},
author = {Zhang, X and Yin, H and Yang, X and Kang, J and Sui, N},
title = {Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {1007-1022},
pmid = {40026814},
issn = {1178-7074},
abstract = {PURPOSE: To explore the mechanism of Zhuyang Tongbian Decoction (ZTD) in treating functional constipation (FC) by observing its effects on intestinal flora composition, the metabolic function of gut microbiota, fecal short-chain fatty acid (SCFA) levels, and serum concentrations of TLR4, NF-κB, TNF-α, and IL-6 in patients with FC.<br><br>PATIENTS AND METHODS: 40 patients with FC were randomly divided into the control group and the treatment group, 20 cases in each group. And 20&#xa0;healthy volunteers were recruited during the same period. The control group was administered lactulose, while the treatment group was treated with ZTD. 16s RNA sequencing technology was used to compare the changes in the structure and diversity of the intestinal flora of patients before and after treatment. Changes in the levels of SCFAs in faeces and the levels of TLR4, NF-&#x3ba;B, TNF-&#x3b1; and IL-6 in serum were analysed. Metagenomics sequencing assessed microbiota metabolic functions.<br><br>RESULTS: The treatment group showed a significant increase in the relative abundance of beneficial bacteria, including Bifidobacterium, Lactobacillus, and Faecalibacterium_prausnitzii (P < 0.05), whereas Desulfobacterota and Ruminococcus were significantly reduced (P < 0.05). Notably, fecal acetic and propionic acid levels were significantly higher in the treatment group (P < 0.05). Serum biomarkers TLR4, NF-&#x3ba;B, TNF-&#x3b1;, and IL-6 decreased significantly (P < 0.05). Metagenomics sequencing showed that Carbohydrate metabolism, Metabolism of cofactors and vitamins, and C5- Branched dibasic acid metabolism were significantly increased in functional abundance (P < 0.05).<br><br>CONCLUSION: ZTD notably improves intestinal flora composition and gut microbiota metabolic function, regulates SCFA levels, and reduces inflammation markers in FC patients. The strain Faecalibacterium_prausnitzii shows significant potential in regulation of intestinal inflammation and may play a crucial role in the treatment efficacy of ZTD for FC.},
}
@article {pmid40026575,
year = {2025},
author = {Shen, W and Wang, D and Li, J and Liu, Y and Wang, Y and Yang, X and Peng, X and Xie, B and Su, L and Wei, Z and He, Q and Wang, Z and Feng, K and Du, W and Deng, Y},
title = {Developing a microfluidic-based epicPCR reveals diverse potential hosts of the mcrA gene in marine cold seep.},
journal = {mLife},
volume = {4},
number = {1},
pages = {70-82},
pmid = {40026575},
issn = {2770-100X},
abstract = {Anaerobic methanotrophic (ANME) microbes play a crucial role in the bioprocess of anaerobic oxidation of methane (AOM). However, due to their unculturable status, their diversity is poorly understood. In this study, we established a microfluidics-based epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) to fuse the 16S rRNA gene and mcrA gene to reveal the diversity of ANME microbes (mcrA gene hosts) in three sampling push-cores from the marine cold seep. A total of 3725 16S amplicon sequence variants (ASVs) of the mcrA gene hosts were detected, and classified into 78 genera across 23 phyla. Across all samples, the dominant phyla with high relative abundance (>10%) were the well-known Euryarchaeota, and some bacterial phyla such as Campylobacterota, Proteobacteria, and Chloroflexi; however, the specificity of these associations was not verified. In addition, the compositions of the mcrA gene hosts were significantly different in different layers, where the archaeal hosts increased with the depths of sediments, indicating the carriers of AOM were divergent in depth. Furthermore, the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria, suggesting the horizontal transfer of the mcrA gene may occur among host members. Finally, some bacterial metagenomes were found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway, which prospectively propose the existence of ANME bacteria. This study describes improvements for a potential method for studying the diversity of uncultured functional microbes and broadens our understanding of the diversity of ANMEs.},
}
@article {pmid40026326,
year = {2024},
author = {Laço, J and Martorell, S and Gallegos, MDC and Gomila, M},
title = {Yearlong analysis of bacterial diversity in hospital sink drains: culturomics, antibiotic resistance and implications for infection control.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501170},
pmid = {40026326},
issn = {1664-302X},
abstract = {Hospitals can carry high levels of bacterial diversity from all types of origins, such as human skin, outside environment and medical equipment. Sink drains in clinical settings are considered reservoirs for pathogenic bacteria and potential sources of hospital-acquired infections (HAI's) and antibiotic resistance genes (ARGs). Therefore, infection control measures are crucial to minimizing the risks associated with these reservoirs. Recent research has focused primarily on intensive care units (ICUs) and known pathogens, often employing metagenomic approaches that do not include bacterial isolation. This study aims to evaluate bacterial diversity using culturomics, extending the investigation beyond the ICU to identify antibiotic-resistant bacteria. A total of four samplings were conducted over 1 year (March 2022 to March 2023) in five different hospital wards [ICU, General Medicine (GM), Hematology (H), Short stay unit (UCE), and Microbiology laboratory (MS)]. All samples were cultured on selective and non-selective culture media, resulting in 1,058 isolates identified using MALDI-TOF MS, with a subset confirmed through 16S rRNA gene sequencing. Isolates retrieved from antibiotic supplemented agar were subjected to antibiotic susceptibility testing. The highest bacterial diversity, as measured by the Shannon index, was observed in the ICU and GM wards, posing significant risks to patients in these areas. While bacterial genera were largely similar across wards and sampling times, with Pseudomonas and Stenotrophomonas being the most prevalent, different species were detected in each sampling, indicating no loss of diversity. This suggests that these environments undergo dynamic changes over time, influenced by their surroundings. The results also indicate a relationship between human activity and drain usage and the presence of Pseudomonas aeruginosa, the most commonly found species across most wards. Antibiotic susceptibility testing revealed that all tested isolates, except for one, were multi-resistant, including clinically relevant species, such as P. aeruginosa and K. pneumoniae. Hospital drains may serve as reservoirs for both known and emerging pathogens exhibiting high antibiotic resistance phenotypes. Their dynamic nature may provide insights into strategies for preventing the colonization of these environments by such species.},
}
@article {pmid40025421,
year = {2025},
author = {Sun, J and Ru, J and Cribbs, AP and Xiong, D},
title = {PyPropel: a Python-based tool for efficiently processing and characterising protein data.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {70},
pmid = {40025421},
issn = {1471-2105},
support = {MR/V010182/1//UKRI Medical Research Council (MRC) career development fellowship/ ; MR/V010182/1//UKRI Medical Research Council (MRC) career development fellowship/ ; },
mesh = {*Software ; *Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Machine Learning ; Sequence Analysis, Protein/methods ; },
abstract = {BACKGROUND: The volume of protein sequence data has grown exponentially in recent years, driven by advancements in metagenomics. Despite this, a substantial proportion of these sequences remain poorly annotated, underscoring the need for robust bioinformatics tools to facilitate efficient characterisation and annotation for functional studies.<br><br>RESULTS: We present PyPropel, a Python-based computational tool developed to streamline the large-scale analysis of protein data, with a particular focus on applications in machine learning. PyPropel integrates sequence and structural data pre-processing, feature generation, and post-processing for model performance evaluation and visualisation, offering a comprehensive solution for handling complex protein datasets.<br><br>CONCLUSION: PyPropel provides added value over existing tools by offering a unified workflow that encompasses the full spectrum of protein research, from raw data pre-processing to functional annotation and model performance analysis, thereby supporting efficient protein function studies.},
}
@article {pmid40025420,
year = {2025},
author = {Zhao, J and Zhang, W and Luo, J and Fang, H and Wang, K},
title = {Clinical application of acute Q fever -induced systemic capillary leak syndrome in a patient by using metagenomic next-generation sequencing: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {300},
pmid = {40025420},
issn = {1471-2334},
support = {No. 2023KY1296//Medical and Health Research Program of Zhejiang Province/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Q Fever/diagnosis/complications/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing ; *Capillary Leak Syndrome/diagnosis ; *Metagenomics ; Anti-Bacterial Agents/therapeutic use ; Coxiella burnetii/genetics/isolation &amp; purification ; },
abstract = {INTRODUCTION: Query fever (Q fever), a zoonotic disease, caused by Coxiella burnetii, is an infectious disease that has long been considered a rare and regionally restricted disease. It can be responsible for endocarditis and endovascular infections. Systemic capillary leak syndrome (SCLS), a rare disease of unknown etiology that most commonly develops in adults 50-70 years of age, is diagnosed clinically based on a characteristic symptomatic triad of hypotension, hemoconcentration (elevated hemoglobin or hematocrit), and serum hypoalbuminemia resulting from fluid extravasation. Although Q fever has increasingly been recognized and reported in recent years, the treatment of Q fever complicated by SCLS, with an etiological diagnosis aided by metagenomic next-generation sequencing (mNGS), remains uncommon.<br><br>CASE PRESENTATION: This report describes a case of acute Q fever with concurrent SCLS in a 54-year-old male who worked in a slaughterhouse. The patient presented with fever, chest tightness, and shortness of breath, accompanied by severe headache. His condition rapidly deteriorated, leading to acute fever, generalized weakness, and hypotension. Due to respiratory failure and shock, he was admitted to the intensive care unit (ICU) for treatment. Despite empirical antibiotic therapy along with fluid resuscitation, his blood pressure continued to decline, and metabolic acidosis and respiratory distress worsened. As his condition failed to improve, tracheal intubation was performed. mNGS detected both Coxiella burnetii in his BALF and blood samples. Based on the mNGS results, he was started on doxycycline, alongside penicillin antibiotics, vasopressors, and continuous renal replacement therapy (CRRT). The patient's condition gradually improved, and he was discharged home after 12 days of treatment. At his 90-day follow-up, he had nearly fully recovered to his pre-illness status.<br><br>CONCLUSIONS: mNGS plays a crucial role in assisting the diagnosis of Q fever, which enables the timely treatment of the underlying disease triggering SCLS. This, combined with restrictive fluid resuscitation strategies, is essential for improving patient outcomes.},
}
@article {pmid40023822,
year = {2025},
author = {Gooskens, J and van Essen, EHR and Kraakman, MEM and Wörz, P and Heddema, ER and Boers, SA},
title = {Community-Acquired Pneumonia Caused by Avian Chlamydia abortus, the Netherlands.},
journal = {Emerging infectious diseases},
volume = {31},
number = {3},
pages = {630-633},
doi = {10.3201/eid3103.241406},
pmid = {40023822},
issn = {1080-6059},
mesh = {Netherlands/epidemiology ; Humans ; Animals ; *Chlamydia/isolation &amp; purification ; *Community-Acquired Infections/microbiology/epidemiology ; *Chlamydia Infections/veterinary/microbiology/epidemiology ; *Birds/microbiology ; Aged ; Male ; Bird Diseases/microbiology/epidemiology ; Pneumonia, Bacterial/veterinary/microbiology/epidemiology ; Chlamydial Pneumonia/microbiology/epidemiology ; },
abstract = {We report avian Chlamydia abortus pneumonia in an immunocompetent elderly patient in the Netherlands after environmental exposure to wild aquatic birds, including seabirds. New molecular surveillance studies are needed in wild and captive birds, as well as increased awareness to establish occurrence, clinical manifestations, and geographic distribution of this rare zoonotic disease.},
}
@article {pmid40023383,
year = {2025},
author = {Zhang, Y and Zhang, H and Zhang, B},
title = {Biological and terrestrial influences on dissolved organic matter in Antarctic surface waters: insights from mass spectrometry and metagenomic analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121252},
doi = {10.1016/j.envres.2025.121252},
pmid = {40023383},
issn = {1096-0953},
abstract = {Global warming increases the surface waters and biodiversity in polar regions. However, the intrinsic biological sources of dissolved organic matter (DOM) in Antarctic surface waters remain poorly understood. This work evaluated the sources and driving mechanisms of DOM in Antarctic lakes systematically, based on fluorescence excitation-emission matrices, ultrahigh-resolution mass spectra, biological detection, and metagenomic analyses. The most abundant DOM in the water was peptides (37.02%), which differed from those in soil (lignins: 26.33%) and penguin guano (lipids: 50.71%). The relative abundance of CHON and CHOP compounds in water was significantly correlated with the distance from the penguin colony (p < 0.05). Both the fluorescence and mass spectrum fingerprints of water and soil/faeces showed low similarities using end-member source tracking methods. This could be attributed to the facilitation of guano-derived nutrients and organic carbon to phytoplankton proliferation, whereas the concentrations of NH4[+]-N, NO3[-]-N, total phosphorus, and total organic carbon were significantly higher in the penguin-intensive area than in the other areas. Algae had significant positive effects on carbohydrates and amino sugars and positive effects on lignins, compared to zooplankton and bacteria. Zooplankton had significantly more positive effects on peptides than phytoplankton. Secondary bacterial metabolic activity can be positively linked with CHO compounds. Carbohydrates and amino sugars co-occurred with carbohydrate-active enzyme genes and nitrogen cycling genes in one module of the co-occurrence network, whereas the other module was characterised by the co-occurrence patterns of condensed aromatic structures with carbohydrate-active enzyme genes and nitrogen cycling genes. These results emphasise the roles of secondary metabolites from algae and bacteria in species-specific sources of DOM, shedding light on the driving mechanisms of the biogeochemical cycling of DOM in the Antarctic water environment.},
}
@article {pmid40023333,
year = {2025},
author = {Liu, H and Zhou, Z and Long, C and Qing, T and Feng, B and Zhang, P and Chen, YP},
title = {Light/dark synergy enhances cyanophycin accumulation in algal-bacterial consortia: Boosted strategy for nitrogen recovery from wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132309},
doi = {10.1016/j.biortech.2025.132309},
pmid = {40023333},
issn = {1873-2976},
abstract = {Recovering the nitrogen-rich biopolymer cyanophycin [(β-Asp-Arg)n] from algal-bacterial consortia enhances the reclamation of value-added chemicals from wastewater. However, the modulation of light/dark conditions on cyanophycin accumulation remain unknown. In this study, the trends and mechanisms of cyanophycin synthesis in algal-bacterial consortia under light/dark conditions were investigated. The results showed that cyanophycin production during the dark periods ranged from 137-150 mg/g MLSS (mixed liquid suspended solids), which was 32 %-38 % higher than those during the light period (p < 0.001). Metatranscriptomics results demonstrated that 50 metagenome-assembled genomes contribute to cyanophycin production, with the Planktothrix genus being the dominant contributor. Metabolomics findings suggested that algal-bacterial consortia produce higher level of arginine for cyanophycin synthesis under light conditions. This study demonstrates the feasibility of increasing cyanophycin production by merging light/dark cycles, and offers a novel strategy for high yield of valuable biopolymers from wastewater substrate.},
}
@article {pmid40023316,
year = {2025},
author = {Olearo, F and Zein, SE and Eugenia, PM and Zapf, A and Rohde, H and Berbari, EF and Wouthuyzen-Bakker, M and , },
title = {Diagnostic accuracy of 16S rDNA PCR, Multiplex PCR and Metagenomic Next-Generation Sequencing in Periprosthetic Joint Infections: A Systematic Review and Meta-Analysis.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.02.022},
pmid = {40023316},
issn = {1469-0691},
abstract = {BACKGROUND: The diagnostic accuracy of 16S rDNA PCR, multiplex PCR (mPCR), and metagenomic next-generation sequencing (mNGS) in periprosthetic joint infections (PJIs) remains unclear.<br><br>OBJECTIVES: To evaluate the diagnostic accuracy of 16S rDNA PCR, mPCR, and mNGS in PJI.<br><br>DATA SOURCES: PubMed and EMBASE (January 1, 2000-March 1, 2024), with no language restrictions.<br><br>STUDY ELIGIBILITY CRITERIA: Studies containing sufficient data to construct a 2&#xd7;2 contingency table allowing for sensitivity and specificity calculation were considered.<br><br>PARTICIPANTS: Adults (&#x2265;18&#xa0;years) with PJI and appropriate control groups.<br><br>TESTS: 16S rDNA PCR, mPCR, and mNGS.<br><br>REFERENCE STANDARD: Diagnosis required adherence to Musculoskeletal Infection Society, Infectious Diseases Society of America (IDSA), International Consensus Meeting, European Bone and Joint Infection Society criteria. Studies employing alternative author-defined criteria were included only if they did not rely solely on positive cultures to define PJI.<br><br>ASSESSMENT OF RISK OF BIAS: QUADAS-2 was used.<br><br>METHODS OF DATA SYNTHESIS: A bivariate model calculated pooled diagnostic odds ratios (DORs), sensitivities, and specificities, each with 95% confidence intervals (CIs).<br><br>RESULTS: Seventy-nine studies were included, comprising 3,940 PJI cases and 4,700 uninfected controls. Pooled sensitivity/specificity were 80.0% (95% CI: 75.4-84.3%)/94.0% (95% CI: 91-96%) for 16S rDNA PCR; 62.2% (52.5-70.9%)/96.2% (93.2-97.9%) for mPCR; and 88.6% (83.3-92.4%)/93.2% (89.5-95.6%) for mNGS. Notably, mNGS had the highest DOR (105.9; 95% CI: 60-186.9). A sensitivity analysis excluding lower-quality studies resulted in increased DORs for all methods.<br><br>DISCUSSION: These molecular techniques display strong diagnostic accuracy for identifying PJI. Although mNGS yielded the highest DOR, numerous technical and practical challenges preclude its routine use for PJI diagnosis. Significant heterogeneity across studies warrants cautious interpretation and underscores the need for future comparative research.},
}
@article {pmid40022926,
year = {2025},
author = {Xu, Y and Wang, J and Chi, Q and Zheng, P and Lv, H and Mu, Y and Shen, J},
title = {Mechanistic insights into substituent-induced hydrolytic debromination and electron flow of bromophenols under nitrate-reducing conditions.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137767},
doi = {10.1016/j.jhazmat.2025.137767},
pmid = {40022926},
issn = {1873-3336},
abstract = {Exogenous electron acceptors, such as nitrate, hold great potential for the bioremediation of wastewater contaminated with bromophenols (BPs). However, research into the mechanisms underlying BPs biodegradation remains in its early stages, particularly regarding the molecular structure and bioremediation performance. This study provides a comprehensive analysis of the mechanisms involved in BPs within a nitrate-reducing system, focusing on the molecular structure of BPs. Therefore, three up-flow bioreactors were operated for 187 days, achieving removal efficiencies of 100 %, 90.4 ± 0.6 % and 50.2 ± 2.8 % for ortho-bromophenol (2-BP), para-bromophenol (4-BP) and meta-bromophenol (3-BP), respectively. Hydrolytic dehalogenase (LinB) was found to play a critical role in BP metabolism. Molecular docking and density functional theory calculations revealed that the geometric structure and electronic effects of the Br-substituent significantly influenced LinB activity and BP reactivity, thereby affecting removal efficiencies. Notably, 2-BP, with a shorter orientation distance, was more readily catalyzed by LinB, as evidenced by metagenomic analyses showing significant increases in the abundance of N-transforming and BP-degrading genes. Furthermore, 2-BP and 4-BP stimulated more robust microbial responses, including dehalogenation (Thauera), denitrification (Delftia), and electron transport (Xanthomonadales). These results provide valuable insights into the environmental fate of BPs at the molecular level and how the Br-substituent influences microbial metabolism.},
}
@article {pmid38392845,
year = {2024},
author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Levy, A and Smith, D and Imrie, A},
title = {Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {38392845},
issn = {2076-0817},
mesh = {Animals ; Western Australia ; *RNA Viruses/genetics/isolation &amp; purification ; Microbiota/genetics ; Virome/genetics ; Mosquito Vectors/microbiology/virology ; Culicidae/virology/microbiology ; Aedes/microbiology/virology ; Biodiversity ; Culex/virology/microbiology ; Transcriptome ; Metagenomics/methods ; Phylogeny ; },
abstract = {Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.},
}
@article {pmid40025414,
year = {2025},
author = {Izhar, MZ and Nawaz, M and Yaqub, T and Avais, M},
title = {Effect of probiotic Lactobacillus plantarum CM49 on microbial profile and lactobacilli counts in milk of mastitic cattle.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {109},
pmid = {40025414},
issn = {1471-2180},
support = {PHEC/ARA/PIRCA/20211/9//Punjab Higher Education Commission, Pakistan/ ; },
abstract = {BACKGROUND: Bovine mastitis is a common udder disease in cattle, mainly caused by bacteria and other infectious agents. Traditionally antibiotics are used for their treatment, but the development of antibiotic resistance has increased the importance of using non antibiotic alternative such as probiotic. In current study a previously in vitro characterized isolate Lactobacillus plantarum CM49 infused into two groups of cattle suffering from clinical mastitis (n = 5) and sub-clinical mastitis (n = 5).<br><br>RESULTS: The bacterial composition and diversity analysis of milk samples before and after probiotic administration was analyzed using 16S rRNA gene base metagenomic analysis and lactobacillus counts were also evaluated using Real time PCR. The results show that there was an increase in abundance of Proteobacteria and decrease in Firmicutes at phylum level in both groups while major mastitogens genera Staphylococcus and Streptococcus abundance was reduced after treatment in sub-clinical mastitis group (SCMG) and clinical mastitis group (CMG) respectively. Lactobacilli counts evaluated through Real time PCR showed an increase in number, furthermore diversity indices showed an increase in diversity after treatment with probiotic.<br><br>CONCLUSION: It is concluded from the results that Lactobacillus plantarum CM49 may serve as promising candidate for improving dysbiosis resulting from mastitis and improving microbial diversity.},
}
@article {pmid40025399,
year = {2025},
author = {Liu, A and Wu, J and Li, J and Li, Q and Zhao, N and Hu, K and Liu, S and Blaiotta, G and Zhou, J},
title = {Uncovering the microbial community dynamics and metabolic pathways of primary organic acids in Sichuan Baoning vinegar through metagenomics.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {3},
pages = {91},
pmid = {40025399},
issn = {1573-0972},
support = {No. 2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; },
abstract = {Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.},
}
@article {pmid40025082,
year = {2025},
author = {Regmi, R and Anderson, J and Burgess, L and Mangelson, H and Liachko, I and Vadakattu, G},
title = {Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {367},
pmid = {40025082},
issn = {2052-4463},
mesh = {*Triticum/microbiology ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; Metagenome ; Metagenomics ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; Archaea/genetics ; South Australia ; },
abstract = {Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned to individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements and abundance profiles across multiple samples. However, cost constraints for sequencing and limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), a DNA proximity ligation technique, has been adapted to accurately bin metagenome-assembled genomes (MAGs) from a single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data from wheat rhizospheres grown in two highly calcareous soils of South Australian region and compared conventional and Hi-C binning methods. Two shotgun metagenomes and Hi-C libraries were generated, assembling 1089 shotgun MAGs across 39 bacterial and one archaeal taxon, including 94 Hi-C based bins. Binning performed using only short read sequences was prone to high contamination, while the addition of Hi-C binning improved MAG quality and identified mobile element-host-infection interaction. This dataset provides important tools for studying microbial communities in wheat rhizosphere soils.},
}
@article {pmid40024121,
year = {2025},
author = {Woo, SY and Park, SB and Lee, SY and Sul, WJ and Chun, HS},
title = {Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137777},
doi = {10.1016/j.jhazmat.2025.137777},
pmid = {40024121},
issn = {1873-3336},
abstract = {Mycotoxin contamination is an important concern in producing traditional fermented soybean paste, though no effective control strategy has been developed. This study investigated the mycotoxin profiles of the intermediate (fermented soybean brick, known as "Meju" in South Korea) and final soybean paste products ("Doenjang") to identify major contaminants and describe microbial diversity with the mycotoxins. Profiling of 323 Meju and Doenjang samples revealed severe aflatoxin (AF) contamination. Metagenomic analysis revealed that the species richness and phylogenetic diversity were significantly higher in AF-free than in AF-contaminated Meju and Doenjang. Certain Aspergillus and Penicillium species were more abundant in AF-free than in AF-contaminated Meju and Doenjang. To control AF levels, we developed a novel mycotoxin-reduction approach that preserves the indigenous microbiome by backslopping fermentation of Meju in both Aspergillus-dominant and Penicillium-dominant modes. Both treatments reduced AF levels by > 95 % at a backslopping rate of > 2.5 %. Our results suggested that backslopping fermentation can effectively reduce AF contamination in traditional soybean fermentation, maintaining food safety standards and artisanal practices.},
}
@article {pmid40023235,
year = {2025},
author = {Fang, J and Yin, B and Wang, X and Pan, K and Wang, WX},
title = {Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {371},
number = {},
pages = {125947},
doi = {10.1016/j.envpol.2025.125947},
pmid = {40023235},
issn = {1873-6424},
abstract = {Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g[-1] dw d[-1]). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.},
}
@article {pmid40022370,
year = {2025},
author = {Li, X and You, Y and Xue, B and Chen, J and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J},
title = {Decoding microbiota and metabolite transformation in inoculated fermented suansun using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics:Impacts of different Lactobacillus plantarum strains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {203},
number = {},
pages = {115847},
doi = {10.1016/j.foodres.2025.115847},
pmid = {40022370},
issn = {1873-7145},
mesh = {*Lactobacillus plantarum/metabolism/genetics ; *Metabolomics/methods ; *Fermentation ; *Gas Chromatography-Mass Spectrometry ; *Metagenomics/methods ; *Microbiota/physiology/genetics ; Flavoring Agents/metabolism ; Transcriptome ; Gene Expression Profiling ; Fermented Foods/microbiology ; Food Microbiology ; },
abstract = {Using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics, we investigated the microbial communities and metabolites in two different Lactobacillus plantarum fermentations. Metagenomics revealed Weissella cibaria dominantly contributed to the DACN766-fermented suansun (LPS1) and Lactiplantibacillus pentosus to the DACN760-fermented suansun (LPS2). GC-MS identified 38 and 40 flavor compounds in LPS1 and LPS2, respectively, with p-cresol, 4-hydroxybenzaldehyde, acetic acid, hexanal, and propionic acid crucial for aroma development. LPS2 exhibited higher levels of p-cresol and acetic acid, contributing to its stronger sour and pungent flavors, which was achieved by regulating many metabolisms like glycolysis and tyrosine metabolism. In contrast, Weissella cibaria plays a role in mitigating off-flavors, resulting in a milder flavor profile in LPS1. Non-targeted metabolomics indicated 70.78% of differential metabolites were upregulated in LPS1. Conversely, the elevated expression of tryptophan and tyrosine underscores the more pronounced sour and odor-producing characteristics observed in LPS2. Metatranscriptomics highlighted the regulation of genes like XFA, XFT, and XFM, which inhibit the formation of the precursors of p-cresol and indole in LPS2. This integrated multi-omics analysis provides deep insights into the fermentation dynamics, facilitating the targeted selection of Lactobacillus plantarum strains with flavor-regulating capabilities.},
}
@article {pmid40022356,
year = {2025},
author = {Li, Y and Wu, Y and Chen, S and Zhao, Y and Li, C and Xiang, H and Wang, D and Wang, Y},
title = {Decoding the aroma landscape of fermented golden pompano: The interplay of ester compounds and symbiotic microbiota as revealed by metagenomics and two-dimensional flavoromics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {203},
number = {},
pages = {115832},
doi = {10.1016/j.foodres.2025.115832},
pmid = {40022356},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; *Esters/metabolism/analysis ; *Microbiota ; Odorants/analysis ; Taste ; Seafood/microbiology ; Flavoring Agents/metabolism ; Animals ; Fermented Foods/microbiology ; Symbiosis ; },
abstract = {Fermented pompano (Trachinotus ovatus) is a traditionally popular fermented seafood throughout Asia. Its distinctive flavor profile is primarily attributed to the microbial metabolic conversion of nutrients, which produces specific volatile compounds. Two-dimensional flavoromics of mature pompano revealed that various volatile flavor compounds accumulate throughout fermentation, with fruity (predominantly esters) and oleogustus (primarily ketones) being key flavor markers. S-curve analysis further demonstrated synergistic and additive interactions between these compounds, which enhance flavor release. Metagenomics and Kyoto Encyclopedia of Genes and Genome analysis revealed that amino acid metabolism was the pivotal pathway for ethyl ester synthesis, with Staphylococcus equorum being positively correlated with esters such as ethyl isobutyrate and ethyl enanthate. This study elucidated the interrelationship between flavor compounds and the microbial community in fermented pompano, which is expected to provide insights into flavor modulation and guide the selection of strains that produce key esters in fermented seafood products.},
}
@article {pmid40022320,
year = {2025},
author = {Cámara-Martos, F and Bolívar, A and Rabasco-Vílchez, L and Lafont-Déniz, F and Luque-Ojeda, JL and Pérez-Rodríguez, F},
title = {Exploring the bioaccessibility, in vitro colonic fermentation, and the impact on the intestinal microbiota of allyl-and benzyl-isothiocyanate from white and Ethiopian mustard.},
journal = {Food research international (Ottawa, Ont.)},
volume = {203},
number = {},
pages = {115781},
doi = {10.1016/j.foodres.2025.115781},
pmid = {40022320},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome ; *Mustard Plant/microbiology/chemistry ; *Colon/microbiology/metabolism ; *Fermentation ; *Isothiocyanates/metabolism ; Humans ; Biological Availability ; Digestion ; Glucosinolates/metabolism/analysis ; Gas Chromatography-Mass Spectrometry ; },
abstract = {The aim of this research was to study the formation and bioaccessibility of allyl- and benzyl-isothiocyanate (ITC) resulting from the gastrointestinal digestion (small and large intestine) of green parts from Ethiopian and white mustard. In addition, a GC-MS methodology was validated to determine these compounds in bioaccessible and non-bioaccessible fraction. Plant clumps were divided into two batches: fresh and freeze-dried samples. ITC bioaccessibility was low in the small intestine, with values ranged between 11 and 53 % and mean values of 26 %. These results are in agreement with the fact that ITCs are poorly water-soluble compounds. Bioaccessibility values for lyophilised samples were lower than those obtained in fresh samples. This could be due to the degradation of the precursor glucosinolates (sinigrin and glucotropaeolin respectively). The simulation of the colonic fermentation reduced allyl - and benzyl - ITC levels from the non-bioaccessible fraction of Ethiopian and white mustard (values between 0.009 and 0.087 mg/g). In both cases, ITCs concentration dropped dramatically, i.e. with a ten-fold reduction. Nevertheless, this result does not necessarily indicate that ITCs have not been produced in the large intestine. Bacterial microbiota plays a key role in generating ITCs; however, ITCs are not always the final products of this process. The metagenomic analysis of colonic samples revealed that ITCs and cruciferous matrix significantly influenced the composition of gut microbiota, inhibiting potentially pathogenic bacteria such as Enterobacter and Klebsiella, while promoting beneficial bacteria such as Bifidobacterium, Faecalibacterium, Blautia, and Ruminococcus. Interestingly, ITCs-rich environments selected bacterial species (i.e. Enterobacter ludwigii) and promoted metabolic pathways involved in glucosinolate/ITCs metabolism.},
}
@article {pmid40022097,
year = {2025},
author = {Ferneyhough, B and Roddis, M and Millington, S and Quirk, J and Clements, C and West, S and Schilizzi, R and Fischer, MD and Parkinson, NJ},
title = {A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.},
journal = {BMC urology},
volume = {25},
number = {1},
pages = {41},
pmid = {40022097},
issn = {1471-2490},
mesh = {Humans ; Female ; Male ; *Metagenomics/methods ; *Microbiota/genetics ; Nanopore Sequencing/methods ; Vagina/microbiology ; Workflow ; Urogenital System/microbiology ; },
abstract = {BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.<br><br>RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.<br><br>CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.},
}
@article {pmid40020351,
year = {2025},
author = {Manna, B and Zhou, X and Singhal, N},
title = {ROS-induced stress promotes enrichment and emergence of antibiotic resistance in conventional activated sludge processes.},
journal = {Water research},
volume = {277},
number = {},
pages = {123366},
doi = {10.1016/j.watres.2025.123366},
pmid = {40020351},
issn = {1879-2448},
abstract = {Since the Great Oxidation Event 2.4 billion years ago, microorganisms have evolved sophisticated responses to oxidative stress. These ancient adaptations remain relevant in modern engineered systems, particularly in conventional activated sludge (CAS) processes, which serve as significant reservoirs of antibiotic resistance genes (ARGs). While ROS-induced stress responses are known to promote ARG enrichment/emergence in pure cultures, their impact on ARG dynamics in wastewater treatment processes remains unexplored. Shotgun-metagenomics analysis of two hospital wastewater treatment plants showed that only 35-53 % of hospital effluent resistome was retained in final effluent. Despite this reduction, approximately 29-36 % of ARGs in CAS showed higher abundance than upstream stages, of which 20-22 % emerged de novo. Beta-lactamases and efflux pumps constituted nearly 47-53 % of these enriched ARGs. These ARGs exhibited significant correlations (p < 0.05) with ROS stress response genes (oxyR, soxR, sodAB, katG and ahpCF). The CAS resistome determined 58-75 % of the effluent ARG profiles, indicating treatment processes outweigh influent composition in shaping final resistome. Proof-of-concept batch reactor experiments confirmed increased ROS and ARG levels under high dissolved oxygen (8 mg/L) compared to low oxygen (2 mg/L) concentrations. Untargeted metaproteomics revealed higher expression of resistant proteins (e.g., OXA-184, OXA-576, PME-1, RpoB2, Tet(W/32/O)) under elevated ROS levels. Our findings demonstrate that CAS processes actively shape effluent resistome through ROS-mediated selection, indicating that treatment processes, rather than initial wastewater composition, determine final ARG profiles. This study indicates that the emergence of ARGs needs to be considered as an integral aspect of wastewater treatment design and operation to prevent antibiotic resistance dissemination.},
}
@article {pmid40020294,
year = {2025},
author = {Zhao, Y and Li, L and Tan, J and Zhao, H and Wang, Y and Zhang, A and Jiang, L},
title = {Metagenomic insights into the inhibitory effect of phytochemical supplementation on antibiotic resistance genes and virulence factors in the rumen of transition dairy cows.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137717},
doi = {10.1016/j.jhazmat.2025.137717},
pmid = {40020294},
issn = {1873-3336},
abstract = {Antimicrobial resistance (AMR) is a major global health concern, with the rumen microbiota of dairy cows serving as an important reservoir for antibiotic resistance genes (ARGs) and virulence factors (VFs). This study explores the impact of dietary phytochemical supplementation on the rumen resistome and virulome of transition dairy cows using metagenomic sequencing. Naringin supplementation reduced the abundance of ARGs by up to 9.0 % and VFs by up to 7.2 % during the transition period, as indicated by metagenomic analysis (P < 0.05). Clinically high-risk ARGs, including those conferring resistance to beta-lactams (mecA), tetracyclines (tetM, tetO), and aminoglycosides (rmtF), were notably downregulated (P < 0.05). Virulence factors associated with adherence, secretion systems, and toxins were also significantly decreased (P < 0.05). Naringin altered the microbial community structure, particularly reducing the abundance of Proteobacteria, a key phylum harboring ARGs and VFs. Despite inducing increased ARG-VF network complexity, naringin supplementation promoted a less pathogenic microbiome with reduced resistance potential. These findings demonstrate the potential of naringin as a natural dietary strategy to mitigate AMR by reducing the risk of ARG and VF dissemination into the environment, while supporting rumen microbiota stability in transition dairy cows.},
}
@article {pmid40022204,
year = {2025},
author = {Debray, R and Dickson, CC and Webb, SE and Archie, EA and Tung, J},
title = {Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {59},
pmid = {40022204},
issn = {2049-2618},
support = {R01AG071684/NH/NIH HHS/United States ; R01AG071684/NH/NIH HHS/United States ; R61AG078470//National Science Foundation/ ; R61AG078470//National Science Foundation/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Papio/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; },
abstract = {BACKGROUND: In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.<br><br>RESULTS: Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.<br><br>CONCLUSIONS: We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.},
}
@article {pmid40021978,
year = {2025},
author = {Lv, Y and Zhang, L and Wang, X and Zhang, Y},
title = {Genomic evidence on the distribution and ecological function of Pseudomonas in hadal zone.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {100},
pmid = {40021978},
issn = {1471-2180},
support = {42306104//National Natural Science Foundation of China/ ; 42188102//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute, Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; },
mesh = {*Pseudomonas/genetics/metabolism/classification ; *Seawater/microbiology ; *Genome, Bacterial/genetics ; *Geologic Sediments/microbiology ; *Phylogeny ; Metagenome ; Genomics ; Carbon/metabolism ; },
abstract = {The hadal zone is the deepest region on Earth. It serves as a depositional zone for the sinking matter from surface ocean and continental margin, aided by its unique V-shaped structure. Due to extreme depth (over 6000 m), normally only organic matter with low degradability typically reaches the bottom of the trench. Concurrently, reports have indicated highly active carbon turnover and dense bacterial cells in the Mariana Trench. There remains a cognitive gap in understanding the connection between this phenomenon and the microbial taxa along with their metabolic activities. Here, we surveyed the Pseudomonas, one of the most widely distributed bacterial genera on Earth. The result revealed widespread distribution of Pseudomonas in the hadal zones. We obtained 21 metagenome-assembled genomes (MAGs) from seawater and sediment samples of the Mariana Trench, including three novel species. Comparative genomic analysis showed that hadal Pseudomonas possess more unique ortholog groups of genes related to energy generation and substances transport, distinct from those in other marine zones. These bacteria exhibit the ability to utilize diverse electron acceptors and accumulate compatible solutes, indicating two key strategies for adaptation for high hydrostatic pressure conditions. Furthermore, predicted genomic capabilities suggest that Pseudomonas could decompose various components of organic matter, particularly aromatics, as supported by metatranscriptomic datasets. These findings significantly enhance our understanding of Pseudomonas diversity and metabolic potential, providing valuable insights into the carbon and nitrogen cycles in hadal trench ecosystems.},
}
@article {pmid40021694,
year = {2025},
author = {Gambardella, N and Costa, J and Martins, BM and Folhas, D and Ribeiro, AP and Hintelmann, H and Canário, J and Magalhães, C},
title = {The role of prokaryotic mercury methylators and demethylators in Canadian Arctic thermokarst lakes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7173},
pmid = {40021694},
issn = {2045-2322},
support = {PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Arctic Regions ; Canada ; *Lakes/microbiology ; *Mercury/metabolism ; Methylation ; Methylmercury Compounds/metabolism/analysis ; Microbiota ; Geologic Sediments/microbiology ; Bacteria/genetics/metabolism/classification ; Permafrost/microbiology ; Seasons ; Metagenomics/methods ; Water Pollutants, Chemical/metabolism ; Environmental Monitoring/methods ; },
abstract = {Permafrost soils are critical reservoirs for mercury (Hg), with the thawing process leading to the release of this element into the environment, posing significant environmental risks. Of particular concern is the methylated form of mercury, monomethylmercury (MMHg), known for its adverse effects on Human health. Microbial communities play a pivotal role in the formation of MMHg by facilitating Hg methylation and in the demethylation of MMHg, slowing the crossing of toxic threshold concentration in the environment. However, the specific microbes involved still need to be understood. This study aimed to identify the microbial drivers behind changes in Hg speciation (MMHg and Hg) in permafrost thaw lakes and assess the significance of the biotic component in Hg biogeochemistry. Sediment samples from two thermokarst lakes in the Canadian sub-Arctic were collected during the winter and summer of 2022. Gene-centric metagenomics using whole-genome sequencing (WGS) was employed to identify key genes involved in mercury methylation (hgcA and hgcB) and demethylation (merA and merB), supported by qPCR analyses. A seasonal decline in microbial diversity, involved in the Hg methylation, and hgcA gene coverage was observed from winter to summer, mirroring patterns in mercury methylation rates. Notably, hgcA sequences were significantly more abundant than merAB sequences, with contrasting seasonal trends. These results indicate a seasonal shift in the microbial community, transitioning from a dominance of mercury methylation in winter to a predominance of mercury demethylation in summer. Environmental drivers of these dynamics were integrated into a conceptual model. This study provide new insights on the microbial processes influencing the Hg cycle in Arctic permafrost undergoing degradation.},
}
@article {pmid40021498,
year = {2025},
author = {Urrea, V and Páez-Triana, L and Velásquez-Ortiz, N and Camargo, M and Patiño, LH and Vega, L and Ballesteros, N and Hidalgo-Troya, A and Galeano, LA and Ramírez, JD and Muñoz, M},
title = {Metagenomic Analysis of Surface Waters and Wastewater in the Colombian Andean Highlands: Implications for Health and Disease.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {162},
pmid = {40021498},
issn = {1432-0991},
support = {BPIN: 2020000100770//Colombian Fund for Science, Technology, and Innovation of Sistema General de Regal&#xed;as/ ; },
mesh = {*Wastewater/microbiology/parasitology ; *Metagenomics ; Colombia ; *Cryptosporidium/genetics/isolation &amp; purification/classification ; Giardia/genetics/isolation &amp; purification/classification ; Bacteria/genetics/classification/isolation &amp; purification ; Humans ; Rivers/microbiology/parasitology ; Water Microbiology ; },
abstract = {Urban water bodies serve as critical reservoirs of microbial diversity, with major implications for public health and environmental quality. This study aimed to characterize the microbial diversity of surface waters and wastewater from the Pasto River in the Colombian Andean Highlands, offering insights that may support water quality monitoring efforts. Sampling was conducted at three river sites and one wastewater location. Standard physicochemical and microbiological analyses were performed, including real-time PCR to detect protozoan pathogens Giardia spp. and Cryptosporidium spp. Metagenomic sequencing provided an in-depth taxonomic and functional profile of microbial communities through two complementary approaches: (i) read-based analysis to identify abundant families and species, both pathogenic and beneficial, and (ii) detection of health-related molecular markers, including antimicrobial resistance markers and virulence factors. Physicochemical analyses showed distinct profiles between wastewater and surface water, with wastewater exhibiting elevated levels of suspended solids (113.6 mg/L), biochemical oxygen demand (BOD, 311.2 mg/L), and chemical oxygen demand (COD, 426.7 mg/L). Real-time PCR detected Giardia spp. DNA in 75% (76/102) of the samples and Cryptosporidium spp. DNA in 94% (96/102) of samples. The metagenomic read-based profiling identified Aeromonas media as a prevalent pathogen and Polaromonas naphthalenivorans as a potential biodegradative agent. The metagenomic assembly produced 270 high-quality genomes, revealing 16 bacterial species (e. g., Acinetobacter johnsonii and Megamonas funiformis) that provided insights into fecal contaminants and native aquatic microbes. Functional profiling further revealed a high prevalence of antimicrobial resistance markers, particularly for tetracyclines, aminoglycosides, and macrolides, with the highest abundance found in wastewater samples. Additionally, virulence factors were notably present in Zoogloea ramigera. The findings underscore the value of metagenomic profiling as a comprehensive tool for water quality monitoring, facilitating the detection of pathogens, beneficial species, and molecular markers indicative of potential health risks. This approach supports continuous monitoring efforts, offering actionable data for water management strategies to safeguard public health and maintain ecological integrity.},
}
@article {pmid40020898,
year = {2025},
author = {Chen, F and Chen, J and Chen, Y and He, Y and Li, H and Li, J and Tian, YS},
title = {Mechanistic insight into degradation of dibutyl phthalate by microorganism in sediment-water environment: metabolic pathway, community succession, keystone phylotypes and functional genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125932},
doi = {10.1016/j.envpol.2025.125932},
pmid = {40020898},
issn = {1873-6424},
abstract = {Despite extensive studies on dibutyl phthalate (DBP) degradation in isolated bacterial cultures, the primary degraders, community dynamics, and metabolic pathways involved in its biotransformation within complex sediment microbial communities remain poorly understood. In this study, we aimed to investigate the biotransformation mechanism of DBP by microorganisms in a sediment-water system by employing gas chromatography-mass spectrometry, 16S rRNA gene sequencing, metagenomic analysis, and bacterial isolation techniques. We observed that DBP biotransformation has three distinct phases: lag, degradative, and stationary. During the degradative phase, DBP gets progressively degraded by microorganisms, resulting in a microbial community with reduced stability and ambiguous boundaries. DBP, primarily metabolised by key phylotypes into monobutyl phthalate (MBP), phthalic acid (PA), and protocatechuic acid, subsequently enters the tricarboxylic acid (TCA) cycle. Through metagenomic analysis, ten functional genes from five genera were identified as crucial for DBP metabolism. Firstly, Arthrobacter degrades DBP into MBP and PA using pheA. Subsequently, Acinetobacter, Massilia, and Arthrobacter convert PA into TCA cycle intermediates using phtBAaAbAcAd and pcaCH. Concurrently, Hydrogenophaga and Acidovorax degrade PA to TCA cycle intermediates through pht1234 and ligAB. Genes related to amino acid synthesis, ABC transporters, and two-component regulatory systems also contribute significantly. Thus, the listed key bacteria, along with their diverse functional genes, collectively exhibit a high capacity for DBP degradation. This study provides insights into the bacterial responses to DBP degradation and offers a theoretical basis for the prevention and control of this pollutant.},
}
@article {pmid40020468,
year = {2025},
author = {Huang, Y and Li, XT and Jiang, Z and Liang, ZL and Liu, W and Liu, ZH and Li, LZ and Yang, ZN and Zhang, GQ and Yin, HQ and Liang, JL and Zhou, N and Liu, SJ and Jiang, CY},
title = {Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage.},
journal = {Water research},
volume = {278},
number = {},
pages = {123367},
doi = {10.1016/j.watres.2025.123367},
pmid = {40020468},
issn = {1879-2448},
abstract = {Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.},
}
@article {pmid40020369,
year = {2025},
author = {Tang, Z and Xu, H and Zhu, R and Li, D and Zhao, Z and Xiao, H and Li, H},
title = {Long-term effects of food waste on erosion resistance and production of methane and sulfide in sewer sediments: New insights into extracellular polymeric substances and genetic response mechanisms.},
journal = {Journal of environmental management},
volume = {377},
number = {},
pages = {124700},
doi = {10.1016/j.jenvman.2025.124700},
pmid = {40020369},
issn = {1095-8630},
abstract = {Discharge of food waste (FW) into sewer systems causes environmental issues, such as sewer blockage and odour problems. This study investigated the long-term effects of FW addition on sediment properties, microbial communities, and metabolic pathways using laboratory-scale reactors for 160-day incubation. The addition of 2 g/L FW increased the critical erosion shear stress of sediments by 40.63% and reduced their self-cleaning capacity by 39.46%. This was attributed to the fact that FW discharge increased extracellular polymeric substances (EPS) in sediments by 82.94%, especially aromatic protein with high hydrophobicity and high content of intermolecular hydrogen bonds, which was supported by the increased genes encoding aminoacyl-tRNA biosynthesis. The denser biofilm on the sediment surface hindered oxygen transfer to deeper sediment zones, and lowered oxidation-reduction potential below -400 mV. Microbial and metagenomic analysis revealed an enrichment of methanogenic archaea (e.g., Methanothrix) and sulfate-reducing bacteria (e.g., Desulforhabdus), along with increased genes for dissimilatory sulfate reduction and methanogenesis pathways of acetate and CO2/H2. These microbial and metabolic shifts led to a 95.49% and 34.99% increase methane and sulfide production in the FW-2 group. Overall, the negative effects of FW discharge into sewers emphasizes the need for more rational policies to manage this issue.},
}
@article {pmid40020131,
year = {2025},
author = {Onohuean, H and Nwodo, UU},
title = {Global systematic mapping of Vibrio species pathogenicity: A PRISMA-guided cluster-based analysis.},
journal = {Medicine},
volume = {104},
number = {9},
pages = {e41664},
doi = {10.1097/MD.0000000000041664},
pmid = {40020131},
issn = {1536-5964},
mesh = {*Vibrio/pathogenicity/genetics ; *Virulence Factors/genetics ; Virulence ; Humans ; Cluster Analysis ; Vibrio Infections/microbiology ; },
abstract = {BACKGROUND: A systematic global map on toxigenesis and genomic virulence of Vibrio spp. was analyzed for research progress to identify the emerging research patterns for establishing a database for designing future interventions.<br><br>METHOD: The databases (Web of Science and Scopus) were analyzed with Voxviewer software to map the global scale of Vibrio spp. or virulence toxin/genes publications and standardized using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) strategies.<br><br>RESULTS: The results identified 1162 (Web of Science n&#x2005;=&#x2005;620, Scopus n&#x2005;=&#x2005;542), while 314 studies qualified for inclusion and were significantly analyzed on virulence toxin/genes. By co-citation analysis, 4-thematic clusters were developed from 6420 citations and a total reference of 9062. Cluster #1 (pathogenesis &amp; virulence factors) and cluster #4 (host response factors) generated the utmost publications and citations (n&#x2005;=&#x2005;40, 643) and the least (n&#x2005;=&#x2005;7, 85) interest by the researcher. Whereas 8-thematic clusters were developed by bibliographic coupling technique analysis, cluster#1 and cluster#8 generated the utmost (n&#x2005;=&#x2005;78, 1684) and least (n&#x2005;=&#x2005;7, 81) publications and citations interest by the researcher.<br><br>CONCLUSIONS: Our findings suggest that Vibrio toxigenesis and virulence factors are a complex field requiring an interdisciplinary approach consisting of interconnected perspectives that have important consequences for academics and policymakers.},
}
@article {pmid40020117,
year = {2025},
author = {Zheng, X and Fan, J and Yin, J and Chu, Y},
title = {The role of gut microbiota and plasma metabolites in ulcerative colitis: Insights from Mendelian randomization analysis.},
journal = {Medicine},
volume = {104},
number = {9},
pages = {e41710},
pmid = {40020117},
issn = {1536-5964},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Colitis, Ulcerative/blood/microbiology ; *Genome-Wide Association Study ; },
abstract = {Emerging research suggests that alterations in gut microbiota composition may play a significant role in the pathogenesis of ulcerative colitis (UC). Plasma metabolites, which are influenced by gut microbiota, have also been implicated, but their role in UC remains unclear. This study aims to determine whether specific plasma metabolites mediate the causal relationship between gut microbiota and UC using Mendelian randomization (MR) analysis. This study employed publicly available summary-level data from genome-wide association studies and metagenomic datasets. Gut microbiota data were derived from the FINRISK cohort (5959 participants), plasma metabolite data from the Canadian Longitudinal Study on Aging (8299 individuals), and UC data from multiple consortia (17,030 cases and 883,787 controls). Forward and reverse MR analyses, supplemented by linkage disequilibrium score regression (LDSC), were conducted to assess causal relationships. Mediation effects of plasma metabolites between gut microbiota and UC were analyzed using the product of coefficients method. Various sensitivity analyses, including MR-Egger and MR-PRESSO, were applied to detect pleiotropy and ensure robust results. The study identified 20 bacterial taxa and 93 plasma metabolites linked to UC. Forward MR analysis showed that Clostridium S felsineum increased UC risk via reduced carnitine levels, with a mediation proportion of 39.77%. Eubacterium callanderi was associated with decreased UC risk through the tryptophan to pyruvate ratio (16.02% mediation). Additionally, species CAG-590 sp000431135 increased UC risk through elevated mannitol/sorbitol levels, mediating 28.38% of the effect. Sensitivity analyses confirmed the robustness of these findings, with minimal heterogeneity and pleiotropy detected. This study highlights the significant role of gut microbiota and their associated plasma metabolites in the pathogenesis of UC. Specific microbial species influence UC through metabolites, suggesting potential therapeutic targets. Modulating carnitine, tryptophan metabolism, or sugar alcohols could offer promising avenues for UC management.},
}
@article {pmid40020100,
year = {2025},
author = {Zheng, H and Li, S and Liang, ZY and Feng, RL and Lu, JX and Dong, YJ and Chen, XP},
title = {M1 enrichment facilitates virus detection in patients with allogeneic hematopoietic stemcell transplantation.},
journal = {Medicine},
volume = {104},
number = {9},
pages = {e41683},
doi = {10.1097/MD.0000000000041683},
pmid = {40020100},
issn = {1536-5964},
support = {0104335//National Institute for Communicable Disease Control and Prevention/ ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Real-Time Polymerase Chain Reaction ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing ; Transplantation, Homologous/adverse effects ; Hematologic Neoplasms/therapy/virology ; Viremia/virology/diagnosis ; Virus Diseases/diagnosis/virology ; Viruses/isolation &amp; purification/genetics/classification ; Young Adult ; },
abstract = {Due to the severe consequences of viral infection in allogeneic hematopoietic stem cell transplantation (allo-HSCT) patients, the routine use of polymerase chain reaction (PCR) screening of viruses is common in clinic, while the sensitivities of molecular methods are not always sufficient for blood samples. We aimed to increase the detection efficiency of viremia in allo-HSCT patients with M1 bead enrichment. Blood samples of allo-HSCT patients with fever were collected. Simultaneously with analyses of real-time PCR without enrichment, M1 bead enrichment followed by real-time PCR was applied to detect possible viruses in these samples, and metagenomic next-generation sequencing analyses were also applied in 10 samples negative with real-time PCR without enrichment. Various species of viruses were detected with M1 enrichment method. Significantly, some viruses that had not been found by real-time PCR without M1 enrichment were also detected by those with M1 enrichment and verified by metagenomic next-generation sequencing analyses. Furthermore, blood samples enriched with M1 beads had lower Ct values of real-time PCR assay than those that had not been treated. In conclusion, M1 bead enrichment increased the detection efficiency of most viruses in hematological malignancy patients.},
}
@article {pmid40019273,
year = {2025},
author = {Hackenberger, D and Imtiaz, H and Raphenya, AR and Alcock, BP and Poinar, HN and Wright, GD and McArthur, AG},
title = {CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0187624},
doi = {10.1128/aem.01876-24},
pmid = {40019273},
issn = {1098-5336},
abstract = {Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here, we describe the Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM), a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and tested two separate probe sets: allCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (n = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. clinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.IMPORTANCEAntimicrobial resistance threatens to undermine all modern medicine and is driven by the spread of antimicrobial resistance genes among pathogens, environments, patients, and animals. DNA sequencing of complex samples, such as wastewater, shows considerable promise for tracking these genes and making risk assessments. However, these methods suffer from high costs and low detection limits, plus a requirement for frequent redesign due to the constantly evolving diversity of resistance genes. Building upon our Comprehensive Antibiotic Resistance Database, our research provides software for on-demand renewal, based on the latest knowledge of resistance gene diversity, of our novel bait-capture hybridization platform that simultaneously reduces cost and increases detection levels for DNA sequencing of complex samples. The significance of our research is in the development of new software tools, reagent synthesis protocols, and hybridization enrichment protocols to provide affordable, high-resolution metagenomics DNA sequencing, which we test using environmental and wastewater samples.},
}
@article {pmid40019271,
year = {2025},
author = {Milani, C and Longhi, G and Alessandri, G and Fontana, F and Viglioli, M and Tarracchini, C and Mancabelli, L and Lugli, GA and Petraro, S and Argentini, C and Anzalone, R and Viappiani, A and Carli, E and Vacondio, F and van Sinderen, D and Turroni, F and Mor, M and Ventura, M},
title = {Functional modulation of the human gut microbiome by bacteria vehicled by cheese.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018025},
doi = {10.1128/aem.00180-25},
pmid = {40019271},
issn = {1098-5336},
abstract = {Since cheese is one of the most commonly and globally consumed fermented foods, scientific investigations in recent decades have focused on determining the impact of this dairy product on human health and well-being. However, the modulatory effect exerted by the autochthonous cheese microbial community on the taxonomic composition and associated functional potential of the gut microbiota of human is still far from being fully dissected or understood. Here, through the use of an in vitro human gut-simulating cultivation model in combination with multi-omics approaches, we have shown that minor rather than dominant bacterial players of the cheese microbiota are responsible for gut microbiota modulation of cheese consumers. These include taxa from the genera Enterococcus, Bacillus, Clostridium, and Hafnia. Indeed, they contribute to expand the functional potential of the intestinal microbial ecosystem by introducing genes responsible for the production of metabolites with relevant biological activity, including genes involved in the synthesis of vitamins, short-chain fatty acids, and amino acids. Furthermore, tracing of cheese microbiota-associated bacterial strains in fecal samples from cheese consumers provided evidence of horizontal transmission events, enabling the detection of particular bacterial strains transferred from cheese to humans. Moreover, transcriptomic and metabolomic analyses of a horizontally transmitted (cheese-to-consumer) bacterial strain, i.e., Hafnia paralvei T10, cultivated in a human gut environment-simulating medium, confirmed the concept that cheese-derived bacteria may expand the functional arsenal of the consumer's gut microbiota. This highlights the functional and biologically relevant contributions of food microbes acquired through cheese consumption on the human health.IMPORTANCEDiet is universally recognized as the primary factor influencing and modulating the human intestinal microbiota both taxonomically and functionally. In this context, cheese, being a fermented food with its own microbiota, serves not only as a source of nourishment for humans, but also as a source of nutrients for the consumer's gut microbiota. Additionally, it may act as a vehicle for autochthonous food-associated microorganisms which undergo transfer from cheese to the consumer, potentially influencing host gut health. The current study highlights not only that cheese microbiota-associated bacteria can be traced in the human gut microbiota, but also that they may expand the functional repertoire of the human gut microbiota, with potentially significant implications for human health.},
}
@article {pmid40018976,
year = {2025},
author = {Yu, T and Gao, J and Yuan, J and Yin, Z and Chen, X and Wu, Y and Dai, R and Yan, D and Chen, H and Wu, Y},
title = {Dietary methionine restriction restores wheat gluten-induced celiac-associated small intestine damage in association with affecting butyric acid production by intestinal flora.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo05757k},
pmid = {40018976},
issn = {2042-650X},
abstract = {Methionine restriction has received some attention in recent years as a novel mode of dietary intervention. Our previous study found that methionine restriction could inhibit the celiac toxic effects of wheat gluten in an in vitro model. However, the role of methionine restriction in gluten-induced celiac intestinal damage remains unclear. The aim of this study was to explore whether dietary methionine restriction could suppress the celiac toxic effects of gluten in an in vivo model, thereby mitigating intestine damage. This study systematically investigated the effects of dietary methionine restriction on celiac characteristic indicators such as symptoms, small intestine damage, and intestinal TG2 and IL-15 expression in a gluten-induced C57BL/6 mouse model. The availability of dietary methionine restriction in different ages (adolescent and adult) was also evaluated. Moreover, mouse cecum contents were assayed and co-analyzed for the metagenome of intestinal flora and target short-chain fatty acid metabolomics, with the goal of further exploring and elucidating critical pathways by which dietary methionine restriction plays a role. We discovered that dietary methionine restriction could effectively ameliorate the gluten-induced celiac-associated small intestine damage by modulating intestinal flora to inhibit butyric acid production. Specifically, dietary methionine restriction could inhibit butyric acid production with the help of s_CAG-485 sp002493045 and s_CAG-475 sp910577815, which in turn affected the mitochondrial function within the intestinal epithelial cells to assist in the repair of intestine damage. This study might provide new insights into modulating dietary patterns to mitigate intestinal damage in celiac disease and the production of novel gluten-free products.},
}
@article {pmid40018750,
year = {2025},
author = {Zhu, X and Deng, H and Yu, M and Yang, S and Cao, Q and Zhao, C and Wang, Y and Jiang, J and Zhang, Y},
title = {Middle Ear Cholesteatoma Complicated By Lemierre's Syndrome: A Case Report and Literature Review.},
journal = {Ear, nose, &amp; throat journal},
volume = {},
number = {},
pages = {1455613251323992},
doi = {10.1177/01455613251323992},
pmid = {40018750},
issn = {1942-7522},
abstract = {Septic thrombophlebitis of the internal jugular vein (IJV), known as Lemierre's syndrome, is a rare complication secondary to infections in the head and neck. Cholesteatoma of the middle ear complicated with Lemierre's syndrome is rarely observed in clinical practice. Currently, the treatment controversy centers on whether anticoagulation therapy is necessary for IJV and distant metastatic emboli induced by Lemierre's syndrome. A 46-year-old female patient with middle ear cholesteatoma underwent modified radical mastoidectomy and tympanoplasty surgery and complicated with Lemierre's syndrome, presenting with intermittent high fever, chills, headache, and left lateral neck pain. Computed tomography (CT) revealed thrombosis and internal gas in the left IJV, while blood culture and blood pathogenic microorganism metagenomic detection were negative. We administered sodium ceftriaxone (1 g every 12 hours) for 3 days. According to the secretion culture results showing 90% Actinomyces europaeus and 10% Corynebacterium without mycolic acid, penicillin (2.4 million IU) was added intravenously every 6 hours. The patient's infection worsened on the first day after surgery. We adjusted to upgrade anti-infection vancomycin 1 g every 12 hours, combined with meropenem (1 g every 8 hours) and metronidazole (0.5 g) every 8 hours for 4 weeks, and subcutaneous injection of enoxaparin 0.4 mL every 12 hours for 1 week, then adjusted to rivaroxaban tablets (15 mg bid). Amoxicillin-clavulanate for 2 weeks and rivaroxaban 10 mg were administered orally for 3 months after discharge. A follow-up neck CT scan with intravenous contrast suggested that the gas in the left IJV had disappeared, but the thrombus persisted. During the 3 month follow-up, the patient's vital signs, blood routine, and D-dimer levels were within the normal range. The surgical area healed well, and the patient reported no discomfort. Lemierre's syndrome represents a potentially-fatal complication that results in considerable mortality and must be identified early and aggressively treated.},
}
@article {pmid40018491,
year = {2025},
author = {Shaikh, RG and Dey, A and Singh, VP and Khandagle, A and M, B and Naik, S and Hasan, A},
title = {Understanding the Impact of the Gut Microbiome on Mental Health: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {1},
pages = {e78100},
pmid = {40018491},
issn = {2168-8184},
abstract = {Mental health is a serious issue, with mental health disorders affecting millions of people globally. Gut microbiota has received considerable attention because of its potential role in the pathogenesis of mental health disorders. This systematic review synthesized 15 studies exploring the effects of the gut microbiome on depression, anxiety, schizophrenia, and bipolar disorder, with qualitative and quantitative insights. The studies were conducted in different countries and employed various methods including 16S rRNA sequencing and metagenomic analysis with sample sizes varying from 50 to 600. Some of the key findings were that depression was associated with reduced microbial diversity and high levels of Firmicutes, and anxiety was associated with low levels of short-chain fatty acid (SCFA)-producing bacteria and high levels of Proteobacteria. Schizophrenia was related to endotoxemia and a reduction in the Lactobacillus count whereas bipolar disorder displayed a shift in the Firmicutes/Bacteroidetes ratio. Of interest, probiotics and dietary changes were as effective as drug treatment leading to symptom alleviation in many patients. It was found that depression was linked to less diverse gut bacteria while anxiety was associated with an increase in inflammatory bacteria. People with bipolar disorder were also found to have different gut bacteria patterns. This review also emphasizes the importance of the gut microbiota in the pathophysiology of mental disorders and the promising value of targeting microbiomes in pharmacological treatment approaches.},
}
@article {pmid40018346,
year = {2025},
author = {Sun, C and Zhang, Z},
title = {SARS-CoV-2 detection via metagenomic next-generation sequencing of bronchoalveolar lavage fluid/sputum in lymphoma patients receiving B-cell-depleting therapy: a case report of two cases.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1434340},
pmid = {40018346},
issn = {2296-858X},
abstract = {We describe two cases of coronavirus disease 2019 (COVID-19) infection in patients with lymphoma receiving B-cell-depleting therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF)/sputum showed ongoing viral replication, despite repeated nasopharyngeal swabs being negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. The patients failed to develop seroconversion of IgG antibodies for SARS-CoV-2. However, they showed favorable clinical outcomes after treatment with nirmatrelvir/ritonavir or molnupiravir, despite the antiviral therapies being initiated later in the clinical course. Our case highlights that in immunocompromised hosts, viral clearance of SARS-CoV-2 in lung tissue may lag behind that in the upper respiratory tract. Thus, alternative diagnostic criteria are necessary, and clinical decisions and interventions should be tailored to each individual case.},
}
@article {pmid40018345,
year = {2025},
author = {Fan, Z and Mei, M and Chen, C},
title = {Pyogenic liver abscess and sepsis caused by mixed anaerobic bacteria in an immunocompetent adult: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1486256},
pmid = {40018345},
issn = {2296-858X},
abstract = {BACKGROUND: Anaerobic bacterial communities in the digestive tract play an important role in digestive tract infections and aspiration pneumonia. However, ectopic infections originating from these communities are uncommon.<br><br>CASE REPORT: We present a rare case of a 64-year-old immunocompetent female was admitted with no significant medical history who developed a pyogenic liver abscess and sepsis caused by multiple anaerobic bacteria of digestive tract origin. Metagenomic next-generation sequencing (mNGS) detected four types of anaerobic bacteria in both peripheral blood and abscess puncture fluid. Culture confirmed the presence of three of these microorganisms. Treatment with a combination of meropenem and metronidazole resulted in the patient's subsequent recovery and discharge.<br><br>CONCLUSION: This report highlights the occurrence of ectopic infections caused by multiple anaerobic bacteria leading to pyogenic liver abscess and sepsis, underscoring the importance of considering anaerobic bacteria and conducting rapid comprehensive pathogen detection in clinical practice.},
}
@article {pmid40017465,
year = {2024},
author = {Mishra, AK and Yadav, P and Sharma, S and Maurya, P},
title = {Comparison of microbial diversity and community structure in soils managed with organic and chemical fertilization strategies using amplicon sequencing of 16 s and ITS regions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1444903},
pmid = {40017465},
issn = {1664-302X},
abstract = {Soil microbial species diversity and distribution of microbial communities are vital for soil and crop health, nutrient cycling, availability, and subsequent plant growth. These soil dynamics are highly influenced and altered by various soil management practices, inputs, and agricultural techniques. In the present study, the effects of chemical and organic management practices on soil microbial diversity and community structure were examined and compared using amplicon sequencing of the 16S and ITS regions. Two contrasting soil samples were selected from each crop fields at the International Rice Research Institute-South Asia Regional Centre (IRRI-SARC) in Varanasi: one field followed conventional chemical fertilizer inputs, while the other implemented natural farming practices, including tillage, on-farm crop residue management, and water management. Soil samples from each field were analyzed for bacterial and fungal diversity. Our findings showed that the two differently managed soils exhibited distinct microbial community compositions, with the organically managed soil exhibiting a higher diversity of decomposer bacteria and fungi, showing 40 unique elements in organic soil samples and 19 in chemically managed soil. Natural farming practices also demonstrated a higher relative abundance of bacterial and fungal phyla. Our results emphasize the significance of sustainable soil management techniques, suggesting that organic inputs can increase soil microbial diversity and richness. The functional roles of these microbial communities in soil ecosystems and their potential impact on crop yield and nutrient cycling warrant further study.},
}
@article {pmid40017391,
year = {2025},
author = {Orru', S and Reissinger, A and Filomena, A and Heitmann, A and Funk, MB and Schmidt-Chanasit, J and Kreß, J and Scheiblauer, H and Cadar, D and Fiedler, SA},
title = {Assessment of the effectiveness of West Nile virus screening by analysing suspected positive donations among blood donors, Germany, 2020 to 2023.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {30},
number = {8},
pages = {},
doi = {10.2807/1560-7917.ES.2025.30.8.2400373},
pmid = {40017391},
issn = {1560-7917},
mesh = {Humans ; *Blood Donors ; *West Nile virus/isolation &amp; purification/genetics/immunology ; *West Nile Fever/diagnosis ; Germany ; *Mass Screening/methods ; *Nucleic Acid Amplification Techniques ; Male ; Female ; Middle Aged ; Adult ; High-Throughput Nucleotide Sequencing ; Antibodies, Viral/blood ; Donor Selection/methods ; Viral Load ; RNA, Viral/genetics ; },
abstract = {BackgroundThe first autochthonous human West Nile virus (WNV)-positive cases in Germany were confirmed in 2019. Risk minimisation measures (RMM) were introduced in 2020; no WNV transfusion-transmitted infections have been reported to date.AimTo analyse German suspected WNV-positive blood donations during annual seasons 2020-23 to review donor testing requirements.MethodsWNV look-back procedures were initiated as per German regulations and additional donor data were collected. Blood samples were analysed by metagenomic next-generation sequencing (mNGS), individual donor nucleic acid amplification technique (ID-NAT)-based testing and antibody (Ab) testing.ResultsSeventy-four cases were followed up after WNV-positive donor mini-pool screening. Forty-five (83%) of 54 samples tested with the cobas WNV assay and 14 (29%) of 49 samples tested with the RealStar WNV assay showed a reactive ID-NAT-based result; the viral load ranged between 70,251 IU/mL and values below quantification limits. Fifteen (23%) of 64 samples serologically tested were reactive with at least one of the three Ab tests performed; the previous WNV-negative donation was nearly always documented > 28 days before. Of 73 samples sequenced, mNGS detected WNV in 26 (36%) and other flaviviruses in 14 (19%) cases.ConclusionIn some suspected cases where a WNV infection was not confirmed, mNGS demonstrated a cross-reaction with other flaviviruses. Ab testing could only detect WNV in late stages of infection. A NAT-based WNV donor screening with a detection limit of at least 120 IU/mL seems to be a sufficiently effective RMM at present. However, a continuous re-evaluation of test strategy is always required.},
}
@article {pmid40017220,
year = {2025},
author = {Zheng, JS and Ye, ZL and Liu, LL},
title = {[Observational Study on the Diagnostic Efficacy of Metagenomic Next-Generation Sequencing for Bloodstream Infections Secondary to Hematologic Diseases in Children].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {1},
pages = {280-285},
doi = {10.19746/j.cnki.issn.1009-2137.2025.01.042},
pmid = {40017220},
issn = {1009-2137},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Hematologic Diseases/complications ; Retrospective Studies ; Child ; *Metagenomics/methods ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications ; Anemia, Aplastic/complications ; Leukemia, Myeloid, Acute/complications ; Lymphohistiocytosis, Hemophagocytic/diagnosis ; Male ; },
abstract = {OBJECTIVE: To explore the clinical application value of metagenomic next-generation sequencing (mNGS) in pathogen detection of bloodstream infection secondary to hematologic diseases in children.<br><br>METHODS: 42 children with bloodstream infections secondary to hematologic diseases admitted to the Children's Hematology and Tumor Center of the Affiliated Hospital of Guangdong Medical University from November 2021 to May 2023 were included in the study, and their clinical data, results of peripheral blood mNGS and traditional blood culture, pathogen distribution characteristics, and diagnostic efficacy of mNGS were retrospectively analyzed.<br><br>RESULTS: Among the 42 children included, there were 2 cases (4.8%) of aplastic anemia (AA), 27 cases (64.3%) of acute lymphoblastic leukemia (ALL), 7 cases (16.7%) of acute myeloid leukemia (AML), 1 case (2.4%) of chronic myeloid leukemia (CML), 2 cases (4.8%) of hemophagocytic lymphohistiocytosis (HLH), 2 cases (4.8%) of non-Hodgkin lymphoma (NHL), and 1 case (2.4%) of Wiskott-Aldrich syndrome (WAS). In mNGS testing, pathogens were detected in 31 peripheral blood samples, with a positive rate of 73.8% (31/42), significantly higher than the pathogen positive rate of 16.7% (7/42) detected by traditional blood culture, and the difference was statistically significant (P < 0.05). Among the pathogen-positive cases detected by mNGS, 23 cases (74.2%) were positive for bacteria, 12 cases (38.7%) were positive for viruses, and 9 cases (29.0%) were positive for fungi. 32.2% (10/31) of the pathogen-positive samples detected by mNGS were mixed pathogens, which could not be effectively detected by traditional blood culture.<br><br>CONCLUSION: Peripheral blood mNGS has advantages in the detection of pathogens of bloodstream infection secondary to hematologic diseases, with a higher detection rate of pathogen positivity than traditional blood cultures. It can detect viruses, rare pathogens and mixed pathogens, and has good clinical application value.},
}
@article {pmid40016914,
year = {2025},
author = {Lu, X and Xu, Y and Liu, Y and Li, F and Feng, Q and Gao, C and Liu, D and Zhou, L and Yang, H and Zhang, J and Cui, F and Chen, Q},
title = {Neutrophil Depletion Reduced the Relative Abundance of Unsaturated Long-Chain Fatty Acid Synthesis Microbiota and Intestinal Lipid Absorption.},
journal = {Cell biochemistry and function},
volume = {43},
number = {3},
pages = {e70060},
doi = {10.1002/cbf.70060},
pmid = {40016914},
issn = {1099-0844},
support = {//This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Suzhou Fundamental Research Project (SJC2023001), and Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges. It was funded by the National Natural Science Foundation of China (Grant No. 81773355)./ ; },
mesh = {Animals ; Mice ; *Neutrophils/metabolism ; *Intestinal Absorption ; Male ; Gastrointestinal Microbiome ; Lipid Metabolism ; Mice, Inbred C57BL ; Fatty Acids, Unsaturated/metabolism ; Rats ; },
abstract = {As immune cells, neutrophils serve as the first line of defense against infections; however, the mechanism by which neutrophils regulate lipid metabolism is unknown. The neutrophil depletion group was treated with 100 μg InVivoMAb anti-mouse Ly6G 6 times, whereas the control group mice were intraperitoneally injected with the same quantity of InVivoMAb rat IgG2a. Body fat content, triglycerides (TGs), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) in the jejunum and ileum, as well as 9 long-chain fatty acids (LCFAs) in the intestinal contents were significantly decreased. Furthermore, genes involved in the absorption of lipids in each segment of the intestine also showed decreased expression. Neutrophil-depletion and control models were administered 25 μCi of [3]H-cholesterol by gavage. The distribution of [3]H cholesterol in the intestinal segment, heart, liver, serum, and feces was not altered by anti-Ly6G antibodies. Metagenomics was applied to investigate uncultured microorganisms in the intestinal contents to identify bacteria containing lipid metabolism genes. At the species level, 12 bacteria were involved in unsaturated LCFA synthesis, among which 2 increased and 10 decreased. The overall relative abundance of these bacteria decreased from 3.102% to 0.734%. Many genes involved in lipid metabolism were also reduced as a result, such as fatty acid synthase and peroxisome proliferator-activated receptor γ. In conclusion, neutrophil depletion does not affect intestinal lipid absorption in the diet but leads to a decrease in the overall relative abundance of gut bacteria involved in unsaturated LCFA synthesis. Consequently, intestinal lipid synthesis and absorption are reduced.},
}
@article {pmid40016913,
year = {2025},
author = {Boukhchtaber, DC and von Meijenfeldt, FAB and Sahonero Canavesi, DX and Dorhout, D and Bale, NJ and Hopmans, EC and Villanueva, L},
title = {Discovering Hidden Archaeal and Bacterial Lipid Producers in a Euxinic Marine System.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70054},
doi = {10.1111/1462-2920.70054},
pmid = {40016913},
issn = {1462-2920},
support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; ALWOP.256//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Spinoza prize 2004| NWO/ ; },
mesh = {*Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Seawater/microbiology ; Membrane Lipids/metabolism ; Black Sea ; Metagenome ; Biosynthetic Pathways/genetics ; },
abstract = {Bacterial membrane lipids are typically characterised by fatty acid bilayers linked through ester bonds, whereas those of Archaea are characterised by ether-linked isoprenoids forming bilayers or monolayers of membrane-spanning lipids known as isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs). However, this understanding has been reconsidered with the identification of branched GDGTs (brGDGTs), which are membrane-spanning ether-bound branched alkyl fatty acids of bacterial origin, though their producers are often unidentified. The limited availability of microbial cultures constrains the understanding of the biological sources of these membrane lipids, thus limiting their use as biomarkers. To address this issue, we identified membrane lipids in the Black Sea using high-resolution accurate mass/mass spectrometry and inferred their potential producers by targeting lipid biosynthetic pathways encoded on the metagenome, in metagenome-assembled genomes and unbinned scaffolds. We also identified brGDGTs and highly branched GDGTs in the suboxic and euxinic waters, potentially attributed to Planctomycetota, Cloacimonadota, Desulfobacterota, Chloroflexota, Actinobacteria and Myxococcota-based on their lipid biosynthetic genomic potential. These findings introduce new possibilities for using specific brGDGTs as biomarkers of anoxic conditions in marine environments and highlight the role of these membrane lipids in microbial adaptation.},
}
@article {pmid40016544,
year = {2025},
author = {Zaminhan-Hassemer, M and Zagolin, GB and Aráujo, BC and Perazza, CA and Barbosa, DA and Menegidio, FB and Coutinho, LL and Tizioto, P and Hilsdorf, AWS},
title = {Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia.},
journal = {Veterinary research communications},
volume = {49},
number = {2},
pages = {120},
pmid = {40016544},
issn = {1573-7446},
mesh = {Animals ; *Propolis/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Cichlids/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; Dietary Supplements/analysis ; },
abstract = {The study aimed to investigate the impact of dietary supplementation with green propolis crude extract on juvenile tilapia's growth and intestinal microbiota. The experiment was conducted in raceway tanks with a volume of 19m[3], comprising two treatments with three replicates each. Fish were assigned to either a control diet or a diet supplemented with 0.67% green propolis crude extract. Each experimental unit consisted of 30 fish, initially averaging 22.38 g ± 0.32 in weight, and which were fed ad libitum for 60 days. Results demonstrated that dietary supplementation with green propolis crude extract significantly improved the growth of juvenile tilapia compared to the control group. Firmicutes, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Cyanobacteria were identified as the predominant bacterial phyla in the intestinal microbiota of both groups. The genera Candidatus xiphinematobacter (Verrucomicrobia) and Somerae (Firmicutes) were consistently abundant across treatments, with Somerae and Dispar as the most prevalent species. Significant differences in alpha diversity were observed between treatments at the genus and species levels according to the Chao 1 index. However, no significant differences were detected in Shannon index diversity between the control and green propolis crude extract groups. Beta diversity analysis revealed distinct clustering between treatments. Linear discriminant analysis Effect Size (LEfSe) highlighted significant differences in bacterial abundance between the control and green propolis crude extract groups. In conclusion, dietary supplementation with green propolis crude extract improved growth. It also modulated the intestinal microbiota of juvenile Thai tilapia.},
}
@article {pmid40016305,
year = {2025},
author = {Oba, M and Sakaguchi, S and Teshima, N and Yokota, T and Takemae, H and Tohei, M and Shimokawa, F and Murakami, M and Mizuno, S and Ishida, H and Murakami, H and Takano, T and Mizutani, T and Tsukada, H and Nagai, M},
title = {Metatranscriptomic identification of novel RNA viruses from raccoon dog (Nyctereutes procyonoides) feces in Japan.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7100},
pmid = {40016305},
issn = {2045-2322},
support = {21K05947//JSPS KAKENHI/ ; },
mesh = {Animals ; *Raccoon Dogs/virology ; *Feces/virology ; Japan ; *RNA Viruses/genetics/isolation &amp; purification/classification ; *Phylogeny ; *Genome, Viral ; Transcriptome ; Metagenomics/methods ; },
abstract = {The raccoon dog (Nyctereutes procyonoides), classified in the order Carnivora within the family Canidae, is native to East Asia and widely distributed throughout Japan due to its adaptability to various environments. Despite the close relationship between raccoon dogs and other animals, viruses infecting raccoon dogs have not been thoroughly investigated in Japan. In this study, we performed metatranscriptomic analyses using fecal samples collected from latrines of wild raccoon dogs in two locations on mainland Japan. Nearly complete viral genomes were identified, including viruses belonging to the genus Kobuvirus (CaKoV), an unclassified canine sapelovirus within the subfamily Ensavirinae (CaSaV), the Genius Mamastrovirus (CaAstV), unclassified hepe-astro-like virus (bastrovirus-like) (Bast-like V), and an unclassified dicistrovirus (DiciV) within the family Dicistroviridae. Phylogenetic analyses revealed that raccoon dog CaKoV, CaSaV, and CaAstV are related to canine strains but form independent clusters specific to raccoon dogs, suggesting they have evolved within this host population. Bast-like V, detected for the first time in raccoon dogs, showed high sequence identity with viruses previously identified in Chinese shrews. The shared insectivorous nature of these hosts and in silico host range predictions suggest that Bast-like Vs may originate from arthropod viruses. Although DiciV is likely of dietary origin due to its arthropod hosts, the large number of sequence reads detected and the phylogenetic clustering of raccoon dog DiciVs with mammalian DiciVs indicate the need to assess their potential infectivity in mammals and the risk of spillover. These findings suggest that raccoon dogs harbor endemic viruses within the canine population and may act as potential vectors for viruses with unknown infectivity in mammals but with spillover risk.},
}
@article {pmid40016229,
year = {2025},
author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE},
title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2038},
pmid = {40016229},
issn = {2041-1723},
mesh = {*Oryza/microbiology/metabolism ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Agriculture/methods ; },
abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.},
}
@article {pmid40015949,
year = {2025},
author = {Hu, M and Xu, Y and Wang, Y and Huang, Z and Wang, L and Zeng, F and Qiu, B and Liu, Z and Yuan, P and Wan, Y and Ge, S and Zhong, D and Xiao, S and Luo, R and He, J and Sun, M and Zhuang, X and Guo, N and Cui, C and Gao, J and Zhou, H and He, X},
title = {Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-332891},
pmid = {40015949},
issn = {1468-3288},
abstract = {BACKGROUND: Gut microbial metabolites are recognised as critical effector molecules that influence the development of colorectal cancer (CRC). Peptidoglycan fragments (PGFs) produced by microbiota play a crucial role in maintaining intestinal homeostasis, but their role in CRC remains unclear.<br><br>OBJECTIVE: Here, we aimed to explore the potential contribution of PGFs in intestinal tumourigenesis.<br><br>DESIGN: The relative abundance of peptidoglycan synthase and hydrolase genes was assessed by metagenomic analysis. Specific PGFs in the faeces and serum of CRC patients were quantified using targeted mass spectrometry. The effects of PGF on intestinal tumourigenesis were systematically evaluated using various murine models of CRC and organoids derived from CRC patients. Downstream molecular targets were screened and evaluated using proteome microarray, transcriptome sequencing and rescue assays.<br><br>RESULTS: Metagenomic analysis across seven independent cohorts (n=1121) revealed a comprehensive reduction in peptidoglycan synthase gene relative abundance in CRC patients. Targeted mass spectrometry identified significant depletion of a specific PGF, N-acetylmuramic acid (NAM) in CRC patients, which decreased as tumours progressed (p<0.001). NAM significantly inhibits intestinal tumourigenesis in various models, including Apc [Min/+], AOM/DSS-treated and MC38 tumour-bearing mice. Additionally, NAM inhibits the growth of patient-derived CRC organoids in a concentration-dependent manner. Mechanistically, NAM inhibits the activation of AKT1 by directly binding to it and blocking its phosphorylation, which is a partial mediator of NAM's anticancer effects.<br><br>CONCLUSION: The PGF NAM protects against intestinal tumourigenesis by targeting the AKT1 signalling pathway. NAM may serve as a novel potential preventive and therapeutic biomarker against CRC.},
}
@article {pmid40015896,
year = {2025},
author = {Zheng, R and Peng, J and Li, Q and Liu, Y and Huang, D and Sheng, Y and Liu, C and Qi, L and Keyhani, NO and Tang, Q},
title = {Alterations in microbial community structures and metabolic function in soil treated with biological and chemical insecticides.},
journal = {Pesticide biochemistry and physiology},
volume = {208},
number = {},
pages = {106304},
doi = {10.1016/j.pestbp.2025.106304},
pmid = {40015896},
issn = {1095-9939},
mesh = {*Insecticides/pharmacology ; *Soil Microbiology ; *Metarhizium/genetics ; *Ivermectin/analogs &amp; derivatives/pharmacology ; *Neonicotinoids/pharmacology ; Nitro Compounds/pharmacology ; Soil/chemistry ; Microbiota/drug effects ; },
abstract = {Entomopathogenic fungi show significant promise as effective and ecological friendly alternatives to chemical insecticides for insect pest control. However, little is known concerning their effects on soil ecosystems, especially in comparison to application of chemical insecticides. Here, we examined the effects of one biological and two chemical insecticides, Metarhizium anisopliae, imidacloprid (IMI) and emamectin benzoate (EMB) on microbial community structure, metabolic functioning, and soil biochemistry. Treatment with EMB and IMI, reduced Actinobacteriota populations, while increasing that of Acidobacteriota. However, these populations were not significantly altered under M. anisopliae treatment. Chemical pesticides also altered fungal communities including potential pathogens. Activities of soil beneficial nitrogen-cycling-related enzymes were reduced after application of IMI and EMB, but were increased after treatment with M. anisopliae. Metagenomics analysis showed that IMI treatment reduced levels of carbon and nitrogen-related metabolic pathways. However, M. anisopliae treatment increased representation of key enzymes involved in the carbon, nitrogen, and sulfur cycling important for maintenance of soil fertility. Insecticides treatments altered the abundance of a number antibiotic resistance genes (ARGs) but not virulence factors (VFs), whereas application of M. anisopliae resulted had only minimal effects. These findings highlight the consequences of use of biological vs. chemical pesticides on soil microbiology can affect plant and ecosystem health indicating that the fungal biological control agent, M. anisopliae likely has far less detrimental and potentially beneficial effects on soil ecology as compared to chemical pesticides.},
}
@article {pmid40015523,
year = {2025},
author = {Ma, WJ and Zhang, HM},
title = {Metagenomics deciphers the function of biochar in alleviating zinc ion stress during sulfur autotrophic denitrification process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132303},
doi = {10.1016/j.biortech.2025.132303},
pmid = {40015523},
issn = {1873-2976},
abstract = {Sulfur autotrophic denitrification (SAD) process has significant potential in treating low carbon/nitrogen ratio wastewater. However, the presence of zinc ions (Zn[2+]) adversely affects the denitrification performance. This study investigated the effect of biochar prepared at 300 °C (BC300) and 600 °C (BC600), as well as dosing strategy, on denitrification performance in the SAD process under Zn[2+] inhibition. Firstly, BC600 had a higher maximum adsorption capacity for Zn[2+] than BC300 in nitrogen-containing wastewater. Surface complexation was mainly adsorption mechanism. BC300 exhibited a greater ability in enhancing denitrification ability than BC600. The strategy of synchronous addition is more effective than pre-adsorption. Firstly, BC300 enhancing humic-like component secretion. BC300 enriched higher abundance of sulfur-oxidizing bacteria. More importantly, BC300 counteracted the negative effect of Zn[2+] by enhancing glycan biosynthesis and metabolism, enriching functional genes, and increased the level of quorum sensing. The study presents a sustainable approach for maintaining denitrification performance under environmental stress.},
}
@article {pmid40015429,
year = {2025},
author = {Wani, SM and Chesti, A and Rehman, S and Chandra Nautiyal, V and Bhat, IA and Ahmad, I},
title = {Repurposing and reusing aquaculture wastes through a biosecure microfloc technology.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121214},
doi = {10.1016/j.envres.2025.121214},
pmid = {40015429},
issn = {1096-0953},
abstract = {Intensive aquaculture waste management is a significant challenge in the aquaculture industry, often contributing to environmental issues. Intensive aquacultural techniques demand new strategies and alternatives aimed to achieving sustainability. Repurposing and reusing wastes through innovative technologies can mitigate their negative impact. Biofloc technology (BFT) or bio-colloidal technology is based on the concept of aquaculture waste utilization by heterotrophic microbial biomass and presents a biosecure and sustainable solution. The dynamics of BFT are shaped by ecological interactions like commensalism, competition, and predation, forming a trophic micro-network consisting of rotifers, ciliates, heterotrophic bacteria, and microalgae. Metagenomic studies showed dominance of microbial communities within the biofloc, such as Cyanobacteria, Nitrosomonas, Proteobacteria, Bacteroidetes, Pseudomonadota, Rhodobacteraceae and Bacillus species that play a crucial role in the mineralization and bioremediation of waste. These microbes also help to break down hazardous toxic compounds into non-toxic, beneficial nutrients, which are subsequently utilized as food by fish and shellfish. Also by recycling waste reduces pollution, improves water quality, and enhances the efficiency of aquaculture system. With increasing incidences of microbial diseases and growing expenses for energy, biosecurity with BFT seems, by all means a sustainable production method for aquaculture. The incorporation of biosecure biofloc technology into aquaculture practices enhances environmental sustainability while optimizing resource use, creating more eco-friendly and cost-effective systems. This review highlights key aspects such as the microbial dynamics, role of metagenomics in identifying the bacterial communities, bioremediation of aquaculture waste, biosecurity concerns, and the biocontrol of pathogenic microbes across various biofloc systems.},
}
@article {pmid40015361,
year = {2025},
author = {Liu, W and Geng, Y and Wang, Y and Zhao, J and Fan, Y and Zhang, X and Xie, W and Zhang, L and Zhang, Z},
title = {Evolution of gut microbiota in psoriatic arthritis treated with IL-17 inhibitor revealed by metagenomics.},
journal = {Joint bone spine},
volume = {},
number = {},
pages = {105868},
doi = {10.1016/j.jbspin.2025.105868},
pmid = {40015361},
issn = {1778-7254},
abstract = {OBJECTIVES: To explore the evolution of gut microbiota in taxonomy and function in PsA patients during IL-17i treatment.<br><br>METHODS: Twenty PsA patients treated with secukizumab were included. Fecal samples were collected before treatment (0 mo.), first month (1 mo.) and third month (3mo.) after treatment, and a total of 60 samples were collected. Shotgun metagenomic sequencing was used to detect all fecal samples.<br><br>RESULTS: In the 1 mo. and 3 mo. after IL-17i treatment, the disease activity in PsA patients decreased significantly. Compared with 0 mo., &#x3b1;-diversity calculated by Shannon index and Pielou index increased significantly at 1 mo. and 3 mo. after treatment. Microbial genes encoding Carbohydrate Active enZymes (CAZy) tended to be upregulated after treatment. After treatment, Bacteroidota phylum expanded, especially the abundance of Phocaeicola genus increased gradually with the treatment time (P<0.05). The abundance of Phocaeicola genus was positively correlated with the &#x3b1;-diversity. The Polysaccharide Lyases and Carbohydrate Esterases in CAZy were significantly positively correlated with most of species in Phocaeicola genus.<br><br>CONCLUSIONS: Treatment with IL-17i induces gut microbiota evolution in PsA patients. The key features of this evolution include increased &#x3b1;-diversity, expansion of the Phocaeicola genus, and upregulation of CAZy. Species within the Phocaeicola genus may be the critical bacteria driving this evolution.},
}
@article {pmid40015321,
year = {2025},
author = {Valadez-Cano, C and Tromas, N and Reyes-Prieto, A and Johnston, L and Huang, Y and Morris, H and Zamlynny, L and Beach, DG and Jamieson, RC and Lawrence, J},
title = {Genetic Diversity and Anatoxin Profiles of Freshwater Benthic Cyanobacteria From Nova Scotia (Canada).},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70067},
doi = {10.1111/1462-2920.70067},
pmid = {40015321},
issn = {1462-2920},
support = {ALLRP 576532-22//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Nova Scotia ; *Cyanobacteria/genetics/metabolism/classification ; *Fresh Water/microbiology ; *Genetic Variation ; *Cyanobacteria Toxins ; *Tropanes/metabolism ; Phylogeny ; Multigene Family ; Bacterial Toxins/genetics/metabolism ; },
abstract = {Some mat-forming cyanobacteria produce harmful cyanotoxins, yet benthic species remain understudied compared to planktonic counterparts. This study assesses the diversity, distribution and toxin production of mat-forming cyanobacteria across lentic and lotic systems in Nova Scotia, Canada. We documented greater cyanobacterial species richness in lentic environments, with six dominant species distributed into two major Microcoleus clades, five of which represent putative novel taxa. Two Microcoleus species with the genetic repertoire to produce anatoxins were prevalent. One has been previously reported in Canada, while the second represents a novel species found exclusively in an environment impacted by discharge from a water treatment plant. We observed variability in the gene clusters responsible for the biosynthesis of anatoxin-a and associated analogues (ATXs), including the discovery of a novel anaG variant with a ~ 1.7 kb insertion in a Microcoleus strain dominating homoanatoxin-producing mats. This extended anaG, encoding a polyketide synthase with an additional methyltransferase domain, coexists with shorter variants, leading to the production of a mixture of ATXs. These findings highlight the genetic diversity of benthic cyanobacteria in freshwater environments, with Microcoleus as the primary contributor to the production of ATXs in both lentic and lotic systems, underscoring their potential to produce harmful toxins.},
}
@article {pmid40015021,
year = {2025},
author = {Velásquez-Reyes, D and García-Alamilla, P and Kirchmayr, MR and Lugo-Cervantes, E and Gschaedler, A},
title = {Contribution of post-harvest processing in cocoa bean: Chemometric and metagenomic analysis in fermentation step.},
journal = {Food chemistry},
volume = {477},
number = {},
pages = {143458},
doi = {10.1016/j.foodchem.2025.143458},
pmid = {40015021},
issn = {1873-7072},
abstract = {Cocoa fermentation is a heterogeneous process, exhibiting a high degree of diversity of flavor, aroma, and microbial communities. A study was conducted to examine cocoa fermentations in five municipalities of a region in Mexico, with the objective of associating post-harvest practices, geographic area, and chemical and microbiological profiles. Through the application of high-performance DNA sequencing, the microbial diversity was identified, and the non-volatile and volatile compounds were identified and quantified by UHPLC-RID/PDA and HS-SPME/GC-MS, respectively. Using PCA, PLS regression and Pearson correlation, post-harvest practices, geographical factors, microbial communities, and volatile and non-volatile compounds were made. The absence of control in cocoa fermentation was associated to Aspergillus, Escherichia, and Bacillus, and reduced the production of essential acids for aroma. This study provides data on the diversity of post-harvest practices and their impact on cocoa quality.},
}
@article {pmid40014853,
year = {2025},
author = {Lee, C and Zaheer, R and Thomas, K and Poulin-Laprade, D and Talbot, G and Diarra, M and Van Domselaar, G and Zovoilis, A and McAllister, TA},
title = {Comparative Metagenomics Reveals Limited Differences in Antimicrobial Resistance Gene Abundance Across Conventional and Natural Livestock Production Systems.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0191},
pmid = {40014853},
issn = {1480-3275},
abstract = {The livestock industry has been a source of concern in terms of antimicrobial resistance (AMR) development and spread, especially from a One Health perspective. Raising livestock without antimicrobials, so called natural (NAT) production is an increasingly popular practice. This study used metagenomics to compare this practice to conventional (CONV) antimicrobial use (AMU) on the microbiome and resistome in the feces of beef cattle and swine and the cecal contents of broiler chickens. In cattle, Bacteroidetes, Euryarchaeota, and Spirochaetes were more abundant (q < 0.01) in CONV than NAT systems, with no differences (q > 0.05) in bacterial profiles in either swine or chickens. Classes of antimicrobial resistant genes (ARG) were not impacted regardless of AMU in any of the livestock species. However, many tetracycline resistance genes were more abundant in CONV as compared to NAT swine (q < 0.05), but this difference was not observed in cattle or chickens. This study confirmed that elimination of AMU does not necessarily result in an immediate decline in the abundance or diversity of ARGs within a single livestock production cycle.},
}
@article {pmid40014144,
year = {2025},
author = {Bhure, M and Savaliya, K and Patil, S and Nehra, C and Pandit, R and Shah, T and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG},
title = {Bioprospecting of 101 facultative rumen bacterial isolates through comprehensive genome analysis.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {265},
pmid = {40014144},
issn = {1573-4978},
support = {BT/AQ/1/SP41105/2020//Department of Biotechnology (DBT), Government of India/ ; },
mesh = {*Rumen/microbiology ; Animals ; *Genome, Bacterial/genetics ; Phylogeny ; Bioprospecting/methods ; Bacteria, Anaerobic/genetics/metabolism/isolation &amp; purification ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; },
abstract = {BACKGROUND: Microbes within the rumen play a pivotal role in the digestion of feed ingested by the ruminants. Researchers have been investigating microbes within rumen to assess its genetic capabilities, which hold immense potential across various fields including agro-industrial advantages. Since rumen is preliminary an anaerobic sac, numerous anaerobic bacteria and fungi have been isolated and characterized, however facultative anaerobic bacteria yet not fully investigated.<br><br>METHODS AND RESULTS: In present study, we isolated, characterized and performed whole genome analysis of 101 facultative anaerobic bacteria from rumen, offering a unique perspective compared to metagenomic approaches. All assembled genomes were of high quality, i.e. completeness 100% (only seven were between 92 and 99.5%) and only two had contamination&#x2009;>&#x2009;5%. We identified 9,542 sequences of Carbohydrate-Active Enzymes (CAZymes). Over 8,136 of these CAZymes were full-length sequences, with 2,048 harbouring signal peptides also. Xylan (n&#x2009;=&#x2009;634), pectin (n&#x2009;=&#x2009;604), and starch (n&#x2009;=&#x2009;312) degrading enzyme sequences were dominant. Several isolates also harbour secondary metabolite biosynthesis gene clusters for various metabolites, including fengycin, lichenysin, bacillibactins, bacilysin etc. All the isolates have metabolic versatility, encompassing pathways such as carbohydrate, amino acid, lipid, and vitamin and cofactor metabolism. Intriguingly, lipoic acid metabolism was absent in most of these facultative bacterial isolates.<br><br>CONCLUSION: This comprehensive study sheds light on the genetic potential of culturable facultative rumen bacteria, emphasizing their pivotal roles in carbohydrate degradation, secondary metabolite production, and metabolic diversity. These findings hold promise for enhancing ruminant nutrition, advancing eco-friendly biomass conversion, and bolstering bioprospecting of industrially important biocules and enzymes biofuel production.},
}
@article {pmid40013924,
year = {2025},
author = {Johnson, T and Jamrozik, E and Ramachandran, P and Johnson, S},
title = {Clinical metagenomics: ethical issues.},
journal = {Journal of medical microbiology},
volume = {74},
number = {2},
pages = {},
doi = {10.1099/jmm.0.001967},
pmid = {40013924},
issn = {1473-5644},
mesh = {Humans ; *Metagenomics/ethics ; Male ; Klebsiella pneumoniae/genetics/isolation &amp; purification ; Klebsiella Infections/diagnosis/microbiology ; Encephalitis/diagnosis/microbiology ; Female ; Hepatitis/microbiology/diagnosis ; Child ; Coinfection/diagnosis/microbiology ; },
abstract = {Metagenomics is increasingly used for diagnosis in hospital settings. It is useful particularly in cases of unknown aetiology, where novel or difficult-to-diagnose pathogens are suspected, and/or following unexplained disease outbreaks. In this paper, we present three use cases that draw on existing reports: one involving a patient in intensive care with encephalitis of unknown aetiology; a second case with likely infection with drug-resistant Klebsiella pneumoniae and an incidental finding of unknown relevance; and a third case situated in an unexplained outbreak of acute hepatitis in children, with severe outcomes due to co-infection. We examine each case in turn, highlighting ethical questions arising in relation to clinical issues including: disclosure to patients of untreatable disease, cost-effectiveness, the value of resistance testing, sensitivity and specificity, uncertain or unexpected findings, patient consent and data sharing. We conclude by proposing recommendations for further research and developing particular pieces of guidance to improve clinical uses of metagenomics for diagnosis.},
}
@article {pmid40013797,
year = {2025},
author = {Bai, Y and Hu, Y and Chen, X and Hu, L and Wu, K and Liang, S and Zheng, J and Gänzle, MG and Chen, C},
title = {Comparative metagenome-associated analysis of gut microbiota and antibiotic resistance genes in acute gastrointestinal injury patients with the risk of in-hospital mortality.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144424},
doi = {10.1128/msystems.01444-24},
pmid = {40013797},
issn = {2379-5077},
abstract = {UNLABELLED: Acute gastrointestinal injury (AGI) is known for its poor long-term prognosis and the associated increase in mortality among intensive care unit (ICU) patients. As the role of the gut microbiome and resistome in AGI remains unclear, the present study aimed to explore the possible associations between dysbacteriosis and in-hospital mortality in ICU patients with gastrointestinal dysfunction. Fecal samples were collected from a prospective cohort of 210 ICU patients with AGI, and shotgun metagenomic sequencing was used to determine the taxonomic composition of gut microbiota and the differences of antibiotic resistance genes (ARGs) between the Death and Survival groups. Compared to the Survival group, patients in the Death group shifted from strict anaerobes to facultative anaerobes in the fecal microbial community, with more Klebsiella but less Prevotella. The co-occurrence patterns revealed that more ARG subtypes were enriched in microbial taxa in the Death group, especially for Clostridium and Methanobrevibacter. Furthermore, the ARG type had large area under the curve (AUCs) in receiver operating characteristic for predicting the disease severity, and a combined gut microbiota-ARG subtype classifiers showed better performance than either of them. Thus, comparative metagenome-associated analysis can help to obtain valuable information about gut microbiota and gene coding for antibiotic resistance in AGI patients.<br><br>IMPORTANCE: A metagenomic-related strategy was conducted to obtain a highly valuable resource to improve understanding of intestinal microbiota dysbiosis and antibiotic resistance genes (ARGs) profiles. The results indicate that intestinal microbiota, including Klebsiella and Prevotella, changed dramatically in intensive care unit (ICU) patients with acute gastrointestinal injury (AGI). Due to longer ICU stays and receiving more antibiotic treatment, the types and correlations of ARGs in the Death group were significantly higher than those in the Survival group. The findings of this study are expected to expand our knowledge of gut microbiota and resistome profiles reflecting gastrointestinal status, accelerate the identification of disease biomarkers, and provide new insights into the prevention and treatment of AGI-related diseases.},
}
@article {pmid40013792,
year = {2025},
author = {Qin, Y and Wang, Q and Lin, Q and Liu, F and Pan, X and Wei, C and Chen, J and Huang, T and Fang, M and Yang, W and Pan, L},
title = {Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0080524},
doi = {10.1128/msystems.00805-24},
pmid = {40013792},
issn = {2379-5077},
abstract = {UNLABELLED: Colon cancer (CC) is one of the most common cancers globally, which is associated with the gut microbiota intimately. In current research, exploring the complex interaction between microbiomes and CC is a hotspot. However, the information on microbiomes in most previous studies is based on fecal, which does not fully display the microbial environment of CC. Herein, we collected mucosal and tissue samples from both the tumor and normal regions of 19 CC patients and clarified the composition of mucosal microbiota by 16S rRNA and metagenomic sequencing. Additionally, RNA-Seq was also conducted to identify the different expression genes between tumor and normal tissue samples. We revealed significantly different microbial community structures and expression profiles to CC. Depending on correlation analysis, we demonstrated that 1,472 genes were significantly correlated with CC tumor microbiota. Our study reveals a significant enrichment of Campylobacter jejuni in the mucosa of CC, which correlates with bile secretion. Additionally, we observe a negative correlation between C. jejuni and immune cells CD4+ Tem and mast cells. Finally, we discovered that metabolic bacterial endosymbiont of Bathymodiolus sp., Bacillus wiedmannii, and Mycobacterium tuberculosis had a significant survival value for CC, which was ignored by previous research. Overall, our study expands the understanding of the complex interplay between microbiota and CC and provides new targets for the treatment of CC.<br><br>IMPORTANCE: This study contributes to our understanding of the interaction between microbiota and colon cancer (CC). By examining mucosal and tissue samples rather than solely relying on fecal samples, we have uncovered previously unknown aspects of CC-associated microbiota. Our findings reveal distinct microbial community structures and gene expression profiles correlated with CC progression. Notably, the enrichment of Campylobacter jejuni in CC mucosa, linked to bile secretion, underscores potential mechanisms in CC pathogenesis. Additionally, observed correlations between microbial taxa and immune cell populations offer new avenues for immunotherapy research in CC. Importantly, this study introduces CC-associated microbiota with survival implications for CC, expanding therapeutic targets beyond conventional strategies. By elucidating these correlations, our study not only contributes to uncovering the potential role of gut microbiota in colon cancer but also establishes a foundation for mechanistic studies of gut microbiota in colon cancer, emphasizing the broader impact of microbiota research on cancer biology.},
}
@article {pmid40013791,
year = {2025},
author = {Walter, JM and Greses, S and Hagen, LH and Schiml, VC and Pope, PB and González-Fernández, C and Arntzen, M},
title = {Anaerobic digestion of microalgae: microbial response and recovery after organic loading disturbances.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0167424},
doi = {10.1128/msystems.01674-24},
pmid = {40013791},
issn = {2379-5077},
abstract = {UNLABELLED: Industrial anaerobic digestion (AD) represents a relevant energy source beyond today's fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, which is frequently caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure. Here, we investigate the effect of the microalgal organic loading rate (OLR) on the fermentation product profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics, and metagenome-centric metaproteomics. Both low- and high-ORL fed systems encountered a sudden decline in methane production during OLR disturbances, followed by a recovery of the methanogenic activity within the microbiome. In the high-OLR disturbances, system failure triggered an upregulation of hydrolytic enzymes, an accumulation of fermentation products, and a shift in the methanogenic population from hydrogenotrophic to acetoclastic methanogens, with the latter being essential for recovery of the system after collapse.<br><br>IMPORTANCE: Anaerobic digestion (AD) with microalgae holds great potential for sustainable energy production, but process instability caused by substrate disturbances remains a significant barrier. This study highlights the importance of understanding the microbial dynamics and system responses during organic loading rate perturbations. By identifying key shifts in microbial populations and enzyme activity, particularly the transition from hydrogenotrophic to acetoclastic methanogens during recovery, this research provides critical insights for improving AD system stability and can contribute to optimizing microalgae-based AD processes for more reliable and efficient methane production.},
}
@article {pmid40013784,
year = {2025},
author = {Midani, FS and Danhof, HA and Mathew, N and Ardis, CK and Garey, KW and Spinler, JK and Britton, RA},
title = {Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107524},
doi = {10.1128/msystems.01075-24},
pmid = {40013784},
issn = {2379-5077},
abstract = {Clostridioides difficile is a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. Although C. difficile is a genetically diverse species, certain ribotypes are overrepresented in human infections, and it is unclear if metabolic adaptations are essential for the emergence of these epidemic ribotypes. To identify ribotype-specific metabolic differences, we therefore tested carbon substrate utilization by 88 C. difficile isolates and looked for differences in growth between 22 ribotypes. As expected, C. difficile was capable of growing on a variety of carbon substrates. Further, C. difficile strains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, although C. difficile Clade 5 is the most evolutionary distant clade and often detected in animals, it displayed robust growth on simple sugars similar to Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy of C. difficile but also demonstrate lineage-specific metabolic capabilities.IMPORTANCEThe gut pathogen Clostridioides difficile utilizes a wide range of carbon sources. Microbial communities can be rationally designed to combat C. difficile by depleting its preferred nutrients in the gut. However, C. difficile is genetically diverse with hundreds of identified ribotypes, and most of its metabolic studies were performed with lab-adapted strains. To identify ribotype-specific metabolic differences, we profiled carbon metabolism by a myriad of C. difficile clinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that genetically newer and older clades grew to a similar level on simple sugars, which contrasts with recent findings that newer clades experienced positive selection on genes involved in simple sugar metabolism. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.},
}
@article {pmid40013331,
year = {2025},
author = {Standley, JM and Marcelino, J and Yu, F and Ellis, JD},
title = {A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14090},
doi = {10.1111/1755-0998.14090},
pmid = {40013331},
issn = {1755-0998},
support = {//University of Florida Entomology and Nematology Gahan Endowment/ ; //Clay County Beekeepers Association/ ; 1019945//USDA/NIFA Multi-State Project/ ; AP22PPQS&amp;T00C189//USDA/APHIS Cooperative Agreement/ ; },
abstract = {Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.},
}
@article {pmid40012972,
year = {2025},
author = {Hu, M and Qiao, X and Zhang, J and Qin, D and Guo, S and Zhao, W and Wang, C},
title = {Case report: Clinical characteristics of anthrax meningoencephalitis: two cases diagnosed using metagenomic next-generation sequencing and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1539314},
pmid = {40012972},
issn = {2296-858X},
abstract = {PURPOSE: To explore the clinical features, diagnosis, treatment, and prognosis of anthrax meningoencephalitis.<br><br>METHODS: The clinical data of two cases of anthrax meningoencephalitis were summarized and the relevant literature was reviewed.<br><br>RESULTS: Both patients, who were farmers, had cutaneous lesions prior to the onset of meningoencephalitis. The clinical manifestations included fever (2/2), headache (2/2), stupor (2/2), meningeal signs (2/2), and lymph node enlargement (2/2). The CSF analysis showed erythrocytes, increased neutrophils, low glucose levels and high protein levels. CSF cytology revealed rod-shaped bacilli. Metagenomic next-generation sequencing of the CSF from both patients detected Bacillus anthracis. Additionally, cultures confirmed the presence of endogenous spores of macrobacteria. Brain imaging revealed subarachnoid hemorrhages and minimal cerebral edema. Despite aggressive antibiotic treatment, both patients died. Fifty-seven articles of the past 70&#x202f;years were reviewed. There were 59 patients of anthrax meningoencephalitis in total, including 46 patients died. Stupor (42/46, 91.3% vs. 3/13, 46.2%, p&#x202f;=&#x202f;0.001), agitation (15/46, 32.6% vs. 0/13, 0.0%, p&#x202f;=&#x202f;0.043) and intracranial hemorrhage (37/46, 80.4% vs. 4/13, 30.8%, p&#x202f;=&#x202f;0.002) were more common in the deceased group. Two types of bactericidal drugs or intrathecal injection drugs presented more often in the surviving group (10/13, 76.9% vs. 13/46, 28.3%, p&#x202f;=&#x202f;0.001), whereas penicillin monotherapy presented more often in the deceased group (23/46, 50.0% vs. 2/13, 15.4%, p&#x202f;=&#x202f;0.026).<br><br>CONCLUSION: Anthrax meningoencephalitis typically presents as a rapidly progressive bacterial meningoencephalitis. The occurrence of stupor, agitation and intracranial hemorrhage is possibly correlated with poor outcome. Two types of bactericidal drugs or intrathecal injection drugs are associated with better prognosis. Metagenomic next-generation sequencing can quickly and accurately detect B. anthracis in CSF.},
}
@article {pmid40012786,
year = {2025},
author = {Stein, M and Brinks, E and Habermann, D and Cho, GS and Franz, CMAP},
title = {Exogenous plasmid capture to characterize tetracycline-resistance plasmids in sprouts obtained from retail in Germany.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538973},
pmid = {40012786},
issn = {1664-302X},
abstract = {This study aimed to characterize antibiotic-resistance plasmids present in microorganisms from sprout samples using exogenous plasmid capture. Fresh mung bean sprouts were predominantly colonized by bacteria from the phyla Proteobacteria and Bacteroidetes. To capture plasmids, a plasmid-free Escherichia (E.) coli CV601 strain, containing a green fluorescent protein gene for selection, was used as the recipient strain in exogenous plasmid capture experiments. Transconjugants were selected on media containing cefotaxime or tetracycline antibiotics. While no cefotaxime-resistant transconjugants were obtained, 40 tetracycline-resistant isolates were obtained and sequenced by Illumina NextSeq short read and Nanopore MinION long read sequencing. Sequences were assembled using Unicycler hybrid assembly. Most of the captured long plasmids carried either the tet(A) or tet(D) resistance gene, belonged to the IncFI or IncFII replicon types, and were predicted as conjugative. While the smaller plasmids contained the tet(A) tetracycline resistance gene as well as additional quinolone (qnrS1), sulfonamide (sul1) and trimethoprim (dfrA1) resistance genes, the larger plasmids only contained the tet(D) resistance gene. An exception was the largest 192 kbp plasmid isolated, which contained the tet(D), as well as sulfonamide (sul1) and streptomycin (aadA1) resistance genes. The smaller plasmid was isolated from different sprout samples more often and showed a 100% identity in size (71,155 bp), while the 180 kbp plasmids showed some smaller or larger differences (in size between 157,683 to 192,360 bp). This suggested that the plasmids obtained from the similar sprout production batches could be clonally related. Nanopore MinION based 16S metagenomics showed the presence of Enterobacter (En.) cloacae, En. ludwigii, En. kobei, Citrobacter (C.) werkmanii, C. freundii, Klebsiella (K.) oxytoca and K. pneumonia, which have previously been isolated from fresh produce in Germany. These bacteria may harbor antibiotic resistance genes on plasmids that could potentially be transferred to similar genera. This study demonstrated that bacteria present in sprouts may act as the donors of antibiotic resistance plasmids which can transfer resistance to other bacteria on this product via conjugation.},
}
@article {pmid40012781,
year = {2025},
author = {Zhao, B and Zhang, R and Jin, B and Yu, Z and Wen, W and Zhao, T and Quan, Y and Zhou, J},
title = {Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492128},
pmid = {40012781},
issn = {1664-302X},
abstract = {Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.},
}
@article {pmid40012777,
year = {2025},
author = {Li, Y and Zhao, J},
title = {Xiaohua Funing decoction ameliorates non-alcoholic fatty liver disease by modulating the gut microbiota and bile acids.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1511885},
pmid = {40012777},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota and bile acids (BAs) have emerged as factors involved in the development of non-alcoholic fatty liver disease (NAFLD). Xiaohua Funing decoction (XFD) is a traditional Chinese medicine formula used for the treatment of NAFLD. Previous studies have indicated that XFD protects liver function, but the underlying mechanism remains unclear.<br><br>METHODS: In this study, a Wistar rat model of NAFLD (Mod) was established via a high-fat diet. The effects of obeticholic acid (OCA) and XFD on Mod rats were subsequently evaluated. Wistar rats in the control (Con) group were fed a standard diet. There were eight rats in each group, and the treatment lasted for 12&#x202f;weeks. Furthermore, metagenomic sequencing and BA metabolomic analyses were performed.<br><br>RESULTS: Compared to the Con group, the Mod group presented significant differences in body and liver weights; serum total cholesterol (TC) and triglyceride (TG) levels; and liver TG, TC, and bile salt hydrolase levels (p&#x202f;<&#x202f;0.05 or p&#x202f;<&#x202f;0.01). Importantly, OCA and XFD administration normalized these indicators (p&#x202f;<&#x202f;0.05 or p&#x202f;<&#x202f;0.01). Pathology of the liver and white fat steatosis was observed in the Mod group, but steatosis was significantly alleviated in the OCA and XFD groups (p&#x202f;<&#x202f;0.05 or p&#x202f;<&#x202f;0.01). The abundances of Bacteroidales_bacterium, Prevotella_sp., bacterium_0.1xD8-71, and unclassified_g_Turicibacter in the Mod group were significantly different from those in the Con group (p&#x202f;<&#x202f;0.05 or p&#x202f;<&#x202f;0.01), whereas the abundance of Bacteroidales_bacterium was greater in the XFD group. A total of 17, 24, and 24 differentially abundant BAs were detected in the feces, liver, and serum samples from the Mod and Con groups, respectively (p&#x202f;<&#x202f;0.05 or p&#x202f;<&#x202f;0.01). In the feces, liver, and serum, XFD normalized the levels of 16, 23, and 14 BAs, respectively, including glycochenodeoxycholic acid, deoxycholic acid, murideoxycholic acid, lithocholic acid, 23-nordeoxycholic acid, and 3&#x3b2;-ursodeoxycholic acid. In addition, glycochenodeoxycholic acid was identified as a potential biomarker of NAFLD.<br><br>DISCUSSION: In summary, our experiments revealed that XFD regulates the gut microbiota and BAs, providing beneficial effects on liver lipid accumulation in NAFLD.},
}
@article {pmid40012717,
year = {2025},
author = {Li, YI and Pagulayan, K and Rau, H and Hendrickson, R and Schindler, AG},
title = {Gut Microbial Composition Is Associated with Symptom Self-Report in Trauma-Exposed Iraq and Afghanistan Veterans.},
journal = {Neurotrauma reports},
volume = {6},
number = {1},
pages = {1-12},
pmid = {40012717},
issn = {2689-288X},
abstract = {Iraq and Afghanistan War-era Veterans are at elevated risk for physical injuries and psychiatric illnesses, in particular the polytrauma triad of mild traumatic brain injury (mTBI), post-traumatic stress disorder (PTSD), and chronic pain. The gut microbiome has been implicated in modulation of critical processes beyond digestion, including immune system functioning and stress responsivity, and may be an important factor in understanding physical and mental health outcomes following deployment and trauma exposure. However, minimal research to date has sought to characterize gut microbiome composition in this population. Male Veterans of the conflicts in Iraq and Afghanistan who previously completed a Veterans Affairs' comprehensive TBI evaluation were enrolled in the current study. Participants completed self-report measures of PTSD symptom severity, pain intensity and interference, fatigue, cognitive symptoms, substance use, and sleep quality. They also submitted fecal samples, and metagenomic sequencing was used to calculate alpha and beta diversity and taxonomic microbial composition. Associations between microbiome data and clinical variables were then examined. Alpha and beta diversity measures were not significantly correlated with clinical outcomes. Fatigue, post-concussive symptoms, executive function symptoms, and cannabis use were associated with differences in gut microbial composition, specifically Verrucomicrobiota. Together, results suggest that altered gut microbiome composition is associated with psychiatric and cognitive symptoms in Veterans and highlight a potential new therapeutic target of interest. Future research is needed to examine whether probiotic treatment is effective for reducing symptoms common in this clinical population.},
}
@article {pmid40011862,
year = {2025},
author = {Blomström, AL and Källse, A and Riihimäki, M},
title = {Detection and genetic characterization of equine viruses in Sweden using viral metagenomics.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {119},
pmid = {40011862},
issn = {1746-6148},
support = {H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; },
mesh = {Animals ; Horses ; Sweden/epidemiology ; *Horse Diseases/virology/epidemiology ; *Metagenomics ; *Virus Diseases/veterinary/virology/epidemiology ; Viruses/classification/isolation &amp; purification/genetics ; Genome, Viral ; },
abstract = {BACKGROUND: Viral infections pose a significant challenge to the equine population, compromising welfare and causing substantial economic losses for the global equine industry. While numerous equine viral pathogens have been identified, many suspected viral infections remain undiagnosed. This highlights the need for further identification and characterization of viruses circulating within the equine population. In this study, we utilized viral metagenomics to investigate viruses present in serum samples and nasal swabs collected from horses in Sweden. The primary focus was on horses presenting with fever, although control horses were also included for comparison.<br><br>RESULT: The viral metagenomic analysis identified several viruses in the investigated samples. Among nasal swabs, the majority of the viral reads were classified as various equine herpesvirues (EHVs), mainly EHV-2 and EHV-5. Other viruses in nasal swabs include but are not limited to EHV-4, Torque teno equus virus 1 (TTeqV1) and equine copiparvovirus (eqCopV). Both TTeqV1 and eqCopV were also detected in the serum samples together with equine circovirus and equine pegivirus. A number of the detected viruses were further genetically characterized and were shown to display high sequence similarity to viruses from the US and/or China. qPCR screening of a selected number of the detected viruses revealed a rather low detection rate (1.6%-9.4%) in individual horses.<br><br>CONCLUSION: This study identified several viruses that circulate in the horse population in Sweden, some of which have not been previously detected in Sweden or Europe. Furthermore, the complete or nearly complete genomes of several of these viruses have been genetically characterized. These new data provide a valuable foundation for developing improved detection assays and conducting larger prevalence studies to assess the potential impact of these viruses on the equine population. Such efforts could ultimately contribute to enhanced equine welfare.},
}
@article {pmid40011766,
year = {2025},
author = {Proctor, DM and Sansom, SE and Deming, C and Conlan, S and Blaustein, RA and Atkins, TK and , and Dangana, T and Fukuda, C and Thotapalli, L and Kong, HH and Lin, MY and Hayden, MK and Segre, JA},
title = {Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40011766},
issn = {1476-4687},
abstract = {Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings[1]. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions[2]. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.},
}
@article {pmid40011381,
year = {2025},
author = {Esquivel-López, A and Rocha-Mendoza, D and Serrano-Maldonado, CE and Escobar-Zepeda, A and Quirasco, M},
title = {Heterologous Expression of Bacteriocins from the Metagenome Mining of Cotija Cheese.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40011381},
issn = {1867-1314},
support = {IN222717//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico-Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (UNAM-PAPIIT)/ ; IN222717//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico-Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (UNAM-PAPIIT)/ ; },
abstract = {Bacteriocins are a heterologous group of ribosomal peptides with antibacterial activity. They are of interest to the pharmaceutical and food industries due to their potential to fight antibiotic-resistant pathogens and improve microbial food safety, respectively. Metagenomic data mining for antibacterial activity is valuable for the information it provides from unstudied genomic sequences. Furthermore, the higher biosynthetic yield obtained by the heterologous expression of putative bacteriocins allows their subsequent purification and characterization. This work aimed to express antilisterial bacteriocins in Escherichia coli after obtaining their gene sequences by in silico mining the bacterial metagenome of Cotija cheese. This artisanal Mexican cheese is manufactured with unpasteurized milk and ripens for at least 3 months. Analyzing the Cotija cheese bacterial shotgun metagenome allowed us to select two sequences (QC1 and QC2) encoding novel Class IId bacteriocins belonging to the lactococcin family. These genes were expressed as (His)6-fusion proteins in E. coli BL21 (DE3) and showed high antimicrobial activity against Listeria monocytogenes, with a minimum inhibitory concentration of 78 µg/mL. QC1 and QC2 were tested against several pathogenic bacteria and showed activity exclusively against L. monocytogenes. QC2 has a novel sequence that showed no matches against the UniProt database. It was purified by Ni[2+] affinity chromatography and retained its activity after heating at 70 °C for 30 min. As the sequences were obtained by genomic mining on a fermented food metagenome, QC1 and QC2 have potential applications as sanitizers in industrial food facilities where L. monocytogenes contamination is the most prevalent.},
}
@article {pmid40010603,
year = {2025},
author = {Han, B and Shi, Y and Zhang, P and Liu, Y and Xu, M and Xia, J and Li, J and Li, Y and Zhang, M and Wang, J and Ren, Z and Yang, F and Chen, Y and Feng, G},
title = {Clinical Application Value of Metagenomic Next-generation Sequencing at Perioperative Period in Patients with Central Nervous System Infections in Neurosurgical Intensive Care Unit.},
journal = {World neurosurgery},
volume = {},
number = {},
pages = {123824},
doi = {10.1016/j.wneu.2025.123824},
pmid = {40010603},
issn = {1878-8769},
abstract = {OBJECTIVE: This study aims to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for diagnosing central nervous system infections (CNSIs) during the perioperative period in neurosurgical intensive care unit (ICU) patients.<br><br>METHODS: In this prospective study, we included patients suspected of CNSIs during the perioperative period who were admitted to the Neurosurgical-ICU at Henan Provincial People's Hospital. Clinical samples were tested using both mNGS and conventional pathogen culture methods. Based on comprehensive clinical diagnoses, patients were categorized into the CNSIs and non-CNSIs groups. The diagnostic performance of mNGS was compared with traditional methods, including time to pathogen detection and evaluation of optimal testing conditions. Additionally, the study assessed whether antibiotic resistance genes detected by mNGS could predict drug resistance phenotypes.<br><br>RESULTS: Between January 2022 and December 2023, 116 patients were enrolled, including 48 in the CNSIs group and 30 in the non-CNSIs group. mNGS identified a greater variety and quantity of pathogens compared to conventional methods. First, mNGS results were consistent with traditional culture in five cases. mNGS exhibited superior sensitivity (85.42% vs. 10.42%) and a higher negative predictive value (80.00% vs. 40.10%) compared to traditional cultures. Second, only 8.33% of CNSIs patients showed identical pathogens in both cerebrospinal fluid (CSF) and blood samples. Third, 28.6% of CSF samples with an mNGS detection interval of over seven days showed complete pathogen consistency, while 60% of samples with a detection interval of less than three days were consistent. Moreover, the antibiotic resistance genes detected by mNGS largely corresponded with the resistance phenotypes identified by antibiotic susceptibility testing.<br><br>CONCLUSION: To sum up, mNGS offers excellent diagnostic accuracy and significant clinical value in CNSIs diagnosis during the perioperative period in the neurosurgical-ICU, complementing traditional culture methods effectively.},
}
@article {pmid40010597,
year = {2025},
author = {Wang, X and Lin, Y and Li, S and Wang, J and Li, X and Zhang, D and Duan, D and Shao, Z},
title = {Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125923},
doi = {10.1016/j.envpol.2025.125923},
pmid = {40010597},
issn = {1873-6424},
abstract = {The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.},
}
@article {pmid40010587,
year = {2025},
author = {Lai, Y and Qu, Y and Liu, H and Yue, Y and Cui, X and Wang, X and Wang, C and Zhang, L and Shi, Y and Huo, M},
title = {Anomalous reduced sequence: Potential hazards of disinfection byproduct chlorate in reclaimed water.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125924},
doi = {10.1016/j.envpol.2025.125924},
pmid = {40010587},
issn = {1873-6424},
abstract = {Chlorine dioxide is used in reclaimed water treatment technologies and generates the inorganic disinfection byproduct (DBP) chlorate (ClO3[-]) during disinfection. Currently, water quality standards for reclaimed water do not specify concentration limits for ClO3[-]. This DBP can infiltrate the soil along with reclaimed water. Ion concentrations are determined by ion chromatography. Metagenomics is used to measure and analyze the genomes of all microorganisms in soil. Results indicate that ClO3[-] remains stable in groundwater, and despite its higher redox potential (+1.21 V), it is not biologically reduced. Instead, NO3[-] with a lower redox potential (+0.94 V), undergoes significant biological reduction. Concurrently, microbial oxidative stress levels increase markedly by 133.77%, significantly stimulating the production of extracellular proteins by over 20.13% and polysaccharides by over 9.68%. Additionally, slight changes in microbial community structure are observed, including the elimination of microorganisms such as Chloroflexota, a slight decrease in species richness, and a minor increase in the regulation of genes related to amino acid metabolism by 2.56%. In terms of microbial ecological risks, ClO3[-] significantly upregulates microbial resistance gene levels by 16.15%, with microorganisms adopting two main strategies to mitigate ClO3[-] toxicity: altering target proteins or nucleic acids (51.70%) and efflux (43.41%). The relative abundance of efflux-related genes increases by 44.72%. Pathogenic bacteria show significant changes in relative abundance (over 156.52%) and community structure, with Acinetobacter junii increasing by 222.22% and Acinetobacter baumannii decreasing by 63.20%. In summary, ClO3[-] infiltrating with reclaimed water may potentially contaminate the groundwater environment. This study provides a comprehensive understanding of the interactions between ClO3[-] and soil microorganisms.},
}
@article {pmid38961050,
year = {2025},
author = {Bandeira, L and Faria, C and Cavalcante, F and Mesquita, A and Martins, C and Martins, S},
title = {Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado.},
journal = {Folia microbiologica},
volume = {70},
number = {1},
pages = {159-175},
pmid = {38961050},
issn = {1874-9356},
support = {421350/2017-2//Instituto Chico Mendes de Conserva&#xe7;&#xe3;o da Biodiversidade/ ; 18/2017//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Actinobacteria/chemistry/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/analysis ; Parks, Recreational ; Brazil ; *Soil Microbiology ; Biodiversity ; Soil/chemistry ; Metagenome ; },
abstract = {Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.},
}
@article {pmid40008244,
year = {2025},
author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G},
title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae141},
pmid = {40008244},
issn = {2730-6151},
abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.},
}
@article {pmid40007957,
year = {2025},
author = {Wang, J and Lv, G and Yang, J and He, X and Wang, H and Li, W},
title = {Impacts of plant root traits and microbial functional attributes on soil respiration components in the desert-oasis ecotone.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1511277},
pmid = {40007957},
issn = {1664-462X},
abstract = {Dividing soil respiration (Rs) into autotrophic respiration (Ra) and heterotrophic respiration (Rh) represents a pivotal step in deciphering how Rs responds to environmental perturbations. Nevertheless, in arid ecosystems beset by environmental stress, the partitioning of Rs and the underlying mechanisms through which microbial and root traits govern the distinct components remain poorly understood. This study was strategically designed to investigate Rs and its components (Ra and Rh), soil properties, and root traits within the desert-oasis ecotone (encompassing the river bank, transitional zone, and desert margin) of northwest China. Employing metagenomics, we quantitatively characterized microbial taxonomic attributes (i.e., taxonomic composition) and functional attributes (specifically, functional genes implicated in microbial carbon metabolism). Field measurements during the growing season of 2019 unveiled a pronounced decline in soil respiration rates along the environmental gradient from the river bank to the desert margin. The mean soil respiration rate was recorded as 1.82 ± 0.41 μmol m[-2] s[-1] at the river bank, 0.49 ± 0.15 μmol m[-2] s[-1] in the transitional zone, and a meager 0.45 ± 0.12 μmol m[-2] s[-1] in the desert margin. Concomitantly, the Ra and Rh components exhibited a similar trend throughout the study period, with Rh emerging as the dominant driver of Rs. Utilizing random forest modeling, we unearthed significant associations between microbial taxonomic and functional features and Rs components. Notably, both Ra and Rh displayed robust positive correlations with the abundance of phosphatidylinositol glycan A, a key player in microbial carbon metabolism. Partial least squares path modeling further elucidated that soil properties and microbial functions exerted direct and positive influences on both Ra and Rh, whereas taxonomic features failed to register a significant impact. When considering the combined effects of biotic and abiotic factors, microbial functional attributes emerged as the linchpin in dictating Rs composition. Collectively, these findings suggest that a trait-based approach holds great promise in more effectively revealing the response mechanisms of Rs composition to environmental changes, thereby offering novel vistas for future investigations into carbon cycling in terrestrial soils.},
}
@article {pmid40007795,
year = {2025},
author = {Li, J and Shi, Y and Hu, L and He, W and Li, Y},
title = {Assessing Gut Microbiome Alterations in Children With Allergic Rhinitis: Associations With Allergen-Specific IgE Levels and Sensitization Patterns.},
journal = {Journal of asthma and allergy},
volume = {18},
number = {},
pages = {269-281},
pmid = {40007795},
issn = {1178-6965},
abstract = {BACKGROUND: The relationship between gut microbiota composition and allergen exposure in children with allergic rhinitis (AR) remains insufficiently explored, particularly concerning variations in gut microbiota at different allergen-specific IgE (sIgE) levels and the distinction between monosensitization and polysensitization to allergens.<br><br>METHODS: We employed metagenomic shotgun sequencing to compare the fecal microbiota of 50&#xa0;healthy controls (HC) to 88 children with AR induced by house dust mites (HDM-AR). We further examined differences in gut microbiota among HDM-AR subgroups with extremely high house dust mite-sIgE (EH-HDM), high HDM-sIgE (H-HDM), as well as between monosensitized (mono-HDM) and polysensitized (poly-HDM) individuals.<br><br>RESULTS: While no significant differences in overall gut microbiome diversity were observed between the HC and HDM-AR groups, a notable increase in the relative abundance of Streptococcus sanguinis within the genus was identified in children with AR. Further analysis revealed a significant enrichment of the Streptococcus genus in the EH-HDM group, particularly highlighting an increased relative abundance of the Streptococcus salivarius. Functional gene analysis via KEGG pathways indicated substantial enrichment in the salivary secretion pathway. Additionally, in comparisons among the HC, mono-HDM, and poly-HDM groups, Streptococcus salivarius emerged as the key differential species, showing a marked increase in the mono-HDM group.<br><br>CONCLUSION: Our study suggests that specific bacterial strains, particularly Streptococcus salivarius, may be potential biomarkers for assessing varying degrees and patterns of HDM sensitization. These findings open the avenues for developing targeted interventions aimed at mitigating the pathophysiology of AR.},
}
@article {pmid40007605,
year = {2025},
author = {Buffet-Bataillon, S and Durão, G and Le Huërou-Luron, I and Rué, O and Le Cunff, Y and Cattoir, V and Bouguen, G},
title = {Gut microbiota dysfunction in Crohn's disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1540352},
pmid = {40007605},
issn = {2235-2988},
mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Feces/microbiology ; Adult ; Female ; Male ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Oxidative Stress ; Dysbiosis/microbiology ; Middle Aged ; Young Adult ; },
abstract = {INTRODUCTION: Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.<br><br>METHODS: We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.<br><br>RESULTS: As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.<br><br>CONCLUSIONS: This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.},
}
@article {pmid40007035,
year = {2025},
author = {De Koch, MD and Sweeney, N and Taylor, JE and Lucas, F and Ratheesh, NK and Lamb, SK and Miller, J and Kraberger, S and Varsani, A},
title = {Diverse Anelloviruses Identified in Leporids from Arizona (USA).},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/v17020280},
pmid = {40007035},
issn = {1999-4915},
mesh = {Animals ; Arizona ; *Genome, Viral ; *Phylogeny ; *Anelloviridae/genetics/classification/isolation &amp; purification ; Host Specificity ; Metagenomics ; Hares/virology ; Genome, Mitochondrial ; Ticks/virology ; Open Reading Frames ; },
abstract = {The communities of viruses studied in rabbits and hares (family Leporidae) have largely been those with clinical significance. Consequently, less is known broadly about other leporid viruses. Anelloviruses (family Anelloviridae) are likely commensal members of the single-stranded DNA virome in mammals. Here, we employ a viral metagenomic approach to identify DNA viruses of leporids and the ticks feeding on them in Arizona, USA. We characterize five complete anellovirus genomes from four leporids belonging to the black-tailed jackrabbit (Lepus californicus, n = 3) and the desert cottontail (Sylvilagus audubonii, n = 1). All five anellovirus genomes share > 69% orf1 gene pairwise nucleotide identity with those found in Iberian hares and thus belong to the species Aleptorquevirus lepor1. Accordingly, we expand the known host range of this anellovirus species to include Iberian hares in Europe and black-tailed jackrabbit and desert cottontail in the USA. We also sequenced the complete mitochondrial genomes of the four leporid hosts (Sylvilagus audubonii, n = 1; Lepus californicus, n = 3) and two ticks (Dermacentor parumapertus, n = 2) found feeding on two black-tailed jackrabbits. These results expand the diversity of anelloviruses in leporids while giving insight into the host genetics of leporids and ticks in Arizona, USA.},
}
@article {pmid40006931,
year = {2025},
author = {Sarker, S and Talukder, S and Athukorala, A and Whiteley, PL},
title = {The Spleen Virome of Australia's Endemic Platypus Is Dominated by Highly Diverse Papillomaviruses.},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/v17020176},
pmid = {40006931},
issn = {1999-4915},
mesh = {Animals ; *Phylogeny ; *Platypus/virology ; *Virome ; *Genome, Viral ; Australia ; *Papillomaviridae/genetics/classification/isolation &amp; purification ; *Spleen/virology ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Genetic Variation ; },
abstract = {The platypus (Ornithorhynchus anatinus), a unique monotreme, represents a pivotal point in mammalian evolution with its distinctive traits, such as electroreception and venom production. Despite its evolutionary significance, the viral diversity within platypuses remains poorly understood. This study employed next-generation sequencing to investigate the virome of the dead platypuses, uncovering a range of novel and divergent viruses. Among the identified viruses were four complete genomes of papillomaviruses (OaPV1-4) exhibiting substantial divergence from known strains, suggesting a novel genus within the subfamily Secondpapillomavirinae. Additionally, five novel parvoviruses were detected, including two with complete genomes, highlighting the complex viral ecosystem of the platypus. Phylogenetic analysis placed these viruses in unique evolutionary branches, further demonstrating the platypus's evolutionary significance. A circular DNA virus, a tombus-like virus, and a nodamuvirus were also identified, expanding the understanding of viral diversity in monotremes. These findings offer crucial insights into viral evolution in one of the most unique mammalian lineages, emphasising the need for further exploration to assess ecological and pathological impacts on platypus populations.},
}
@article {pmid40006910,
year = {2025},
author = {Haagmans, R and Charity, OJ and Baker, D and Telatin, A and Savva, GM and Adriaenssens, EM and Powell, PP and Carding, SR},
title = {Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/v17020155},
pmid = {40006910},
issn = {1999-4915},
support = {BB/R012490/1//BBSRC/ ; BB/X011054/1//BBSRC/ ; BB/X011054/1//BBSRC/ ; BB/X011011/1//BBSRC/ ; BB/CCG1860/1//BBSRC/ ; Project Grant//ME Research UK/ ; PhD studentship//Invest in ME Research/ ; PhD studentship//UEA Faculty Medicine and Health/ ; },
mesh = {*Metagenomics/methods ; *Feces/virology ; Humans ; *DNA Viruses/genetics/classification/isolation &amp; purification ; Reproducibility of Results ; *RNA Viruses/genetics/isolation &amp; purification/classification ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Viral/genetics ; Nucleic Acid Amplification Techniques/methods ; Genome, Viral ; },
abstract = {Whole transcriptome amplification (WTA2) and sequence-independent single primer amplification (SISPA) are two widely used methods for combined metagenomic sequencing of RNA and DNA viruses. However, information on the reproducibility and bias of these methods on diverse viruses in faecal samples is currently lacking. A mock community (MC) of diverse viruses was developed and used to spike faecal samples at different concentrations. Virus-like particles (VLPs) were extracted, nucleic acid isolated, reverse-transcribed, and PCR amplified using either WTA2 or SISPA and sequenced for metagenomic analysis. A bioinformatics pipeline measured the recovery of MC viruses in replicates of faecal samples from three human donors, analysing the consistency of viral abundance measures and taxonomy. Viruses had different recovery levels with VLP extraction introducing variability between replicates, while WTA2 and SISPA produced comparable results. In comparing WTA2- and SISPA-generated libraries, WTA2 gave more uniform coverage depth profiles and improved assembly quality and virus identification. SISPA produced more consistent abundance, with a 50% difference between replicates occurring in ~20% and ~10% of sequences for WTA2 and SISPA, respectively. In conclusion, a bioinformatics pipeline has been developed to assess the methodological variability and bias of WTA2 and SISPA, demonstrating higher sensitivity with WTA2 and higher consistency with SISPA.},
}
@article {pmid40005922,
year = {2025},
author = {Chrzastek, K and Seal, BS and Kulkarni, A and Kapczynski, DR},
title = {Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification.},
journal = {Veterinary sciences},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/vetsci12020162},
pmid = {40005922},
issn = {2306-7381},
abstract = {A whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, Ornithobacterium rhinotracheale (ORT) and a putative prophage candidate were found in one of the swab samples. A multi-locus sequence typing (MLST) scheme of the ORT genome involved the adk, aroE, fumC, gdhA, pgi, and pmi genes. Antibiotic resistant analysis demonstrated tetracycline-resistan t ribosomal protection protein, tetQ, the aminoglycoside-(3)-acetyltransferase IV gene, aminoglycoside antibiotic inactivation and macrolide resistance, and the ermX gene in the ORT genome. A putative prophage candidate was predicted using Prophage Hunter and PHAST, while BLAST analyses were utilized to identify genes encoding bacteriophage proteins. Interestingly, genes encoding endolysins were detected in bacteriophage genomes. The gene products encoded in the prophage sequence were most closely related to bacteriophages in the N4-like family among the Authographiviridae in the Caudovirales. This study demonstrates the potential of sWGS for the rapid detection and characterization of etiologic agents found in clinical samples.},
}
@article {pmid40005859,
year = {2025},
author = {Chen, H and Qing, Y and Xu, L and Zhu, L and Yin, W and Li, S and Kuang, S and Zhou, Y and Xu, Z},
title = {Prevalence and Molecular Characterization of Porcine Parvovirus 2 in Southwest China During 2020-2023.},
journal = {Veterinary sciences},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/vetsci12020099},
pmid = {40005859},
issn = {2306-7381},
abstract = {Porcine parvovirus (PPV) is a non-enveloped, single-stranded linear DNA virus that induces reproductive disorders in sows, particularly abortions in primiparous sows. This study investigated the prevalence of PPV in the southwestern region and conducted molecular characterization of PPV strains. An epidemiological survey was conducted on 1534 aborted fetuses from the southwestern region between 2020 and 2023, revealing an abortion rate of 3.00% due to PPV2, with the highest rate of 3.77% in Sichuan. Additionally, 2973 blood samples from sows were tested using ELISA, showing a PPV2 antibody positivity rate of 73.03% to 90%. Through shotgun metagenomics, PPV2 SC2020 was identified in aborted fetal samples from a pig farm in Pengzhou, Sichuan. PCR sequencing analysis yielded seven PPV2 genomic sequences, and the phylogenetic analysis of eight PPV2 strains with thirty reference strains showed distinct evolutionary branches. The virus was successfully isolated from PPV2-positive samples, and the phylogenetic analysis of PPV2 SC2020 revealed ORF1 gene homology of 94.9% to 99.3% and the ORF2 gene homology of 93.1% to 98.0%, with 34 reference strains. Homologous recombination analysis indicated that SC2020 is a recombinant strain of HeB03 and S1.},
}
@article {pmid40005817,
year = {2025},
author = {Tavano, F and Napoli, A and Gioffreda, D and Palmieri, O and Latiano, T and Tardio, M and di Mola, FF and Grottola, T and Büchler, MW and Gentile, M and Latiano, A and Mazza, T and Perri, F},
title = {Could the Microbial Profiling of Normal Pancreatic Tissue from Healthy Organ Donors Contribute to Understanding the Intratumoral Microbiota Signature in Pancreatic Ductal Adenocarcinoma?.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020452},
pmid = {40005817},
issn = {2076-2607},
support = {Ricerca Corrente program 2022-2024//Italian Minister of Health/ ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is associated with intratumoral microbiota changes. However, defining the normal pancreatic microbial composition remains a challenge. Herein, we tested the hypothesis that the microbial profiling of normal pancreatic tissue from healthy organ donors (HC) could help in determining the signature of microbiota in PDAC. Matched pairs of tumor and normal tissues from PDAC patients (n = 32) and normal pancreatic tissues from HC (n = 17) were analyzed by 16S rRNA gene sequencing. Dissimilarities in all the beta metrics emerged in both normal samples and tumor samples, compared to HC (Bray-Curtis dissimilarity and Jaccard distance: p = 0.002; weighted UniFrac distances: p = 0.42 and p = 0.012, respectively; unweighted UniFrac distance: p = 0.009); a trend toward a lower Faith's phylogenetic distance was found at the tumor level vs. HC (p = 0.08). Within PDAC, a lower Faith's phylogenetic distance (p = 0.003) and a significant unweighted UniFrac distance (p = 0.024) were observed in tumor samples vs. normal samples. We noted the presence of a decreased abundance of bacteria with potential beneficial effects (Jeotgalicoccus) and anticancer activity (Acinetobacter_guillouiae) in PDAC vs. HC; bacteria involved in immune homeostasis and suppression of tumor progression (Streptococcus_salivarius, Sphingomonas) were reduced, and those implicated in tumor initiation and development (Methylobacterium-Methylorubrum, g_Delftia) were enhanced in tumor samples vs. normal samples. Metagenomic functions involved in fatty acid synthesis were reduced in normal samples compared to HC, while peptidoglycan biosynthesis IV and L-rhamnose degradation were more abundant in tumor samples vs. normal samples. Future prospective studies on larger populations, also including patients in advanced tumor stages and considering all potential existing confounding factors, as well as further functional investigations, are needed to prove the role of microbiota-mediated pathogenicity in PDAC.},
}
@article {pmid40005798,
year = {2025},
author = {Di, H and Zhang, M and Ning, Z and Liu, C and He, Z and Wang, S and Kong, S and Gan, S and Sun, W and Xu, Z and Ti, J},
title = {Metagenomic Insights into the Abundance of Iron-Reducing Microorganisms in a Petroleum-Contaminated Iron-Rich Aquifer.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020433},
pmid = {40005798},
issn = {2076-2607},
abstract = {In petroleum-contaminated aquifers, iron (III) serves as an electron acceptor, enabling microbial degradation of organic matter. While previous studies have focused on iron reduction and organic matter degradation under laboratory conditions, research on iron-associated microorganisms in petroleum-contaminated aquifers is limited. To explore the diversity and distribution of such microorganisms in natural settings, this study used metagenomic analysis of an iron-rich, petroleum-contaminated aquifer. Sixteen groundwater samples from both pollution source and background areas were collected for species annotation and functional gene identification. Results show more than 7000 species were identified as iron-reducing microorganisms (IRMs), including several previously well-characterized iron-reducing species (e.g., Geobacter luticola and Geobacter sulfurreducens). However, the majority of IRMs were not found in existing iron-reducing microbial databases. Some of them, such as Sulfurospirillum sp. and Extensimonas perlucida, could be taxonomically classified at the species level, while most were only annotated as unclassified bacteria. In the contamination source zone, these microorganisms proliferated extensively, which led to hydrocarbon degradation predominantly driven by iron reduction in the aquifer. This study enhances our understanding of hydrocarbon-degrading microorganisms and supports the management of petroleum-contaminated sites.},
}
@article {pmid40005739,
year = {2025},
author = {Fu, Z and Zhang, H and Yang, Z and Liu, Y and Wang, P and Zhang, J and Chi, H},
title = {Metagenomic and Metabolomic Analyses Reveal the Role of a Bacteriocin-Producing Strain of Enterococcus faecalis DH9003 in Regulating Gut Microbiota in Mice.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020372},
pmid = {40005739},
issn = {2076-2607},
abstract = {To investigate the regulatory effect of a bacteriocin-producing strain of Enterococcus faecalis DH9003 on the gut microbiota of mice, 15 healthy C57 male mice were randomly administered an equal volume of sterile normal saline (HD, control group, n = 7) and E. faecalis DH9003 (YD, treatment group, n = 8) via gavage. Metagenomic and metabolomic analyses were performed to determine the composition and metabolic function of the intestinal microbiota in mice. The results showed that the relative abundance of Firmicutes continuously increased over time in YD compared to HD. The number of E. faecalis DH9003 increased slowly and remained steady from days 7 to 28, indicating that E. faecalis DH9003 could colonize a considerable number of mouse guts via intragastric administration. Supplementation with E. faecalis DH9003 demonstrated a regulatory effect on the intestinal microbiota composition of mice, causing a shift in the relative abundance of Bacteroidetes and Firmicutes at the phylum level. In addition, a total of 2426 different metabolites were found in mouse feces, including 1286 and 1140 metabolites in positive and negative modes, respectively. Vitamin B6 and succinate were the most regulated and downregulated metabolites in negative ion mode, and the most upregulated and downregulated metabolites in positive ion mode were N-methyl-glutamic acid and N-octanoyl sphingosine. In conclusion, E. faecalis DH9003 can colonize mice gut, affecting the gut microbiota and metabolic competence. This strain therefore offers considerable potential for application as a probiotic.},
}
@article {pmid40005729,
year = {2025},
author = {Chao, S and Zhang, Y and Hu, Y and Chen, Y and Li, P and Sun, Y and Song, L and Hu, Y and Wang, H and Wu, J and Lv, B},
title = {Transgenic Maize of ZmMYB3R Shapes Microbiome on Adaxial and Abaxial Surface of Leaves to Promote Disease Resistance.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020362},
pmid = {40005729},
issn = {2076-2607},
support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; },
abstract = {The phyllosphere is one of the largest habitats for microorganisms, and host genetic factors play an important role during the interaction between microorganisms and the phyllosphere. Therefore, the transgene may also lead to changes in the maize phyllosphere. ZmMYB3R was identified as a drought-tolerant gene in Arabisopsis. Here, we employed metagenomic sequencing to analyze the microbiome of the adaxial and abaxial leaf surfaces on ZmMYB3R-overexpressing (OE) and wild-type (WT)·maize, aiming to dissect the possible associations between ZmMYB3R and changes in phyllosphere microbiome functioning. Our results revealed that overexpressing ZmMYB3R altered the alpha and beta diversity of the phyllosphere microbiome. In OE plants, more beneficial microbes accumulated on the phyllosphere, while pathogenic ones diminished, especially on the abaxial surface of ZmMYB3R leaves. Further analysis of disease resistance-related metabolic pathways and abundances of disease resistance genes revealed significant differences between OE and WT. The inoculation experiment between OE and WT proved that ZmMYB3R increased the disease resistance of maize. In conclusion, the results reveal that transgenes affect the phyllosphere microbiome, and ZmMYB3R might alter leaf disease resistance by reshaping the phyllosphere microbiome structure. These findings help us understand how ZmMYB3R regulates leaf disease resistance and may facilitate the development of disease control by harnessing beneficial microbial communities.},
}
@article {pmid40005715,
year = {2025},
author = {Wu, H and Shi, C and Xu, T and Dai, X and Zhao, D},
title = {Characterization and Optimization of Cellulose-Degrading Bacteria Isolated from Fecal Samples of Elaphurus davidianus Through Response Surface Methodology.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020348},
pmid = {40005715},
issn = {2076-2607},
support = {23YFYSHZ00080//Chinese Academy of Sciences - Tianjin cooperation project/ ; Tianjin Bureau of Planning and Natural Resources//Tianjin Bureau of Planning and Natural Resources/ ; },
abstract = {The screening of cellulose-degrading microorganisms from herbivores and the optimization of fermentation conditions are of great significance for the utilization of cellulose resources. In this study, we initially employed a metagenomic analysis to investigate the fecal microbiota of both captive and semi-free-ranging Père David's deer (Elaphurus davidianus) under varying environmental conditions. Subsequently, we isolated and cultured cellulase-degrading microorganisms from the fecal samples using Congo red medium. There was consistency in the dominant phyla and genera of gut microorganisms between the two groups, with only differences in abundance. Then, a cellulose-degrading strain identified as Bacillus pumilus XM was isolated after a morphological analysis and molecular identification by 16S rRNA amplicon. In addition, a series of single factor experiments and response surface analysis were conducted to determine the optimal conditions for best cellulase activity. The optimum temperature, culture time, and shaking speed for the reaction of cellulase produced by the strain Bacillus pumilus XM were 34 °C, 28 h, and 154 r/min, respectively. Under these conditions, the cellulase activity reached a maximum of 10.96 U/mL, which was relatively close to the predicted value of 10.975 U/mL. The results have enriched the existing bacterial resources and laid a foundation for the development of new enzymes, providing a theoretical basis for the rational utilization of cellulase from wild animal resources.},
}
@article {pmid40005661,
year = {2025},
author = {Van Poelvoorde, LAE and Karlsson, EA and Dupont-Rouzeyrol, M and Roosens, NHCJ},
title = {Can Wastewater Surveillance Enhance Genomic Tracking of Climate-Driven Pathogens?.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020294},
pmid = {40005661},
issn = {2076-2607},
support = {ACIP 648-2023//Institut Pasteur/ ; },
abstract = {Climate change heightens the threat of infectious diseases in Europe, necessitating innovative surveillance methods. Based on 390 scientific papers, for the first time, this review associates climate-related pathogens, data related to their presence in wastewater, and associated available genomic detection methods. This deep analysis reveals a wide range of pathogens that can be tracked through methods such as quantitative and digital PCR, as well as genomic pathogen enrichment in combination with sequencing and metagenomics. Nevertheless, significant gaps remain in the development of methods, particularly for vector-borne pathogens, and in their general harmonization relating to performance criteria. By offering an overview of recent advancements while identifying critical gaps, we advocate for collaborative research and validation to integrate detection techniques into surveillance frameworks. This will enhance public health resilience against emerging infectious diseases driven by climate change.},
}
@article {pmid40005646,
year = {2025},
author = {Choi, Y and Jeong, J and Han, Y and Han, M and Yu, B and Han, K},
title = {Exploring Competitive Relationship Between Haemophilus parainfluenzae and Mitis Streptococci via Co-Culture-Based Molecular Diagnosis and Metabolomic Assay.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020279},
pmid = {40005646},
issn = {2076-2607},
support = {RS-2024-00355393//the Ministry of Education of the Republic of Korea and the National Research Foundation of Korea/ ; },
abstract = {Various bacterial strains with nitrate-reducing capacity (NRC), such as Haemophilus, Actinomyces, and Neisseria, are known to promote NH3 production, control pH in the oral cavity, and inhibit the growth of aciduric bacteria. However, experimental evidence on various estimated bacterial networks within the salivary microbiome is insufficient. This study aims to explore potential bacterial compositional competition observed within saliva samples from dental caries patients through a co-culture assay of mitis Streptococci, which is a primary colonizer in the salivary microbiome, and nitrate-reducing bacteria Haemophilus parainfluenzae. We investigated bacterial growth efficiency change by co-culture time using the qRT-PCR method. In addition, we applied LC/Q-TOF-based metabolites screening to confirm metabolic interactions between oral bacterial species and their association with dental caries from a metabolomics perspective. As a result, we first found that the nitrate reduction ability of H. parainfluenzae is maintained even in a co-culture environment with the mitis Streptococci group through a nitrate reduction test. However, nitrate reduction efficiency was hindered when compared with monoculture-based nitrate reduction test results. Next, we designed species-specific primers, and we confirmed by qRT-PCR that there is an obvious competitive relationship in growth efficiency between H. parainfluenzae and two mitis Streptococci (S. australis and S. sanguinis). Furthermore, although direct effects of nitrate reduction on competition have not been identified, we have potentially confirmed through LC/Q-TOF-based metabolite screening analysis that the interaction of various metabolic compounds synthesized from mitis Streptococci is driving inter-strain competition. In particular, we constructed a basic reference core-metabolites list to understand the metabolic network between each target bacterial species (H. parainfluenzae and mitis Streptococci) within the salivary microbiome, which still lacks accumulated research data. Ultimately, we suggest that our data have potential value to be referenced in further metagenomics and metabolomics-based studies related to oral health care.},
}
@article {pmid40005640,
year = {2025},
author = {Cao, X and Cui, Q and Li, D and Liu, Y and Liu, K and Li, Z},
title = {Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020273},
pmid = {40005640},
issn = {2076-2607},
support = {2022YSKY-57//Integrated analysis of soil hydrologic function of returning farmland to forest (grass) in Basic Scientific Research Youth Exploration Project of Central public welfare research Institute of Chinese Research Academy of Environmental Sciences, China/ ; },
abstract = {The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustainable use of land resources are key to addressing its ecological challenges. Soil microbial communities are vital to ecosystem functioning, and land use is a major human factor influencing their structure and diversity. Existing research on the Huanghe alluvial plain primarily focuses on soil physicochemical properties and moisture content, with relatively limited attention given to soil microorganisms. Therefore, this study, using the Wudi Tanyang Forest Farm in the Huanghe alluvial plain as a case study, employs high-throughput metagenomic sequencing to analyze the composition and diversity of soil bacteria, eukaryota, archaea, and virus communities in five different land use types (Tamarix chinensis forest, Fraxinus chinensis forest, farmland, wetland, and grassland). The results indicate that: (1) At the phylum level, the top three bacteria communities were Pseudomonadota, Acidobacteriota, and Actinomycetota; the top three in the eukaryota communities were Ascomycota, Mucoromycota, and Basidiomycotina; the top three in the archaea communities were Nitrososphaerota, Euryarchaeota, and Candidatus Thermoplasmatota; and the virus communities were dominated by Uroviricota; (2) The microbial community structure of the Tamarix chinensis forest and the Fraxinus chinensis forest was similar, and was significantly different from the other three land use types; (3) The land use type had a significant effect on the diversity of the soil microbial communities, with a higher diversity in the wetland and grassland soils; (4) The dominant species of the soil microbial communities under different land use types showed significant differences. This study provides theoretical support for land use optimization and sustainable soil management in the Huanghe alluvial plain region.},
}
@article {pmid40005630,
year = {2025},
author = {Song, X and Chen, G and Zheng, L and Shen, J and Xue, C and Chang, Y},
title = {Microbiota Involved in the Degradation of Tremella fuciformis Polysaccharide and Microbial Enzymatic Potential Revealed by Microbiome and Metagenome.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020263},
pmid = {40005630},
issn = {2076-2607},
support = {2023YFD2100605//the National Key R&amp;D Program of China/ ; },
abstract = {Tremella fuciformis, as a traditional edible fungus in Asian countries, is rich in polysaccharides with a variety of bioactivities. Nevertheless, its high molecular weight and complex structure have caused limitations in its application and structural analysis. In this study, we successfully screened a Tremella fuciformis polysaccharide-degrading bacterium from the soil by enriching and screening. The mixed bacterium consisted mainly of Verrucomicrobium (55.4%) and Lysobacter (43.8%), which released extracellular enzymes that enabled the degradation of Tremella fuciformis polysaccharides. The functional annotation using microbiome and metagenome combined with bioinformatics revealed its active carbohydrate metabolism, binding, and catalysis. It exposed the enzymatic potential of the bacterium and provided a basis for the exploration of hydrolytic enzymes for hardly degradable polysaccharides in fungi.},
}
@article {pmid40005614,
year = {2025},
author = {Lee, JL and Yourek, G},
title = {The Microbiome of Catfish (Ictalurus punctatus) Treated with Natural Preservatives During Refrigerated Storage.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020244},
pmid = {40005614},
issn = {2076-2607},
abstract = {Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers' growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (-4 to -5 Log CFU/g vinegar and -0.1 to -4 Log CFU/g other treatments in aquaculture and -1 to -2 Log CFU/g vinegar and -0.2 to -0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. Pseudomonas, Janthinobacterium, and Camobacteriaceae were the dominant bacteria species in the early point for store-bought fish. Still, Pseudomonas was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. Chryseobacterium, CK-1C4-19, and Cetobacterium were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, Pseudomonas in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products.},
}
@article {pmid40005601,
year = {2025},
author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH},
title = {Alleviation of Acute Heat Stress in Broiler Chickens by Dietary Supplementation of Polyphenols from Shredded, Steam-Exploded Pine Particles.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020235},
pmid = {40005601},
issn = {2076-2607},
support = {2020193C10-2022-BA01//Korea Forest Service/ ; No. RS-2024-00350745//Ministry of Science and ICT/ ; },
abstract = {Reducing the detrimental effects of heat stress (HS) in poultry is essential to minimize production losses. The present study evaluates the effects of dietary polyphenols prepared from underutilized wood byproducts on the growth, gut health, and cecal microbiota in broilers subjected to acute heat stress (AHS). One hundred eight one-day-old Indian River broilers were fed with 0%, 0.5%, or 1% polyphenols from shredded, steam-exploded pine particles (PSPP) in their diet. On the 37th day, forty birds were equally distributed among four groups containing either a control diet at thermoneutral temperatures (NT0%) or AHS temperatures with 0% (AHS0%), 0.5% (AHS0.5%), and 1% (AHS1%) PSPP-supplemented diets. The temperature in the NT room was maintained at 21.0 °C, while, in the AHS room, it was increased to 31 °C. AHS negatively influenced performance parameters and increased rectal temperature (RT) in broilers. The AHS0% group showed a higher expression of NOX4, HSP-70, and HSP-90 genes, while the expression was lower in PSPP-supplemented birds. In the jejunum, mRNA expression of SOD was increased in all the birds under AHS compared to NT. The expression of the CLDN1 and ZO2 genes was increased in AHS0%, while that of the ZO1 and MUC2 genes was increased in PSPP-supplemented birds. HS tends to increase TLR2 and TLR4 gene expression in chickens. The significantly modified genera were Bariatricus, Sporobacter, Sporanaerobacter, and Natranaerovirga. Concludingly, AHS negatively influences the performance parameters, RT, stress, gut-health-related genes, and pathogenic penetration, but PSPP supplementation reduces its bad impact by overcoming the stress and gut-health-related genes, increasing favorable bacterial abundance and reducing pathogenic penetration in chickens.},
}
@article {pmid40005600,
year = {2025},
author = {Misu, IJ and Kayess, MO and Siddiqui, MN and Gupta, DR and Islam, MN and Islam, T},
title = {Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020233},
pmid = {40005600},
issn = {2076-2607},
abstract = {The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts.},
}
@article {pmid40005589,
year = {2025},
author = {Warkhade, Y and Schaerer, LG and Bigcraft, I and Hazen, TC and Techtmann, SM},
title = {Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020222},
pmid = {40005589},
issn = {2076-2607},
support = {Merck Future Insight Prize//Merck KGaA/ ; },
abstract = {Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.},
}
@article {pmid40005401,
year = {2025},
author = {Straume, Z and Krūmiņa, N and Elbere, I and Rozenberga, M and Erts, R and Rudzīte, D and Proskurina, A and Krumina, A},
title = {Impact of Vitamins, Antibiotics, Probiotics, and History of COVID-19 on the Gut Microbiome in Ulcerative Colitis Patients: A Cross-Sectional Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {2},
pages = {},
doi = {10.3390/medicina61020284},
pmid = {40005401},
issn = {1648-9144},
support = {1.1.1.1/21/A/029//the European Regional Development Fund (ERDF)/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Female ; *Colitis, Ulcerative/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *COVID-19 ; *Vitamins/therapeutic use ; Adult ; Middle Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Probiotics/therapeutic use ; *SARS-CoV-2 ; Aged ; },
abstract = {Background and Objectives: The human gut microbiome is essential for the health of the host and is affected by antibiotics and coronavirus disease 2019 (COVID-19). The gut microbiome is recognized as a contributing factor in the development of ulcerative colitis. Specific vitamins and probiotics have been demonstrated to positively influence the microbiome by enhancing the prevalence of expected beneficial microorganisms. Materials and Methods: Forty-nine ulcerative colitis (UC) outpatients from Riga East Clinical University Hospital were enrolled in this cross-sectional study from June 2021 to December 2021. All patients were divided into groups based on history of COVID-19 (COVID-19 positive vs. COVID-19 negative) in the last six months. Information about antibiotic, probiotic, and vitamin intake were outlined, and faecal samples were collected. The MetaPhlAn v.2.6.0 tool was used for the taxonomic classification of the gut microbiome metagenome data. Statistical analysis was performed using R 4.2.1. Results: Of the 49 patients enrolled, 31 (63%) were male and 18 (37%) were female. Coronavirus disease 2019 was found in 14 (28.6%) patients in the last 6 months. Verrucomicrobia was statistically significantly lower in the COVID-19 positive group (M = 0.05; SD = 0.11) compared to the COVID-19 negative group (M = 0.5; SD = 1.22), p = 0.03. Antibiotic non-users had more Firmicutes in their microbiome than antibiotic users (p = 0.008). The most used vitamin supplement was vitamin D (N = 18), fifteen (42.9%) of the patients were COVID-19 negative and 3 (21.4%) were COVID-19 positive over the last six months (p > 0.05). Vitamin C users had more Firmicutes in their gut microbiome compared to non-users (Md = 72.8 [IQR: 66.6; 78.7] vs. Md = 60.1 [IQR: 42.4; 67.7]), p = 0.01. Conclusions: Antibiotic non-users had more Firmicutes than antibiotic users in their gut microbiome. Only vitamin C had statistically significant results; in users, more Firmicutes were observed. A mild course of COVID-19 may not influence ulcerative colitis patients' gut microbiome.},
}
@article {pmid40005052,
year = {2025},
author = {Zang, P and Chen, P and Chen, J and Sun, J and Lan, H and Dong, H and Liu, W and Xu, N and Wang, W and Hou, L and Sun, B and Zhang, L and Huang, J and Wang, P and Ren, F and Liu, S},
title = {Alteration of Gastrointestinal Function and the Ameliorative Effects of Hericium erinaceus Polysaccharides in Tail Suspension Rats.},
journal = {Nutrients},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/nu17040724},
pmid = {40005052},
issn = {2072-6643},
support = {242300421105//Henan Natural Science Foundation of Excellent Young Scholars/ ; },
mesh = {Animals ; *Rats, Sprague-Dawley ; *Gastrointestinal Microbiome/drug effects ; *Hericium ; Rats ; Male ; *Polysaccharides/pharmacology ; Hindlimb Suspension ; Dysbiosis ; Dietary Supplements ; Gastrointestinal Tract/drug effects ; Gastrointestinal Diseases/drug therapy/prevention &amp; control ; Weightlessness Simulation ; },
abstract = {Background/Objectives: Long-term spaceflight in a microgravity environment frequently results in gastrointestinal dysfunction, presenting substantial challenges to astronauts' health. Hericium erinaceus, a plant recognized for its dual use as food and medicine, contains a key functional component called Hericium erinaceus polysaccharide (HEP), which is purported to promote gastrointestinal health. This study aims to investigate the protective effects of HEP against gastrointestinal disturbances induced by simulated weightlessness and to elucidate its regulatory mechanisms. Methods: Sprague Dawley rats subjected to a tail suspension model were administered either a standard diet or a diet supplemented with 0.125% HEP over a period of 4 weeks (the intake of HEP is approximately 157.5 mg/kg bw/d, n = 8), metagenomics and targeted metabolomics to investigate the effects of HEP on gastrointestinal hormone secretion disorders, gut microbiota dysbiosis, and intestinal barrier damage induced by simulated weightlessness. Results: Dietary supplementation with HEP was observed to significantly alleviate weightlessness-induced gastrointestinal hormone disruptions, enhancing motility and intestinal barrier function while reducing inflammation. In addition, HEP improved gut microbiota by boosting beneficial bacteria as Oscillibacter sp.1-3, Firmicutes bacterium ASF500, and Lactobacillus reuteri, while reducing harmful bacteria like Escherichia coli and Mucispirillum schaedleri at the species level. Furthermore, HEP altered the serum metabolic profile of the rats, reducing inflammation by upregulating the tryptophan metabolism pathway and enhancing the production of short-chain fatty acids. Conclusions: HEP effectively protects against gastrointestinal dysfunction induced by simulated weightlessness by regulating hormone secretion and maintaining intestinal homeostasis.},
}
@article {pmid40004244,
year = {2025},
author = {Blankestijn, JM and Baalbaki, N and Beijers, RJHCG and Cornelissen, MEB and Wiersinga, WJ and Abdel-Aziz, MI and Maitland-van der Zee, AH and , },
title = {Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041781},
pmid = {40004244},
issn = {1422-0067},
support = {LSHM20104; LSHM20068//Health Holland/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology ; *Feces/microbiology/virology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Aged ; *SARS-CoV-2/isolation &amp; purification ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut-lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV1, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID.},
}
@article {pmid40004174,
year = {2025},
author = {Cui, Y and Guan, H and Okyere, SK and Hua, Z and Deng, Y and Deng, H and Ren, Z and Deng, J},
title = {Microbial Guardians or Foes? Metagenomics Reveal Association of Gut Microbiota in Intestinal Toxicity Caused by DON in Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041712},
pmid = {40004174},
issn = {1422-0067},
support = {. 32273072//This research was supported by National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Trichothecenes/toxicity ; *Metagenomics/methods ; Cytokines/metabolism ; Intestinal Mucosa/metabolism/microbiology/pathology ; Zonula Occludens-1 Protein/metabolism/genetics ; Male ; Colon/microbiology/metabolism/pathology/drug effects ; Jejunum/microbiology/pathology/metabolism/drug effects ; Occludin/metabolism/genetics ; Intestines/microbiology/pathology/drug effects ; },
abstract = {The role of gut microbiota has become a research hotspot in recent years; however, whether the gut microbiota are involved in the alleviation or exacerbation of Deoxynivalenol (DON) toxicity has not been fully studied. Therefore, the objective of this study was to investigate whether the gut microbiota are involved in reducing or aggravating the intestinal damage induced by DON in mice. Mice that received or did not receive antibiotic-induced intestinal flora clearance were orally given DON (5 mg kg/bw/day) for 14 days. At the end of the experiment, serum, intestinal tissue samples and colon contents were collected for further analysis. DON caused development of severe histopathological damage, such as necrosis and inflammation of the jejunum and colon in mice without gut microbiota clearance. The levels of tight junction proteins ZO-1 and occludin were reduced in the jejunum and colon of mice without gut microbiota clearance. In addition, the mRNA and protein levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) were increased in mice without gut microbiota clearance. The presence of microbiota exacerbate the intestinal damage induced by DON via changes in gut microbiota abundance and production of gut damaging metabolites.},
}
@article {pmid40003915,
year = {2025},
author = {Chao, X and Fan, Z and Wu, J and Ye, C and Wang, X and Li, R and Chen, S and Zhang, X and Fang, C and Luo, Q},
title = {Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041448},
pmid = {40003915},
issn = {1422-0067},
support = {2022B0202100002//Key-Area Research and Development Program of Guangdong Province/ ; 2024B03J1353//Science and Technology Program of Guangzhou City/ ; 2023ZD04064//STI2030-Major Projects/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Poultry Diseases/microbiology/genetics ; *Metagenomics/methods ; *Salmonella Infections, Animal/microbiology/genetics ; Cecum/microbiology ; RNA, Messenger/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Alternative Splicing ; Salmonella/genetics/pathogenicity ; RNA-Seq/methods ; Gene Expression Profiling ; Metagenome ; Gene Expression Regulation ; },
abstract = {The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.},
}
@article {pmid40003912,
year = {2025},
author = {Chatzokou, D and Tsarna, E and Davouti, E and Siristatidis, CS and Christopoulou, S and Spanakis, N and Tsakris, A and Christopoulos, P},
title = {Semen Microbiome, Male Infertility, and Reproductive Health.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041446},
pmid = {40003912},
issn = {1422-0067},
mesh = {Male ; Humans ; *Microbiota ; *Semen/microbiology ; *Infertility, Male/microbiology ; *Reproductive Health ; Female ; Reproductive Techniques, Assisted ; Spermatozoa/microbiology ; Fertility ; Pregnancy ; },
abstract = {The semen microbiome, once believed to be sterile, is now recognized as a dynamic ecosystem containing a diverse range of microorganisms with potential implications for male fertility and reproductive health. We aimed to examine the relationship between the semen microbiome, male infertility, and reproductive outcomes, highlighting the transformative role of next generation sequencing techniques and bioinformatics in exploring this intricate interaction, and we present a critical review of the published literature on this issue. Current evidence suggests a complex association between the composition of the semen microbiome and male fertility, with certain bacterial genera, such as Lactobacillus and Prevotella that exert opposing effects on sperm quality and DNA integrity. In addition, the influence of the semen microbiome extends beyond natural fertility, affecting assisted reproductive technologies and pregnancy outcomes. Despite considerable progress, challenges remain in standardizing methodologies and interpreting findings. In conclusion, we identify the lack of a definitive management proposal for couples presenting with this phenomenon, and we underline the need for an algorithm and indicate the questions raised that point toward our goal for a strategy. Continued research is essential to clarify the role of the semen microbiome in male reproductive health and to advance the development of personalized fertility management approaches.},
}
@article {pmid40003742,
year = {2025},
author = {Castillo, D and Abella, E and Sinpoo, C and Phokasem, P and Chantaphanwattana, T and Yongsawas, R and Cervancia, C and Baroga-Barbecho, J and Attasopa, K and Noirungsee, N and Disayathanoowat, T},
title = {Gut Microbiome Diversity in European Honeybees (Apis mellifera L.) from La Union, Northern Luzon, Philippines.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020112},
pmid = {40003742},
issn = {2075-4450},
support = {2022//Mekong - Lancang Special Fund/ ; },
abstract = {Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region.},
}
@article {pmid40002888,
year = {2025},
author = {Fu, Z and Jia, Y and Zhao, J and Guo, Y and Xie, B and An, K and Yuan, W and Chen, Y and Zhong, J and Tong, Z and Liu, X and Su, P},
title = {Perioperative Multi-Kingdom Gut Microbiota Alters in Coronary Artery Bypass Grafting.},
journal = {Biomedicines},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/biomedicines13020475},
pmid = {40002888},
issn = {2227-9059},
support = {(Cardiovascular Surgery)//National clinical key specialty construction project/ ; },
abstract = {Background: Coronary artery bypass grafting (CABG) is one of the main treatments for coronary heart disease (CHD). Gut microbiota, including bacteria, fungi, archaea, and virus, has been reported to be associated with CHD. However, the changes in the multi-kingdom gut microbiota after CABG are not yet clear. This study aimed to explore the changes in multi-kingdom gut microbiota during the early postoperative period of CABG. Methods: We collected fecal samples from 40 patients before and 1 week after CABG surgery. Metagenomic sequencing was used to detect the microbial spectrum and gene functions in the patients' fecal samples. Results: Post-CABG patients exhibited significant changes in the composition of multi-kingdom gut microbiota and gene functions. Among bacteria, beneficial species such as Bifidobacterium, Bacteroides, and Blautia were significantly reduced after CABG, while the harmful species Enterococcus was significantly increased. In fungi, Schizosaccharomyces pombe was significantly decreased in the postoperative group, while Saccharomyces cerevisiae and Aspergillus chevalieri were significantly increased postoperatively. Spearman correlation analysis indicated that Schizosaccharomyces pombe had positive interactions with beneficial bacteria such as Lachnospiraceae, Ruminococcus, and Blautia. Among archaea, the preoperatively enriched Methanomethylovorans-SGB40959 was significantly reduced postoperatively, and Spearman correlation analysis showed a significant positive interaction with probiotics Ruminococcus and Dorea. In viruses, the phage Enterococcus virus EFP01, which infects Enterococcus, was significantly increased postoperatively and showed a significant positive interaction with Enterococcus. Additionally, postoperative dysregulation of gene functions such as the Phosphoenolpyruvate-dependent Sugar Phosphotransferase System (PTS), Transposition, DNA-mediated, and Transposase Activity was observed, and Spearman correlation analysis indicated significant correlations between the dysregulated gene functions and the microbial communities. Conclusions: This study comprehensively revealed the changes in multi-kingdom species post-CABG. The reduction of beneficial microorganisms and the increase of harmful microorganisms after surgery are of significant clinical importance for understanding the overall health status of post-CABG patients and for optimizing postoperative treatment plans. Future research needs to further explore how to improve the prognosis of post-CABG patients by modulating the gut microbiota.},
}
@article {pmid40002576,
year = {2025},
author = {Pais, RJ and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R and Bessa, LJ},
title = {Exploring AI-Driven Machine Learning Approaches for Optimal Classification of Peri-Implantitis Based on Oral Microbiome Data: A Feasibility Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/diagnostics15040425},
pmid = {40002576},
issn = {2075-4418},
support = {2022.01430.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
abstract = {Background: Machine learning (ML) techniques have been recently proposed as a solution for aiding in the prevention and diagnosis of microbiome-related diseases. Here, we applied auto-ML approaches on real-case metagenomic datasets from saliva and subgingival peri-implant biofilm microbiomes to explore a wide range of ML algorithms to benchmark best-performing algorithms for predicting peri-implantitis (PI). Methods: A total of 100 metagenomes from the NCBI SRA database (PRJNA1163384) were used in this study to construct biofilm and saliva metagenomes datasets. Two AI-driven auto-ML approaches were used on constructed datasets to generate 100 ML-based models for the prediction of PI. These were compared with statistically significant single-microorganism-based models. Results: Several ML algorithms were pinpointed as suitable bespoke predictive approaches to apply to metagenomic data, outperforming the single-microorganism-based classification. Auto-ML approaches rendered high-performing models with Receiver Operating Characteristic-Area Under the Curve, sensitivities and specificities between 80% and 100%. Among these, classifiers based on ML-driven scoring of combinations of 2-4 microorganisms presented top-ranked performances and can be suitable for clinical application. Moreover, models generated based on the saliva microbiome showed higher predictive performance than those from the biofilm microbiome. Conclusions: This feasibility study bridges complex AI research with practical dental applications by benchmarking ML algorithms and exploring oral microbiomes as foundations for developing intuitive, cost-effective, and clinically relevant diagnostic platforms.},
}
@article {pmid40002490,
year = {2025},
author = {Thirupathi, K and Ghozy, S and Reda, A and Ranatunga, WK and Ruben, MA and Armin, Z and Mereuta, OM and Prabhjot, S and Dai, D and Brinjikji, W and Kallmes, DF and Kadirvel, R},
title = {Metagenomic Insights into Microbial Signatures in Thrombi from Acute Ischemic Stroke Patients Undergoing Endovascular Treatment.},
journal = {Brain sciences},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/brainsci15020157},
pmid = {40002490},
issn = {2076-3425},
abstract = {Background: Variability in recanalization success during endovascular treatment for acute ischemic stroke (AIS) has led to increased interests in thrombus composition and associated cellular materials. While evidence suggests that bacteria may influence thrombus characteristics, limited data exist on microbiological profiles of thrombi in stroke patients. Objectives: Characterization of bacterial communities present in thrombi of AIS patients undergoing mechanical thrombectomy, providing insights into microbial contributions to stroke pathogenesis and treatment outcomes. Methods: Thrombi were collected from 20 AIS patients. After extracting metagenome, 16S rDNA sequencing was performed. Bioinformatic analysis included taxonomy and diversity assessments. The presence of bacterial DNA and viable bacteria in thrombi was validated using polymerase chain reaction (PCR) and bacterial culturing followed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis, respectively. Results: 16S rDNA was amplified in 19/20 thrombi (95%). Analysis identified a diverse microbial community, with Corynebacterium spp. as the most prevalent genus, followed by Staphylococcus spp., Bifidobacterium spp., Methylobacterium spp., and Anaerococcus spp. Alpha diversity analyses (Shannon index: 4.0-6.0 and Simpson index: 0.8-1.0) revealed moderate to high microbial diversity across samples; beta diversity demonstrated distinct clustering, indicating inter-patient variability in microbial profiles. PCR confirmed the presence of DNA specific to dominant bacterial taxa identified through sequencing. Culturing showed the presence of Staphylococcus epidermidis and Enterococcus faecalis in some clots as identified through MALDI analysis. Conclusions: This study shows bacterial communities present in AIS patients' thrombi, suggesting a potential link between microbial signatures and thrombus characteristics.},
}
@article {pmid40002376,
year = {2025},
author = {Smirnova, YD and Hanetseder, D and Derigo, L and Gasser, AS and Vaglio-Garro, A and Sperger, S and Brunauer, R and Korneeva, OS and Duvigneau, JC and Marolt Presen, D and Kozlov, AV},
title = {Osteosarcoma Cells and Undifferentiated Human Mesenchymal Stromal Cells Are More Susceptible to Ferroptosis than Differentiated Human Mesenchymal Stromal Cells.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/antiox14020189},
pmid = {40002376},
issn = {2076-3921},
support = {ICM-2020-00212//OeAD-GmbH/ ; MPC-2022-00040//OeAD-GmbH/ ; 953134//European Union's Horizon 2020; H2020-NMBP-TR-IND-2020/ ; 877452//Austrian Research Promotion Agency (FFG)/ ; P-33799//Austrian Science Fund (FWF)/ ; },
abstract = {Current research suggests that promoting ferroptosis, a non-apoptotic form of cell death, may be an effective therapy for osteosarcoma, while its inhibition could facilitate bone regeneration and prevent osteoporosis. Our objective was to investigate whether the susceptibility to and regulation of ferroptosis differ between undifferentiated (UBC) and differentiated (DBC) human bone marrow stromal cells, as well as human osteosarcoma cells (MG63). Ferroptosis was induced by either inhibiting glutathione peroxidase 4 (GPX4) using RSL3 or blocking all glutathione-dependent enzymes through inhibition of the glutamate/cysteine antiporter with Erastin. Lipid peroxidation was assessed using the fluorescent probe BODIPY™581/591C11, while Ferrostatin-1 was used to inhibit ferroptosis. We demonstrate that neither Erastin nor RSL3 induces ferroptosis in DBC. However, both RSL3 and Erastin induce ferroptosis in UBC, while Erastin predominantly induces ferroptosis in MG63 cells. Our data suggest that ferroptosis induction in undifferentiated hBMSCs is primarily regulated by GPX4, whereas glutathione S-Transferase P1 (GSTP1) plays a key role in controlling ferroptosis in osteosarcoma cells. In conclusion, targeting the key pathways involved in ferroptosis across different bone cell types may improve the efficacy of cancer treatments while minimizing collateral damage and supporting regenerative processes, with minimal impact on cancer therapy.},
}
@article {pmid40002058,
year = {2025},
author = {Tenea, GN and Cifuentes, V and Reyes, P and Cevallos-Vallejos, M},
title = {Unveiling the Microbial Signatures of Arabica Coffee Cherries: Insights into Ripeness Specific Diversity, Functional Traits, and Implications for Quality and Safety.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/foods14040614},
pmid = {40002058},
issn = {2304-8158},
support = {7874/2023//Universidad T&#xe9;cnica del Norte/ ; },
abstract = {Arabica coffee, one of the most valuable crop commodities, harbors diverse microbial communities with unique genetic and functional traits that influence bean safety and final coffee quality. In Ecuador, coffee production faces challenges due to the spread of pathogenic organisms across cultivars, leading to reduced yields and compromised quality. This study employed a shotgun metagenomic approach to characterize the indigenous microbial diversity present in the cell biomass of fermented coffee cherries from three Coffea arabica varieties: Typica (Group A), Yellow Caturra (Group B), and Red Caturra (Group C), originating from the Intag Valley in northern Ecuador, at two ripe stages: green (immature fruits) and ripe (red/yellow mature fruits). Gene prediction and functional annotation were performed using multiple databases, including EggNOG, COG, KEGG, CAZy, CARD, and BacMet, to explore the potential impact of microbial communities on bean quality and safety. Metagenomic sequencing generated over 416 million high-quality reads, averaging 66 million clean reads per sample and yielding a total of 47 Gbps of data. Analysis revealed distinct differences in species abundance based on the coffee variety and ripening stage. A total of 799,658 protein-coding sequences (CDSs) were predicted, of which 205,937 genes were annotated with EggNOG, 181,723 with COG, 155,220 with KEGG, and 10,473 with CAZy. Additionally, 432 antibiotic resistance genes (ARGs) were identified using CARD, and 8974 biocide and metal resistance genes (BMRGs) were annotated with BacMet. Immature cherries exhibited enriched pathways associated with resistance to antibiotics such as fluoroquinolones, penams, rifamycin, macrolides, carbapenems, and cephalosporins. The abundance of these pathways varied with the ripening stage and variety. Furthermore, green cherries showed a significant increase in BMRGs associated with resistance to substances including hydrochloric acid, copper, nickel, hydrogen peroxide, arsenic, and zinc. Among mature cherries, Typica and Red Caturra shared similar profiles, while Yellow Caturra displayed a divergent microbial and functional profile. These study findings emphasize the interplay between microbial diversity, ripening stages, and coffee varieties, providing a foundation for innovative approaches to enhance coffee quality through microbiome management.},
}
@article {pmid40002014,
year = {2025},
author = {Yan, C and Huang, Z and Tu, R and Zhang, L and Wu, C and Wang, S and Huang, P and Zeng, Y and Shi, B},
title = {Revealing the Differences in Microbial Community and Quality of High-Temperature Daqu in the Southern Sichuan-Northern Guizhou Region.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/foods14040570},
pmid = {40002014},
issn = {2304-8158},
support = {KY202301//Scientific Research Cooperation Project of Sichuan University - Luzhou Laojiao Culture and Technology Innovation Research Center/ ; },
abstract = {High-temperature Daqu is crucial to Jiang-flavor Baijiu production in the Southern Sichuan-Northern Guizhou region of China. However, the complex interplay among microorganisms, enzymes, and metabolites in the Daqu from this region requires further investigation. This study compared four high-temperature Daqu samples from this region, analyzing their physicochemical properties, enzyme activities, volatile compounds, and microbial community composition and function, and exploring the influence of microorganisms on the saccharification and aroma-formation function of Daqu in combination with correlation analysis. The microbial communities in the Daqu samples exhibited functional redundancy, with Desmospora sp. 8437 being consistently dominant (3.6-7.3%). Members of the family Bacillaceae were the principal factors contributing to the differences in starch degradation capacity, protein degradation capacity, and pyrazine content among the Daqu samples, mainly through the amylases and proteases they produce. Kroppenstedtia spp. were principal factors causing the differences in aldehyde and ketone contents, primarily via the lipid degradation enzymes they synthesize. Overall, the bacterial community composition of Daqu greatly influenced its characteristics. This study provided a theoretical basis for understanding the diversity of high-temperature Daqu in the Southern Sichuan-Northern Guizhou region.},
}
@article {pmid40001366,
year = {2025},
author = {Ortiz-Severín, J and Hojas, I and Redin, F and Serón, E and Santana, J and Maass, A and Cambiazo, V},
title = {From Metagenomes to Functional Expression of Resistance: floR Gene Diversity in Bacteria from Salmon Farms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/antibiotics14020122},
pmid = {40001366},
issn = {2079-6382},
support = {Convocatoria Nacional Subvenci&#xf3;n a Instalaci&#xf3;n en la Academia Convocatoria a&#xf1;o 2021 Folio SA77210027//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt 1211893//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n number 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Basal Center grant FB210005//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID-MILENIO-ICN2021_044//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {Background. The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. Methods. Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover floR gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. Results. Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The floR gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference floR. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the floR sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. Conclusions. This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms.},
}
@article {pmid40001165,
year = {2025},
author = {Awasthi, S and Hiremath, VM and Nain, S and Malik, S and Srinivasan, V and Rose, P and Choudhury, A and Grover, R and Sharma, R},
title = {Microbial landscape of Indian homes: the microbial diversity, pathogens and antimicrobial resistome in urban residential spaces.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {25},
pmid = {40001165},
issn = {2524-6372},
support = {CLP0030, CNP0011//Reckitt (India) Ltd, India/ ; JRF//CSIR/ ; },
abstract = {BACKGROUND: Urban dwellings serve as complex and diverse microbial community niches. Interactions and impact of house microbiome on the health of the inhabitants need to be clearly defined. Therefore, it is critical to understand the diversity of the house microbiota, the presence and abundance of potential pathogens, and antimicrobial resistance.<br><br>RESULTS: Shotgun metagenomics was used to analyze the samples collected from 9 locations in 10 houses in New Delhi, India. The microbiota includes more than 1409 bacterial, 5 fungal, and 474 viral species en masse. The most prevalent bacterial species were Moraxella osloensis, Paracoccus marcusii, Microbacterium aurum, Qipengyuania sp YIMB01966, and Paracoccus sphaerophysae, which were detected in at least 80 samples. The location was the primary factor influencing the microbiome diversity in the Indian houses. The overall diversity of different houses did not differ significantly from each other. The surface type influenced the microbial community, but the microbial diversity on the cemented and tiled floors did not vary significantly. A substantial fraction of the bacterial species were potentially pathogenic or opportunistic pathogens, including the ESKAPE pathogens. Escherichia coli was relatively more abundant in bedroom, foyer, and drawing room locations. Analysis of the house microbiome antimicrobial resistome revealed 669 subtypes representing 22 categories of antimicrobial resistance genes, with multidrug resistance genes being the most abundant, followed by aminoglycoside genes.<br><br>CONCLUSIONS: This study provides the first insight into the microbiomes of houses in New Delhi, showing that these houses have diverse microbiomes and that the location within the house significantly influences the microbiota. The presence of potential pathogens and a repertoire of antimicrobial resistance genes reflect possible health risks, as these could lead to infectious disease transmission. This study builds a framework for understanding the microbial diversity of houses in terms of geographical location, environment, building design, cleaning habits, and impact on the health of occupants.},
}
@article {pmid40001114,
year = {2025},
author = {Feng, X and Cheng, J and Jiang, L and Lin, J and Ye, Z and Pang, Q and Liu, J},
title = {The application of endoscopic debridement combined with metagenomic next-generation sequencing technology in primary spinal infections: a retrospective study.},
journal = {Journal of orthopaedic surgery and research},
volume = {20},
number = {1},
pages = {195},
pmid = {40001114},
issn = {1749-799X},
support = {2024HMZD05//the Key Research Foundation of Ningbo No.2 Hospital/ ; 2024021//Zhejiang provincial key clinical specialty/ ; 2022-F15//the project of Ningbo leading medical &amp; Health Discipline/ ; 2023HMJQ03//the Distinguished Young Scholars of Ningbo No.2 Hospital/ ; },
mesh = {Humans ; Retrospective Studies ; *Debridement/methods ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; *Endoscopy/methods ; Adult ; Spinal Diseases/surgery/microbiology ; Bacterial Infections/microbiology/diagnosis ; },
abstract = {PURPOSE: Spinal endoscopy is a novel minimally invasive spinal surgery technique used in recent years to treat various degenerative spinal diseases. Metagenomic next-generation sequencing (mNGS) is a new method for identifying infectious microorganisms in infectious diseases. We aim to evaluate the application effect of combining spinal endoscopy with mNGS in diagnosing and treating spinal infections.<br><br>METHODS: The clinical data of 62 patients with suspected spinal infectious diseases admitted from January 2020 to December 2023 were retrospectively analyzed. All patients underwent spinal endoscopy to obtain tissue specimens, histopathological examination, routine bacterial culture, and mNGS sequencing. Describe the pathogenic microbial spectrum of spinal infection, and compare the differences in sensitivity (true positive rate) and specificity (true negative rate) between the two detection methods. White blood cell (WBC) erythrocyte deposition rate (ESR), C-reactive protein (CRP), visual analog scale (VAS), Japanese Orthopaedic Association (JOA) score, Oswestry Disability Index (ODI), and other clinical results were analyzed.<br><br>RESULTS: In 62 cases, mNGS, microbiological culture, serologic testing, and pathologic examination results were obtained. 49 cases of spinal infections and 13 cases of non-spinal infections were finally diagnosed clinically. Among the 49 patients with spinal infections, there were 31 cases of purulent bacterial infections, 8 cases of tuberculosis infections, and 10 cases of infections with unspecified etiological microorganisms. Among the 13 cases of non-spinal infections, there were 3 cases of spinal tumors, 6 cases of Modic changes of the endplates, and 4 cases of endplate fracture. The positive rate of microbial culture was 36.73% (18/49), and the positive rate of the mNGS test was 71.43% (35/49), which was statistically different from each other (P&#x2009;<&#x2009;0.01). The sensitivity of the mNGS test was 71.43%, and the specificity of the mNGS test was 84.62%. At the 3-month follow-up, WBC, ESR, and CRP levels were normalized. The VAS, JOA score, and ODI of the lower back and legs at each follow-up point after surgery were significantly improved compared with those before surgery, and the difference was statistically significant (P&#x2009;<&#x2009;0.01).<br><br>CONCLUSION: Metagenomic sequencing technology is fast, efficient, and accurate in detecting pathogenic microorganisms, and has high diagnostic value in the diagnosis and treatment of spinal infections. Spinal endoscopic debridement combined with mNGS can achieve good clinical results.},
}
@article {pmid40000989,
year = {2025},
author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P},
title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {90},
pmid = {40000989},
issn = {1471-2180},
support = {32201393//National Natural Science Foundation of China/ ; },
abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.},
}
@article {pmid39999781,
year = {2025},
author = {Chrismas, N and Yahr, R},
title = {Genomics: A window into the molecular mystery box of lichen symbiosis.},
journal = {Current biology : CB},
volume = {35},
number = {4},
pages = {R139-R141},
doi = {10.1016/j.cub.2025.01.034},
pmid = {39999781},
issn = {1879-0445},
mesh = {*Lichens/genetics/physiology/microbiology ; *Symbiosis/genetics ; *Genomics ; Metagenomics ; },
abstract = {How is a symbiosis built? Lichen metagenomic and metatranscriptomic surveys comparing growth stages, experimental treatments and environmental settings identify a catalogue of candidate genes - and microbial partners - in a developing model system.},
}
@article {pmid39999861,
year = {2025},
author = {Mejia, G and Jara-Servin, A and Hernández-Álvarez, C and Romero-Chora, L and Peimbert, M and Cruz-Ortega, R and Alcaraz, LD},
title = {Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf019},
pmid = {39999861},
issn = {1574-6941},
abstract = {Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 OTUs across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (p ≤ 0.05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into Bacteria (93.7%) and Eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertiliser use in agriculture.},
}
@article {pmid39999355,
year = {2025},
author = {Ahmed, AA and Park, SY and Smollin, MJ and Lindner, MS and Sarmiento Clemente, A and Del Valle Penella, A and Laufer, PM and Sanchez-Vegas, C and Cotilla, MR and Melish, ME and Trieu, C and Kabani, NA and Cooper, J and Lloyd, AR and Kimberlin, DW and Arnold, JC and Jordan-Villegas, A and Patterson, LE and Foster, CE and Yagupsky, P},
title = {Plasma Microbial Cell-free DNA Sequencing for the Detection of Kingella kingae Pediatric Spinal Infections.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004743},
pmid = {39999355},
issn = {1532-0987},
abstract = {BACKGROUND: Diagnosis of Kingella kingae skeletal system infections is made challenging by the microbe's fastidious nature. Detection and quantification of circulating microbial cell-free DNA (mcfDNA) in plasma by the Karius Test, a commercial metagenomic sequencing test, may offer promise in diagnosing pediatric spinal infections caused by difficult-to-culture organisms such as K. kingae.<br><br>METHODS: Plasma mcfDNA sequencing detections of K. kingae from April 2018 to December 2020 were reviewed to identify pediatric (age <18 years) patients. Medical charts of those with spinal infections were reviewed, and mcfDNA sequencing diagnostic performance was compared with usual care tests (ie, cultures, polymerase chain reaction).<br><br>RESULTS: Ten children with K. kingae spinal infections were identified across 7 institutions. The median age was 16.5 months (range 11-23 months). All case-patients had vertebral osteomyelitis with 9 having spondylodiscitis. Compared with usual care tests, mcfDNA sequencing was significantly more sensitive (McNemar's test 6.25, 2-tailed P = 0.0133). It was the only method of microbiological diagnosis in 9 patients, providing results in a median of 2.5 days (range 2-5 days) from sample collection. K. kingae mcfDNA was detected despite antibiotic pretreatment in 5/5 case-patients. Pathogen-tailoring of antimicrobial coverage was undertaken in 9 children.<br><br>CONCLUSION: Plasma mcfDNA sequencing offers a rapid, noninvasive method of detecting K. kingae causing pediatric spinal infections. This culture-independent approach may facilitate diagnosis, despite antibiotic pretreatment and subsequently targeted therapy and potentially obviate the need for biopsy.},
}
@article {pmid39999339,
year = {2025},
author = {Hohmann, M and Iliasov, D and Larralde, M and Johannes, W and Janßen, KP and Zeller, G and Mascher, T and Gulder, TAM},
title = {Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00042},
pmid = {39999339},
issn = {2161-5063},
abstract = {Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.},
}
@article {pmid39998665,
year = {2025},
author = {Szóstak, N and Budnik, M and Tomela, K and Handschuh, L and Samelak-Czajka, A and Pietrzak, B and Schmidt, M and Kaczmarek, M and Galus, &#x141; and Mackiewicz, J and Mackiewicz, A and Kozlowski, P and Philips, A},
title = {Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {4},
pages = {110},
pmid = {39998665},
issn = {1432-0851},
support = {2017/25/B/NZ5/01949//Narodowe Centrum Nauki/ ; POIR.04.01.02-00-0025/17-00//Narodowe Centrum Bada&#x144; i Rozwoju/ ; },
mesh = {Humans ; *Melanoma/drug therapy/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lymphocytes/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Mycobiome ; Aged ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; Adult ; Skin Neoplasms/immunology/drug therapy/microbiology ; Fungi/immunology ; },
abstract = {Research has shown that the microbiome can influence how the immune system responds to melanoma cells, affecting the course of the disease and the outcome of the therapy. Here, we used the metagenomic approach and flow cytometry analyses of blood cells to discover correlations between gut fungi of metastatic melanoma patients enrolled in anti-PD-1 therapy and lymphocytes in their blood.We analyzed the patterns of associations before the first administration of anti-PD-1 therapy (BT, n = 61) and in the third month of the therapy (T3, n = 37), allowing us to track changes during treatment. To understand the possible impact of gut fungi on the efficacy of anti-PD-1 therapy, we analyzed the associations in clinical beneficiaries (CB, n = 37) and non-beneficiaries (NB, n = 24), as well as responders (R, n = 28) and non-responders (NR, n = 33).Patients with LDH < 338 units/L, overall survival (OS) > 12, CB, as well as R, had lower levels of Shannon diversity (p = 0.02, p = 0.05, p = 0.05, and p = 0.03, respectively). We found that the correlation pattern between intestinal fungi and lymphocytes was specific to the type of response, positive or negative. When comparing CB and NB groups, correlations with opposite directions were detected for C. albicans, suggesting a response-specific immune reaction. For CB, M. restricta exhibited a set of correlations with different types of lymphocytes, with prevalent positive correlations, suggesting a robust immune response in the CB group. This result extends our former research, where M. restricta and C. albicans were associated with an increased risk of melanoma progression and a poorer response to anti-PD-1 treatment.},
}
@article {pmid39998261,
year = {2025},
author = {Woh, PY and Chen, Y and Kumpitsch, C and Mohammadzadeh, R and Schmidt, L and Moissl-Eichinger, C},
title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0218324},
doi = {10.1128/spectrum.02183-24},
pmid = {39998261},
issn = {2165-0497},
abstract = {The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically Methanobrevibacter species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (n = 21), fingolimod (n = 20), glatiramer acetate (n = 14), interferon (n = 18), natalizumab (n = 6), or ocrelizumab/rituximab (n = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of Methanobrevibacter smithii and M. sp900766745 compared to untreated patients. Notably, M. sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for M. smithii and M. sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.},
}
@article {pmid39998243,
year = {2025},
author = {Brochu, HN and Zhang, Q and Song, K and Wang, L and Deare, EA and Williams, JD and Icenhour, CR and Iyer, LK},
title = {Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258224},
doi = {10.1128/spectrum.02582-24},
pmid = {39998243},
issn = {2165-0497},
abstract = {Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.},
}
@article {pmid39998226,
year = {2025},
author = {Martino, C and Kellman, BP and Sandoval, DR and Clausen, TM and Cooper, R and Benjdia, A and Soualmia, F and Clark, AE and Garretson, AF and Marotz, CA and Song, SJ and Wandro, S and Zaramela, LS and Salido, RA and Zhu, Q and Armingol, E and Vázquez-Baeza, Y and McDonald, D and Sorrentino, JT and Taylor, B and Belda-Ferre, P and Das, P and Ali, F and Liang, C and Zhang, Y and Schifanella, L and Covizzi, A and Lai, A and Riva, A and Basting, C and Broedlow, CA and Havulinna, AS and Jousilahti, P and Estaki, M and Kosciolek, T and Kuplicki, R and Victor, TA and Paulus, MP and Savage, KE and Benbow, JL and Spielfogel, ES and Anderson, CAM and Martinez, ME and Lacey, JV and Huang, S and Haiminen, N and Parida, L and Kim, H-C and Gilbert, JA and Sweeney, DA and Allard, SM and Swafford, AD and Cheng, S and Inoyue, M and Niiranen, T and Jain, M and Salomaa, V and Zengler, K and Klatt, NR and Hasty, J and Berteau, O and Carlin, AF and Esko, JD and Lewis, NE and Knight, R},
title = {SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.},
journal = {mBio},
volume = {},
number = {},
pages = {e0401524},
doi = {10.1128/mbio.04015-24},
pmid = {39998226},
issn = {2150-7511},
abstract = {The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract's glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2's spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity in vitro. Moreover, we engineered the common probiotic Escherichia coli Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.},
}
@article {pmid39998220,
year = {2025},
author = {Kwak, Y and Argandona, JA and Miao, S and Son, TJ and Hansen, AK},
title = {A dual insect symbiont and plant pathogen improves insect host fitness under arginine limitation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0358824},
doi = {10.1128/mbio.03588-24},
pmid = {39998220},
issn = {2150-7511},
abstract = {Some facultative bacterial symbionts are known to benefit insects, but nutritional advantages are rare among these non-obligate symbionts. Here, we demonstrate that the facultative symbiont Candidatus Liberibacter psyllaurous enhances the fitness of its psyllid insect host, Bactericera cockerelli, by providing nutritional benefits. L. psyllaurous, an unculturable pathogen of solanaceous crops, also establishes a close relationship with its insect vector, B. cockerelli, increasing in titer during insect development, vertically transmitting through eggs, and colonizing various tissues, including the bacteriome, which houses the obligate nutritional symbiont, Carsonella. Carsonella supplies essential amino acids to its insect host but has gaps in some of its essential amino acid pathways that the psyllid complements with its own genes, many of which have been acquired through horizontal gene transfer (HGT) from bacteria. Our findings reveal that L. psyllaurous increases psyllid fitness on plants by reducing developmental time and increasing adult weight. In addition, through metagenomic sequencing, we reveal that L. psyllaurous maintains complete pathways for synthesizing the essential amino acids arginine, lysine, and threonine, unlike the psyllid's other resident microbiota, Carsonella, and two co-occurring Wolbachia strains. RNA sequencing reveals the downregulation of a HGT collaborative psyllid gene (ASL), which indicates a reduced demand for arginine supplied by Carsonella when the psyllid is infected with L. psyllaurous. Notably, artificial diet assays show that L. psyllaurous enhances psyllid fitness on an arginine-deplete diet. These results corroborate the role of L. psyllaurous as a beneficial insect symbiont, contributing to the nutrition of its insect host.IMPORTANCEUnlike obligate symbionts that are permanently associated with their hosts, facultative symbionts rarely show direct nutritional contributions, especially under nutrient-limited conditions. This study demonstrates, for the first time, that Candidatus Liberibacter psyllaurous, a facultative symbiont and a plant pathogen, enhances the fitness of its Bactericera cockerelli host by supplying an essential nutrient arginine that is lacking in the plant sap diet. Our findings reveal how facultative symbionts can play a vital role in helping their insect hosts adapt to nutrient-limited environments. This work provides new insights into the dynamic interactions between insect hosts, their symbiotic microbes, and their shared ecological niches, broadening our understanding of symbiosis and its role in shaping adaptation and survival.},
}
@article {pmid39998197,
year = {2025},
author = {Sahu, RP and Sar, P},
title = {Metagenome-assembled genomes of acetogenic enrichment obtained from deep subsurface archean granitoids of Koyna Seismogenic Zone, Koyna, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0092224},
doi = {10.1128/mra.00922-24},
pmid = {39998197},
issn = {2576-098X},
abstract = {We report 14 metagenome-assembled genomes (MAGs) of acetogenic bacteria (acetogens) enriched from deep (1,679-2,912 m below surface), hot (55°C-74 °C) granitoids of the Koyna Seismogenic Zone, India. These MAGs include Thermoanaerobacter pseudethanolicus, Exiguobacterium alkaliphilum, Moorella humiferrea, Caldanaerobacter subterraneus, etc. The study allowed access to the genomes of deep biosphere acetogens.},
}
@article {pmid39998193,
year = {2025},
author = {Tobun, OA and Adebusoye, SA and Ilori, MO},
title = {Comparative metagenomic analysis of 16S RNA amplicon sequencing of bacterial population of an industrial site contaminated with halogenated anilines.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085624},
doi = {10.1128/mra.00856-24},
pmid = {39998193},
issn = {2576-098X},
abstract = {Here, we use 16S rRNA gene sequencing to identify bacterial communities in three soil samples from contaminated soils with halogenated anilines and empty soil (serving as control) in Lagos state, Nigeria. BNE, BLB, and BLC had unique operational taxonomic units (OTUs) of 160, 1,797, and 4,815, respectively. Proteobacteria were the dominant phyla across all samples.},
}
@article {pmid39998179,
year = {2025},
author = {Lu, C and Wu, Y and Zhang, Z and Mao, L and Ge, X and Wu, A and Sun, F and Jiang, Y and Peng, Y},
title = {Estimated size of the total genome and protein space of viruses.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068324},
doi = {10.1128/msphere.00683-24},
pmid = {39998179},
issn = {2379-5042},
abstract = {Recent metagenomic studies have identified a vast number of viruses. However, the systematic assessment of the true genetic diversity of the whole virus community on our planet remains to be investigated. Here, we explored the genome and protein space of viruses by simulating the process of virus discovery in viral metagenomic studies. Among multiple functions, the power function was found to best fit the increasing trends of virus diversity and was, therefore, used to predict the genetic space of viruses. The estimate suggests that there are at least 8.23e+08 viral operational taxonomic units and 1.62e+09 viral protein clusters on Earth when assuming the saturation of the virus genetic space, taking into account the balance of costs and the identification of novel viruses. It is noteworthy that less than 3% of the viral genetic diversity has been uncovered thus far, emphasizing the vastness of the unexplored viral landscape. To saturate the genetic space, a total of 3.08e+08 samples would be required. Analysis of viral genetic diversity by ecosystem yielded estimates consistent with those mentioned above. Furthermore, the estimate of the virus genetic space remained robust when accounting for the redundancy of sampling, sampling time, sequencing platform, and parameters used for protein clustering. This study provides a guide for future sequencing efforts in virus discovery and contributes to a better understanding of viral diversity in nature.IMPORTANCEViruses are the most abundant and diverse biological entities on Earth. In recent years, a large number of viruses have been discovered based on sequencing technology. However, it is not clear how many kinds of viruses exist on Earth. This study estimates that there are at least 823 million types of viruses and 1.62 billion types of viral proteins. Remarkably, less than 3% of this large diversity has been uncovered to date. These findings highlight the enormous potential for discovering new viruses and reveal a significant gap in our current understanding of the viral world. This study calls for increased attention and resources to be directed toward viral discovery and metagenomics and provides a guide for future sequencing efforts, enhancing our knowledge of viral diversity in nature for ecology, biology, and public health.},
}
@article {pmid39998061,
year = {2025},
author = {Zhang, S and Zhao, C and Liu, G and Guo, L and Zhang, R and Yan, J and He, J and Guo, C},
title = {Monitoring of Pathogens Carried by Imported Flies and Cockroaches at Shenzhen Ports.},
journal = {Tropical medicine and infectious disease},
volume = {10},
number = {2},
pages = {},
doi = {10.3390/tropicalmed10020057},
pmid = {39998061},
issn = {2414-6366},
support = {2022YFC2302804//National Health Commission Medical Science and Technology development research center/ ; },
abstract = {This study tested the efficacy of xenomonitoring using contaminated flies and cockroaches at ports in Shenzhen by analysing sample data from imported flies and cockroaches from October 2023 to April 2024 to identify the pathogens they carried. Among all the samples of flies and cockroaches collected, Musca domestica vicina and Blattella germanica accounted for the highest proportion, 27.59% and 66.47%, respectively. Their positive rates for carrying Staphylococcus aureus were also the most significant, reaching 4.35% and 6.47%, respectively. The imported flies and cockroaches mainly came from Asia, with the highest proportion coming from Hong Kong, at 97.71% and 92.11%, respectively. Metagenomic sequencing indicated that the pathogens carried by the flies and cockroaches from different regions of Asia were generally similar but showed some differences. Flies from Southeast Asia, East Asia, South Asia, and West Asia and cockroaches from Southeast Asia, East Asia, and West Asia harboured unique opportunistic pathogens capable of causing gastrointestinal and respiratory infections in humans. Specifically, flies carried pathogens such as Campylobacter jejuni, Bacillus anthracis, Bacteroides fragilis, and Bordetella bronchiseptica, while cockroaches carried B. fragilis, Clostridium tetani, and Bacillus cereus. Our findings provide data support for future risk assessments of pathogens carried by imported vectors.},
}
@article {pmid39997957,
year = {2025},
author = {Muhie, S and Gautam, A and Mylroie, J and Sowe, B and Campbell, R and Perkins, EJ and Hammamieh, R and Garcia-Reyero, N},
title = {Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics.},
journal = {Toxics},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/toxics13020142},
pmid = {39997957},
issn = {2305-6304},
abstract = {Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.},
}
@article {pmid39997213,
year = {2025},
author = {Calado, R and Leal, MC and Silva, RXG and Borba, M and Ferro, A and Almeida, M and Madeira, D and Vieira, H},
title = {Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery.},
journal = {Marine drugs},
volume = {23},
number = {2},
pages = {},
doi = {10.3390/md23020089},
pmid = {39997213},
issn = {1660-3397},
support = {UIDB/50017/2020 + UIDP/50017/2020 + LA/P/0094/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; (Project N&#xba;. C644915664-00000026)//"BLUE BIOECONOMY PACT", co-funded by the Next Gen-eration EU European Fund, under the incentive line "Agendas for Business Innovation" within Component 5-Capitalization and Business Innovation of the Portuguese Recovery and Resili-ence Plan (RRP), specifi/ ; },
mesh = {*Anthozoa/metabolism ; Animals ; *Coral Reefs ; *Biological Specimen Banks ; Bioprospecting ; Laboratories ; Humans ; Biological Products ; },
abstract = {Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and this is currently hampered by multiple ethical and technological constraints. Living coral displays, research laboratories, and biobanks currently offer an opportunity to continue to unravel coral chemodiversity, acting as "Noah's Arks" that may continue to support the bioprospecting of molecules of interest. This issue is even more relevant if one considers that tropical coral reefs currently face unprecedent threats and irreversible losses that may impair the biodiscovery of molecules with potential for new products, processes, and services. Living coral displays provide controlled environments for studying corals and producing both known and new metabolites under varied conditions, and they are not prone to common bottlenecks associated with bioprospecting in natural coral reefs, such as loss of the source and replicability. Research laboratories may focus on a particular coral species or bioactive compound using corals that were cultured ex situ, although they may differ from wild conspecifics in metabolite production both in quantitative and qualitative terms. Biobanks collect and preserve coral specimens, tissues, cells, and/or information (e.g., genes, associated microorganisms), which offers a plethora of data to support the study of bioactive compounds' mode of action without having to cope with issues related to access, standardization, and regulatory compliance. Bioprospecting in these settings faces several challenges and opportunities. On one hand, it is difficult to ensure the complexity of highly biodiverse ecosystems that shape the production and chemodiversity of corals. On the other hand, it is possible to maximize biomass production and fine tune the synthesis of metabolites of interest under highly controlled environments. Collaborative efforts are needed to overcome barriers and foster opportunities to fully harness the chemodiversity of tropical corals before in-depth knowledge of this pool of metabolites is irreversibly lost due to tropical coral reefs' degradation.},
}
@article {pmid39995421,
year = {2025},
author = {Freyria, NJ and de Oliveira, TC and Meng, A and Pelletier, E and Lovejoy, C},
title = {Shotgun metagenomics reveals the flexibility and diversity of Arctic marine microbiomes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf007},
pmid = {39995421},
issn = {2730-6151},
abstract = {Polar oceanographic regions are exposed to rapid changes in temperature, salinity, and light fields that determine microbial species distributions, but resilience to an increasingly unstable climate is unknown. To unravel microbial genomic potential of the Northern Baffin Bay's polynya, we constructed eight metagenomes from the same latitude but targeting two sides of Pikialasorsuaq (The North Water) that differ by current systems, stratification, and temperature regimes. Samples from the surface and subsurface chlorophyll maximum (SCM) of both sides were collected 13 months apart. Details of metabolic pathways were determined for 18 bacteria and 10 microbial eukaryote metagenome-assembled genomes (MAGs). The microbial eukaryotic MAGs were associated with the dominant green algae in the Mamiellales and diatoms in the Mediophyceae, which tended to respectively dominate the eastern and western sides of Pikialasorsuaq. We show that microbial community taxonomic and functional signatures were ca. 80% similar at the latitude sampled with only 20% of genes associated with local conditions. From the metagenomes we found genes involved in osmotic regulation, antifreeze proteins, and photosystem protection, with hydrocarbon biodegradation and methane oxidation potential detected. The shared genomic compliment was consistent with adaptation to the Arctic's extreme fluctuating conditions, with implications for their evolutionary history and the long-term survival of a pan-arctic microbiome. In particular, previously unrecognized genetic capabilities for methane bio-attenuation and hydrocarbon metabolism in eukaryotic phytoplankton suggest adaptation to dark conditions that will remain, despite climate warming, in the high latitude offshore waters of a future Arctic.},
}
@article {pmid39995022,
year = {2025},
author = {Thangavel, M and Sneha, MJX and Mani, I and Surendrababu, A and Rajapriya, P and Arulselvan, P and Alarfaj, AA and Thangavelu, I and Pandi, M},
title = {Diversity of Endophytic Fungi in Plant Species: Traditional vs. Metagenomic Approaches.},
journal = {Chemistry &amp; biodiversity},
volume = {},
number = {},
pages = {e202402792},
doi = {10.1002/cbdv.202402792},
pmid = {39995022},
issn = {1612-1880},
abstract = {Plant microbiomes impact plant life, with fungi's unique characteristics influencing classification. Cultivation technologies influence fungal classification, and research links soil fungi with plant hosts. This study utilizes morphological and phylogenetic methods, along with NGS data from ITS2 secondary structure predicted endophytes, to identify plant leaves using both traditional and high-resolution techniques. Various topology of the study site was examined. Recent ecological studies highlight unculturable taxa, or dark taxa, where many species cannot sporulate or be cultured emphasizing the need for metagenomics approaches. The study gathered 68,791 reads from S. auriculata with 101 OTU's, 58,620 from C. spinosa with 219 OTU'S, and 66,087 from Z. mauritiana with 193 OTU's, with the majority of OTUs were related to Colletotrichum (69%) and a minimum of Ustilago (16%). A total of 49 fungal isolates were obtained from traditional methods, while 513 fungal OTU's were retrieved through metagenomic methods, confirming the presence of a highly abundant fungus population in plant samples. The study reveals that using the ITS short amplicon sequencing technique provides distinct insights into endophytic fungal communities in three plant samples. In conclusion, analysing plant fungal components using a combination of culture dependent and culture independent techniques may be a novel strategy.},
}
@article {pmid39994640,
year = {2025},
author = {Wu, J and Qi, Y and Zhang, W and Liu, L and Chen, J and Yang, Y and Zhang, X and Liu, X and Shi, Y},
title = {Metagenomic next-generation sequencing for etiological diagnosis of an unexpected rabies case with unclear exposure history.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {258},
pmid = {39994640},
issn = {1471-2334},
abstract = {BACKGROUND: Rabies is an acute and lethal zoonotic disease caused by the rabies virus (RABV). After onset, there are no effective drugs or treatment methods.<br><br>CASE PRESENTATION: A 49-year-old female from Hefei, Anhui Province, China, presented to a local hospital with fever, pruritus, chest distress, and shortness of breath. During the consultation, the patient exhibited agitation and was later admitted to the intensive care unit (ICU) in the local hospital for endotracheal intubation and mechanical ventilation due to worsened agitation and dyspnea. Cerebrospinal fluid (CSF) and blood samples were collected and pathogenic microorganism identification was performed by culture and mNGS. However, all results were negative. In addition, the patient did not display typical rabies-specific symptoms such as aerophobia, hydrophobia or photophobia from onset to admission. Subsequently, saliva samples were collected for mNGS detection following consultation with experts at our hospital. Nucleic acid sequences uniquely aligned to the rabies virus (RABV) were identified in these samples. The result was further confirmed by local Center for Disease Control and Prevention (CDC) through RT-qPCR which detected part of the N gene of RABV in the saliva sample. The patient was then transferred to the ICU for isolation. Unfortunately, the patient died on the 10th day of admission due to multiple organ failure. The detection of human rabies virus IgG antibodies reported positive during the advanced stage of the disease during the hospitalization. We consistently verified with the patient's family member that there was no clear history of animal bites and no history of RABV vaccination. Furthermore, we performed phylogenetic analysis of partial L and G gene sequences of RABV obtained by mNGS (designated HFG23-L and HFG23-G, respectively), the results showed that both HFG23-L and HFG23-G belonged to the China I lineage, and shared 99.7% similarity with the Fengtai strain isolated from dogs in Beijing.<br><br>CONCLUSIONS: The identification of unique RABV sequence through mNGS in the patient's saliva sample suggested that mNGS could serve as a valuable screening tool for the etiological diagnosis of rabies, especially when timely laboratory testing was unavailable or when patients lacked non-specific prodromal symptom and clear exposure history.},
}
@article {pmid39993154,
year = {2025},
author = {Yang, K and Zhang, L and Ruiz-Valencia, A and Song, X and Vogel, TM and Zhang, X},
title = {Heterogeneity in the Composition and Catabolism of Indigenous Microbiomes in Subsurface Soils Cocontaminated with BTEX and Chlorinated Aliphatic Hydrocarbons.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10071},
pmid = {39993154},
issn = {1520-5851},
abstract = {The effectiveness of in situ bioremediation can be affected by an insufficient understanding of high site/soil heterogeneity, especially in cocontaminated soils and sediments. In this study, samples from multiple locations within a relatively small area (20 × 20 m[2]) contaminated with benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) were compared to examine their physicochemical and microbial properties. Unsupervised clustering analysis of 16S rRNA gene amplicon and metagenome shotgun sequencing data indicates that the indigenous community differentiated into three distinct patterns. In Cluster 1, Pseudomonas, with multiple monooxygenases and glutathione S-transferase (GST), was enriched in samples contaminated with high concentrations of BTEX and CAHs. Cluster 2 contained a high fraction of cometabolic degraders. Cluster 3 was dominated by Ralstonia and organohalide-respiring bacteria (OHRBs) mediating the reductive dechlorination of CAHs. Significant differences in composition and function among microbiomes were attributed to the differential distribution of organic pollutants, even in such a small area. Incorporating genomic features with physicochemical data can significantly enhance the understanding of the heterogeneities in soil and their impacts on microbial communities, thereby providing valuable information for the optimization of bioremediation strategies.},
}
@article {pmid39992229,
year = {2025},
author = {Bai, Z and Zhang, YZ and Pang, Y and Imoto, S},
title = {PharaCon: A new framework for identifying bacteriophages via conditional representation learning.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf085},
pmid = {39992229},
issn = {1367-4811},
abstract = {MOTIVATION: Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. However, these models are typically pre-trained with self-supervised tasks that do not consider label variance in the pre-training data. This presents a challenge for phage identification as pre-training on mixed bacterial and phage data may lead to information bias due to the imbalance between bacterial and phage samples.<br><br>RESULTS: To overcome this limitation, we proposed a novel conditional BERT framework that incorporates label classes as special tokens during pre-training. Specifically, our conditional BERT model attaches labels directly during tokenization, introducing label constraints into the model's input. Additionally, we introduced a new fine-tuning scheme that enables the conditional BERT to be effectively utilized for classification tasks. This framework allows the BERT model to acquire label-specific contextual representations from mixed sequence data during pre-training and applies the conditional BERT as a classifier during fine-tuning and we named the fine-tuned model as PharaCon. We evaluated PharaCon against several existing methods on both simulated sequence datasets and real metagenomic contig datasets. The results demonstrate PharaCon's effectiveness and efficiency in phage identification, highlighting the advantages of incorporating label information during both pre-training and fine-tuning.<br><br>AVAILABILITY: The codes of PharaCon are now available in: https://github.com/Celestial-Bai/PharaCon.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid39992148,
year = {2025},
author = {Fang, J and Chen, H and Hamal, K and Liu, D},
title = {CD86 immunohistochemical staining for the detection of Talaromyces marneffei in lesions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0206324},
doi = {10.1128/spectrum.02063-24},
pmid = {39992148},
issn = {2165-0497},
abstract = {Talaromycosis is an invasive fungal disease caused by the pathogenic thermodimorphic fungus Talaromyces marneffei (TM), which is often overlooked in tropical and subtropical regions of Asia. In view of the diversity of clinical manifestations in patients with TM infection, early diagnosis remains challenging. We assessed the sensitivity and specificity of a novel immunohistochemical staining by performing CD86 immunohistochemical staining on 56 tissue sections from patients with talaromycosis who had fungal culture or metagenomic next-generation sequencing confirmed to exist in clinical specimens, as well as 26 patients with other fungi that had been culture-proven. Hematoxylin and eosin and periodic acid Schiff (PAS) stains were also applied to each specimen. We found that anti-CD86 antibody can label TM pathogens in 38 HIV-negative specimens (38/42) and 14 HIV-positive specimens (14/14); conversely, PAS staining yielded positive results in seven cases of HIV-negative specimens (7/42) and 13 cases of HIV-positive specimens (13/14). Additionally, CD86 immunohistochemical staining was negative in other fungi. Importantly, CD86 immunohistochemical staining significantly outperformed PAS staining in terms of localizing and highlighting TM yeasts, as well as demonstrating the specificity of 100% and a significantly higher sensitivity compared to PAS staining at 92.9% versus 35.7% (P < 0.05, McNemar test). Our findings suggest that CD86 immunohistochemical staining has the potential for the rapid diagnosis of talaromycosis.IMPORTANCETalaromycosis is an opportunistic endemic disease without typical clinical manifestations that has emerged as a fungal disease impacting the survival and mortality of immunocompromised individuals and HIV-positive individuals in endemic regions. Nonetheless, talaromycosis is completely curable if it is accurately diagnosed and treated effectively at an early stage. Rapid pathological diagnosis relies on the unique morphological features of Talaromyces marneffei observed under the microscope. This study introduces a novel pathological diagnostic approach, CD86 immunohistochemical staining, to enhance the early detection of TM-infected lesions.},
}
@article {pmid39992132,
year = {2025},
author = {Rodríguez-Ramos, J and Sadler, N and Zegeye, EK and Farris, Y and Purvine, S and Couvillion, S and Nelson, WC and Hofmockel, KS},
title = {Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0161624},
doi = {10.1128/msystems.01616-24},
pmid = {39992132},
issn = {2379-5077},
abstract = {Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.},
}
@article {pmid39992097,
year = {2025},
author = {Salamzade, R and Kalan, LR},
title = {Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0153824},
doi = {10.1128/msystems.01538-24},
pmid = {39992097},
issn = {2379-5077},
abstract = {Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over the past decade have advanced our understanding of both microbial pangenomes and BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis of BGCs, including delineation of BGC boundaries and clustering of BGCs across genomes. We further summarize key findings from microbial comparative genomics studies on BGC conservation across taxa and habitats and discuss the potential fitness effects of BGCs in different settings. Afterward, recent research showing the importance of genomic context on the production of secondary metabolites and the evolution of BGCs is highlighted. These studies draw parallels to recent, broader, investigations on gene-to-gene associations within microbial pangenomes. Finally, we describe mechanisms by which microbial pangenomes and BGCs evolve, ranging from the acquisition or origination of entire BGCs to micro-evolutionary trends of individual biosynthetic genes. An outlook on how expansions in the biosynthetic capabilities of some taxa might support theories that open pangenomes are the result of adaptive evolution is also discussed. We conclude with remarks about how future work leveraging longitudinal metagenomics across diverse ecosystems is likely to significantly improve our understanding on the evolution of microbial genomes and BGCs.},
}
@article {pmid39991711,
year = {2025},
author = {Lin, T},
title = {Editorial: New techniques in microbiome research - volume II: Host-microbiome interactions using 'meta-omics' techniques.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1541881},
pmid = {39991711},
issn = {2235-2988},
}
@article {pmid39991687,
year = {2025},
author = {Pan, Y and Jiao, FY},
title = {Helicobacter pylori infection and gastric microbiota: Insights into gastric and duodenal ulcer development.},
journal = {World journal of gastroenterology},
volume = {31},
number = {7},
pages = {100044},
pmid = {39991687},
issn = {2219-2840},
mesh = {Humans ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/isolation &amp; purification/genetics/pathogenicity ; *Duodenal Ulcer/microbiology ; *Gastrointestinal Microbiome ; *Stomach Ulcer/microbiology ; *Gastric Mucosa/microbiology/pathology ; Metagenomics/methods ; Stomach/microbiology/pathology ; Dysbiosis/microbiology ; },
abstract = {Helicobacter pylori (H. pylori) infection plays a critical role in gastric diseases, impacting the microbiota structure in gastric and duodenal ulcers. In their study, Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls, revealing significant changes in microbial diversity and composition. This article reviews their findings, emphasizing H. pylori's role in gastric ulcers and the need for further research on its impact on duodenal ulcers. We evaluate the study's strengths and limitations, suggesting future research directions to enhance our understanding of H. pylori's contribution to ulcerative diseases.},
}
@article {pmid39991683,
year = {2025},
author = {Darnindro, N and Abdullah, M and Sukartini, N and Rumende, CM and Pitarini, A and Nursyirwan, SA and Fauzi, A and Makmun, D and Nelwan, EJ and Shatri, H and Rinaldi, I and Tanadi, C},
title = {Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.},
journal = {World journal of gastroenterology},
volume = {31},
number = {7},
pages = {100051},
pmid = {39991683},
issn = {2219-2840},
mesh = {Humans ; Indonesia/epidemiology ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; *Colonoscopy ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; Metagenomics/methods ; Bacteria/isolation &amp; purification/genetics/classification ; },
abstract = {BACKGROUND: Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide. Several studies have shown an association between gut microbiota and colorectal cancer. Gut microbiota is unique and can be influenced by geographic factors and habits. This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.<br><br>AIM: To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.<br><br>METHODS: This case-control study included 59 subjects (35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr. Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital. Microbiota examination was performed using 16S rRNA sequencing. Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs (Oxford Nanopore Technologies platform).<br><br>RESULTS: Patients with colorectal cancer had a higher median index value on the Shannon index (3.28 vs 2.82, P > 0.05) and a lower value on the Simpson index (0.050 vs 0.060, P > 0.05). Significant differences in beta diversity were observed at the genus (P = 0.002) and species levels (P = 0.001). Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the dominant phyla. The genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found more frequently in colorectal cancer, while Faecalibacterium, Haemophilus, and Phocaeicola were more frequently found in non-colorectal cancer. The relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Enterococcus faecalis, Campylobacter hominis, and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer. Meanwhile, Faecalibacterium prausnitzii, Faecalibacterium duncaniae, and Prevotella copri were more commonly found in non-colorectal cancer.<br><br>CONCLUSION: Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer. This study was reviewed and approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia (No. KET-1517/UN2.F1/ETIK/PPM.00.02/2023).},
}
@article {pmid39991100,
year = {2025},
author = {Bajinka, O and Ouedraogo, SY and Li, N and Zhan, X},
title = {Multiomics as instrument to promote 3P medical approaches for the overall management of respiratory syncytial viral infections.},
journal = {The EPMA journal},
volume = {16},
number = {1},
pages = {217-238},
pmid = {39991100},
issn = {1878-5077},
abstract = {Respiratory syncytial viral (RSV) infection is a leading persisting pulmonary disease-causing agent. It causes loss of lives especially among infants, old ages, and adults immunocompromised individuals. This viral pathogen infects children more especially those under the age of 2 and may lead to death. It causes 3 million hospitalizations and up to 60,000 deaths annually for under the age of 5. The most vulnerable are immunocompromised individuals and asthmatic children with suboptimal antiviral defenses. It is associated with bronchiolitis, pneumonia, and bronchopneumonia. Despite all the current interventions and clinical trials, the only available therapeutic strategies for this viral infection are palliative care. Therefore, it is imperative to understand the pathogenicity of RSV and the corresponding host immune response to depict a sort of a targeted intervention. With the increasingly cutting-edge methods in harnessing the pathogenicity of this viral infection, high throughput systems including omics technological advances are at the spotlight. For instance, the associated genes with RSV complications for the host, the set of microbiome identified as operational taxonomic unit, the upregulated or downregulated metabolites, the protein subtypes, and the small molecules can help explain the viral microenvironment. Moreover, these big data will lead to RSV patients' stratification through individualized patient profiles that will bring in targeted prevention and treatment algorithms tailored to individualized patients' profiles. Through this, the virus and host interactions based on the pathogenicity of infection will provide a strong ground for depicting the prevention, prediction, and personalized medicine (3PM) for RSV. The 3PM approach brought cutting edge functional medicine to the healthcare givers, thus conferring targeted prevention and precision medicine while observing personalized treatment as well as preventive regularities. The viral replication mechanisms against the host defense mechanisms are crucial for the development of safe and effective therapy. Integrative personal omics profiles, whose analysis is based on the combined proteomics, transcriptomics, genomics, proteoformics, metabolomics, and autoantibody profiles, are very robust for predicting the risk of RSV infection. The targeted prevention will emerge from the patient stratification when the diagnosis is accurately predicted. In addition, the personalized medical services will give an effective prognostic assessment for RSV complications.},
}
@article {pmid39990777,
year = {2025},
author = {Zhu, X and Cao, L and Wang, J and Lu, X and Huang, Z and Wen, X and Bian, L and Wu, C and Zou, M},
title = {Identification of Pathogens in HIV-Infected Patients Using Metagenomic Next-Generation Sequencing (mNGS) as Compared to Conventional Microbiological Tests (CMTs).},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {929-940},
pmid = {39990777},
issn = {1178-6973},
abstract = {BACKGROUND: The rapid and accurate identification of infectious pathogens in HIV-infected patients remains a challenge. Metagenomic next-generation sequencing (mNGS) is a panpathogen assay for rapid diagnosis of infectious diseases. Here, the diagnostic value of mNGS was evaluated in HIV-infected patients and compared with conventional microbiological tests (CMTs).<br><br>METHODS: This study was conducted on 216&#xa0;hIV-infected patients with suspected opportunistic infections. Infectious pathogen detection was done by mNGS and conventional microbiological tests, respectively.<br><br>RESULTS: A total of 195 patients (90.2%) were positive for microbial pathogens by mNGS, while 135 patients (62.5%) were positive for microbial pathogens by CMTs. Mixed infection was identified in 92 patients by mNGS, and 41 patients were detected with mixed infection by CMTs. Fungi and virus mixed infection was the most frequent pattern detected by mNGS (32, 14.8%) and CMTs (22, 10.2%). The CD4+ T cell count in patients with mixed pathogens was significantly lower than that in patients infected with a single pathogen. Pathogens were quickly identified by mNGS in 151 patients (69.9%), and appropriate treatments were initiated. In 47 patients antibacterial agents were adjusted based on mNGS results, in 39 patients antifungal agents were changed, and 35 patients had antiviral agents added.<br><br>CONCLUSION: mNGS is a valuable tool and enhances rapid microbiological identification in HIV-infected patients. Combined with CMTs, mNGS may facilitate personalized antimicrobial treatment strategies and increase survival.},
}
@article {pmid39990197,
year = {2025},
author = {Cheng, H and Li, H and Zhao, Y and Yang, K and Wang, J and Tan, B and Ma, X},
title = {Transcriptome analysis reveals modulations in glycosylation profiles of the mucosal barrier and their potential interaction with gut microbiota in weaned piglets.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {20},
number = {},
pages = {226-238},
pmid = {39990197},
issn = {2405-6383},
abstract = {The current study aims to investigate the potential interaction between glycosylation profiles of the Ningxiang breed (NX) and Western Duroc × Landrace × Yorkshire breed (DLY) weaned piglets, and their characteristic microbes, employing integrated analyses of transcriptomics and metagenomics. Twenty-four (12 NX and 12 DLY) at 28 days of age were transported into an experimental house and fed the same weaned piglet diet. The trail period was 7 days. Results revealed that the NX piglets had a higher growth-to-feed ratio, body weight gain scale, and lower pathological score of intestinal injury compared with the DLY piglets (P < 0.01). DLY piglets displayed elevated mRNA expression levels of MUC2 and MUC5AC in colonic mucosal tissue than NX piglets (P < 0.05). Within the O-linked glycosylated differentially expressed genes (DEGs), FNTA, GALNT18, POMGNT1, POMGNT2, and POMT1 were significantly upregulated in DLY piglets relative to NX piglets (P < 0.05). Conversely, C1GALT2, GALNT1, KMT2C, and OGT were significantly downregulated in DLY piglets compared to NX piglets (P < 0.05). The KMT2C gene was hardly expressed in the transcriptome of DLY piglets. At the phylum taxonomic level, NX piglets had a higher abundance of Firmicutes, while DLY piglets had a higher abundance of Proteobacteria. At the genus taxonomic level, NX piglets had a higher abundance of Lactobacillus, whereas DLY piglets had a higher abundance of Collinsella, Enterococcus and Escherichia. The results of the correlation between intestinal differential bacteria and O-chain glycosylated DEG showed that C1GALT2, GALNT1 and KMT2 were associated with Lactobacillus_pontis showed a positive correlation (R = 0.67). Through comparative analysis of differentially glycosylated genes and their associated functions, this study highlights the potential role of reduced expression of GALNT1 and KMT2C genes, involved in O-linked protein and glycan reactions, in impairing the intestinal barrier function of DLY piglets. Furthermore, members of the Lactobacillus and Prevotella genera may actively contribute to the regulation of piglet colon glycosylation profiles.},
}
@article {pmid39990142,
year = {2025},
author = {Rodriguez, P and Berg, JS and Deng, L and Vogel, H and Okoniewski, M and Lever, MA and Magnabosco, C},
title = {Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1504355},
pmid = {39990142},
issn = {1664-302X},
abstract = {Most of our knowledge of deep sedimentary life comes from marine environments; however, despite their relatively small volume, lacustrine sediments constitute one of the largest global carbon sinks and their deep sediments are largely unexplored. Here, we reconstruct the microbial functional and taxonomic composition of an 8,000-year Holocene sedimentary succession from meromictic Lake Cadagno (Switzerland) using shotgun metagenomics and 16S rRNA gene amplicon sequencing. While younger sediments (<1,000 years) are dominated by typical anaerobic surface sedimentary bacterial taxa (Deltaproteobacteria, Acidobacteria, and Firmicutes), older layers with lower organic matter concentrations and reduced terminal electron acceptor availability are dominated by taxa previously identified as "persistent populations" within deep anoxic marine sediments (Candidatus Bathyarchaeia, Chloroflexi, and Atribacteria). Despite these dramatic changes in taxonomic community composition and sediment geochemistry throughout the sediment core, higher-order functional categories and metabolic marker gene abundances remain relatively consistent and indicate a microbial community capable of carbon fixation, fermentation, dissimilatory sulfate reduction and dissimilatory nitrate reduction to ammonium. As the conservation of these metabolic pathways through changes in microbial community compositions helps preserve the metabolic pathway connectivity required for nutrient cycling, we hypothesize that the persistence of these functional groups helps enable the Lake Cadagno sedimentary communities persist amidst changing environmental conditions.},
}
@article {pmid39990124,
year = {2025},
author = {Carpenter, RE and Almas, S and Tamrakar, VK and Sharma, R},
title = {Dataset for comparative analysis of precision metagenomics and traditional methods in urinary tract infection diagnostics.},
journal = {Data in brief},
volume = {59},
number = {},
pages = {111339},
pmid = {39990124},
issn = {2352-3409},
abstract = {This study presents a comprehensive dataset comparing three diagnostic methodologies-microbial culture, polymerase chain reaction (PCR), and precision metagenomics (precision metagenomics)-for the detection and classification of uropathogens in urine samples from patients with suspected urinary tract infections (UTIs). While microbial culture remains the gold standard for UTI diagnosis, it has limitations in sensitivity, particularly for fastidious or non-culturable microorganisms. PCR offers higher sensitivity but is restricted to pre-targeted organisms, limiting its diagnostic range. Precision Metagenomics, a target-agnostic sequencing method, provides a more inclusive approach by enabling the identification of a broad spectrum of pathogens, including bacteria, viruses, fungi, and parasites, without prior knowledge of the organisms. The dataset includes 47 urine samples, each analyzed by microbial culture, PCR, and precision metagenomics, followed by bioinformatic classification using the Explify® platform. precision metagenomics identified significantly more uropathogens (62 distinct organisms) compared to PCR (19 organisms) and microbial culture (13 organisms), with 98 % of samples testing positive for polymicrobial infections via precision metagenomics. The precision metagenomics method demonstrated superior diagnostic yield by detecting pathogens that were missed by both microbial culture and PCR, particularly in culture-negative and PCR-negative cases. This dataset holds substantial reuse potential for further research into the microbiome of urinary tract infections, pathogen discovery, antimicrobial resistance studies, and the development of more accurate diagnostic models for UTI management. By offering insights into both polymicrobial infections and rare pathogens, this dataset supports the advancement of diagnostic strategies for complex and chronic UTIs.},
}
@article {pmid39989955,
year = {2025},
author = {Cronin, P and Siegers, J and Heang, V and Tok, S and Sin, S and Sievers, B and Omondi, V and Nuon, S and Chhel, K and Nouhin, J and Chim, V and Seng, B and Hak, M and San, S and Tum, S and Claes, F and Firth, C and Su, Y and Smith, G and Karlsson, E},
title = {Air sampling accurately captures circulating zoonotic viral diversity emerging from poultry live-animal markets.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5682962/v1},
pmid = {39989955},
issn = {2693-5015},
abstract = {Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose threats to humans (1) but has not been utilized for zoonotic agents. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission (2). Traditional sampling strategies are time-consuming, expensive, threaten animal welfare and have significant occupational biosafety risks. In this study, we assessed the performance of metagenomics on environmental samples (ES) compared to traditional poultry swabs for detecting avian viral pathogens in LBMs in Cambodia. ES, including air, cage swabs, and carcass wash water, were collected alongside throat and cloacal swabs from domestic chickens and ducks across twelve sampling visits in two LBMs over a 15-month period. Viral nucleic acids were extracted and sequenced using a capture probe-based metagenomics approach. Our results show that metagenomics on ES outperformed traditional poultry samples in detecting the highly pathogenic Influenza A/H5N1, including circulating clades 2.3.4.4b and 2.3.2.1c, which were found in the environment but missed by poultry swabs on multiple occasions. Environmental metagenomics was also highly sensitive in the detection of over 40 other viruses from key pathogen families such as Astroviridae , Coronaviridae , Picornaviridae , and Retroviridae . Viral contigs from ES showed high similarity to those from poultry swabs further highlighting the accuracy of this approach. Our findings highlight metagenomics on ES can precisely and effectively replicate metagenomic results from traditional surveillance samples, offering broader coverage and enhanced detection of avian pathogens. This robust approach could be pivotal for mitigating zoonotic spillover, controlling pathogen transmission at LBMs, and enhancing pandemic preparedness strategies.},
}
@article {pmid39988326,
year = {2025},
author = {Zheng, X and Zou, W and Zou, S and Ye, J and Bao, Z and Song, Y},
title = {Diagnostic Significance of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Suspected Pulmonary Infection.},
journal = {Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imm.13911},
pmid = {39988326},
issn = {1365-2567},
support = {2020J11134//Science and Technology Projects of Fujian Province/ ; },
abstract = {Immunocompromised hosts are highly vulnerable to lung infections, but the efficacy of traditional diagnosis is unsatisfactory. Metagenomic next-generation sequencing (mNGS) has high throughput and broad coverage. Its value in different types of immunocompromised patients has yet to be fully explored. Therefore, the study aims to evaluate the value of mNGS in immunocompromised patients. Clinical data from immunocompromised patients with suspected pulmonary infection (PI) (September 2018-2021) were retrospectively analysed. Patients were categorised into PI (87 cases) and non-pulmonary infection (NPI, 14 cases) groups. The diagnostic performance between mNGS and conventional microbiological tests (CMTs) was compared. Subgroup analyses were also conducted based on whether the patients received organ transplantation, including the comparison of the diagnostic performance of mNGS and culture and the spectrum of characteristics among them. mNGS demonstrated significantly elevated diagnostic sensitivity (p < 0.001) over traditional methods, with a pronounced advantage in identifying mixed PIs (p < 0.05). Among immunocompromised cohorts, mNGS outperformed cultures, showing higher positivity rates in both organ transplant (p < 0.001) and non-transplant patients (p < 0.001). Mixed infections, predominantly bacterial-fungal, were more prevalent in transplant recipients with reduced lymphocytes and CD4[+] T cells. Pathogen profiles differed, with Pneumocystis jirovecii, Cytomegalovirus, and Pseudomonas aeruginosa predominating in organ transplant recipients, and P. jirovecii, P. aeruginosa, Streptococcus pneumoniae and Streptococcus pallidum in non-transplant individuals. mNGS is valuable in diagnosing PI and mixed infections in immunocompromised patients, which may be particularly suitable for identifying mixed infections in patients with organ transplants and low lymphocyte and CD4[+] T lymphocyte counts.},
}
@article {pmid39988254,
year = {2025},
author = {Hou, W and Yu, J and Shi, H and Xu, J and Chen, SS and Shaban, SS and Kim, Y and Bai, J},
title = {As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125903},
doi = {10.1016/j.envpol.2025.125903},
pmid = {39988254},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) and pathogenic bacteria pose significant challenges to human health, and hydrodynamic processes complicate their transmission mechanisms in lake ecosystems, particularly in tropical regions. Lake Victoria supports abundant water resources and provides livelihoods for millions of people, yet the environmental behavior of ARGs and pathogenic bacteria remains unclear. Herein, the novel insights into the co-occurrence patterns and transmission mechanisms of ARGs and pathogenic bacteria in Lake Victoria was investigated via molecular techniques and a hydrodynamic model. The results showed that as a large reservoir of ARGs and pathogenic bacteria, a total of 172 ARG subtypes and 93 pathogenic bacteria were identified in Lake Victoria. ARGs were spread through mobile genetic elements (tnpA4 and int2), enhancing the antibiotic resistance and virulence factors (secretion systems, regulatory factors, and toxins) of various pathogenic bacteria. The hydrodynamic model indicated that surface wind-driven currents and bottom compensatory flows shaped the outward dispersion of ARGs and pathogenic bacteria from the gulf. The NCM model suggested that water exchange accelerated the diffusion of antibiotics and pathogens, likely enhancing the deterministic assembly process of ARGs and the stochastic assembly process of pathogens. The PLS-PM model revealed that hydrodynamics directly influenced the accumulation of ARGs and pathogenic bacteria, and subsequently affected the diffusion and distribution patterns of ARGs and pathogens by facilitating the propagation of MGEs. Our study overcomes the limitations associated with lake and microenvironmental scale, providing insights and understanding into the transmission mechanisms of ARGs and pathogenic bacteria.},
}
@article {pmid39987875,
year = {2025},
author = {Pourrostami Niavol, K and Andaluri, G and Achary, MP and Suri, RPS},
title = {How does carbon to nitrogen ratio and carrier type affect moving bed biofilm reactor (MBBR): Performance evaluation and the fate of antibiotic resistance genes.},
journal = {Journal of environmental management},
volume = {377},
number = {},
pages = {124619},
doi = {10.1016/j.jenvman.2025.124619},
pmid = {39987875},
issn = {1095-8630},
abstract = {With the spread of antibiotic resistance genes (ARGs) in the environment, monitoring and controlling ARGs have become an emerging issue of concern in biological processes. Moving bed biofilm reactors (MBBR) have been gaining attention for application in wastewater treatment. Since the performance of MBBR depends on operational parameters and biocarriers, selection of suitable biocarriers and start-up conditions are vital for efficiency of MBBRs. This study investigates the effects of different carbon-to-nitrogen (C/N) ratios and carrier types on the fate of selected ARGs and microbial communities in four MBBR systems using two conventional (K3 and sponge biocarrier (SB)) and two modified carriers (Fe-Ca@SB and Ze-AC@SB). Results showed that the modified biocarriers achieved higher NH4-N removal and better simultaneous nitrification and denitrification (SND) performance (90%) at C/N of 20. However, as the C/N ratio decreased to 10 and 7, the performance of all bioreactors was approximately similar. Moreover, COD removal of 90% was achieved in all reactors regardless of C/N ratio and carrier type. Further studies on the fate of selected ARGs (tetA, blaTEM, ampR) showed that the C/N ratio could affect the abundance of target ARGs, especially for K3 biocarrier, with tetA being the most abundant gene. Also, as the C/N ratio decreased, intl1 was enriched using K3 and SB. However, for Ze-AC@SB, the increase in the abundance of ARGs and intl1 was the lowest making it a reliable carrier not only in MBBR performance but in the control of ARGs. Metagenomic studies showed that the C/N ratio and carrier type could alter the diversity and structure of the bacterial communities in different MBBR systems, with Proteobacteria being the most abundant phylum in all four systems.},
}
@article {pmid39987826,
year = {2025},
author = {Liu, Y and Chen, H and Liu, C and Wang, R and Zhang, Z},
title = {Effects and mechanisms of reclaimed water irrigation and tillage treatment on the propagation of antibiotic resistome in soil.},
journal = {The Science of the total environment},
volume = {968},
number = {},
pages = {178935},
doi = {10.1016/j.scitotenv.2025.178935},
pmid = {39987826},
issn = {1879-1026},
abstract = {Reclaimed water irrigation can alleviate water resource pressure, while soil tillage is a common agricultural practice to increase crop yield. However, both of these practices may lead to the propagation of antibiotic resistance genes (ARGs). To date, there has been little research that has systematically investigated this issue. To fill this gap, this study has conducted microcosmic experiments to reveal the effect and mechanisms of using reclaimed water for irrigation and tillage treatment on the propagation of ARGs in soil, by utilizing high-throughput sequencing-based metagenomic assembly analysis approaches. The results showed irrigation significantly enhanced the abundance and diversity of ARGs in the soil. Compared to the initial soil, the total coverage of ARGs in the irrigated soil increased by 14.0 % (without tillage) to 22.7 % (with tillage). In particular, tillage treatment facilitated the enhancement of antibiotic resistome in the environment. The analysis with null model suggested soil tillage enabled ecological drift (52.4 %-66.7 %) to dominate the ARGs. Quantitative source apportionment using a machine learning-based microbial source tracking tool showed the irrigation exhibited considerable effect on the ARGs in the soil, with an average contribution of about 13.3 %-17.0 %. Network analysis revealed a close association of ARGs with mobile genetic elements (MGEs) and virulence factors, indicating potential dissemination risk of ARGs in the soil. Microbial communities, MGEs, and environmental factors collectively shaped the ARGs in the environment. Relatively, soil tillage enhanced the complex and stability of network structure and led to the colonization of ARGs in modular manner, resulting in higher contribution of ecological drift to soil resistome. Findings of this study will contribute to the management of resistome risks in reclaimed water utilization and agricultural activities for protecting soil ecosystem safety and public health.},
}
@article {pmid39987648,
year = {2025},
author = {Zampieri, A and Carraro, L and Mohammadpour, H and Rovere, GD and Milan, M and Fasolato, L and Cardazzo, B},
title = {Presence and characterization of the human pathogenic Vibrio species in the microbiota of Manila clams using cultural and molecular methods.},
journal = {International journal of food microbiology},
volume = {433},
number = {},
pages = {111113},
doi = {10.1016/j.ijfoodmicro.2025.111113},
pmid = {39987648},
issn = {1879-3460},
abstract = {The North Adriatic lagoons and the Po River Delta are important areas for farming Manila clams (Ruditapes philippinarum). These areas have been heavily impacted by climate change, reducing livestock numbers and increasing pathogen spread. Shellfish, particularly clams, are primary vectors for Vibrio pathogens affecting humans. In this study, the occurrence of human pathogenic Vibrio species on Manila clams was investigated using an integrated approach that combined culture-dependent and culture-independent techniques. Samples were collected over three years from farming areas in the northeastern Adriatic lagoons and the Po River Delta, regions seriously impacted by climate change and pollution. In this study, species of the human pathogen Vibrio were analyzed in the clam microbiota and characterized using recA-pyrH metabarcoding and shotgun metagenomics. Human pathogenic Vibrio species were widespread in the clam microbiota, especially in summer, demonstrating that the environmental conditions on the northern Adriatic coasts allowed the growth of these bacteria. V. parahaemolyticus and V. vulnificus were also quantified using qPCR in <50 % of summer samples Shotgun metagenomics revealed the similarity of V. parahaemolyticus strains to other worldwide genomes, enabling improved pathogen identification and tracking. In the future, climate change could cause these conditions to become even more favorable to these bacteria, potentially increasing pathogen spread. Consequently, enhanced monitoring and control of both the environment and seafood products should be planned to ensure food safety.},
}
@article {pmid39987284,
year = {2025},
author = {Barcan, AS and Humble, JL and Kasaragod, S and Sajib, MSI and Barcan, RA and McGinnity, P and Welch, TJ and Robertson, B and Vamanu, E and Bacigalupo, A and Llewellyn, MS and Samsing, F},
title = {Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {18},
pmid = {39987284},
issn = {2524-4671},
support = {H.G. no. 118/2023.//Agency for Student Loans and Scholarships/ ; H.G. no. 118/2023.//Agency for Student Loans and Scholarships/ ; BB/T016280/1//BBSRC/ ; },
abstract = {BACKGROUND: The development, progression, and dissemination of antimicrobial resistance (AMR) are determined by interlinked human, animal, and environmental drivers, which pose severe risks to human and livestock health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. In addition to the judicious use and implementation of stewardship programs, mitigating the spread of antibiotic resistance requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long-term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistent (MDR) plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture.<br><br>RESULTS: Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors simulating the teleost gut, which were developed for the SalmoSim gut system. The model system was then inoculated with the Escherichia coli strain ATCC 25922 carrying the plasmid pM07-1 and treated with florfenicol at a concentration of 150&#xa0;mg/L in fish feed media for 5 days prior to the washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including those involving gram-negative and gram-positive taxa, and, crucially, the transfer and persistence of the plasmid continued once florfenicol treatment was withdrawn.<br><br>CONCLUSIONS: Our findings highlight the role of the commensal teleost gut flora as a reservoir for AMR even once antimicrobial selective pressure has been withdrawn. Our system also provides a model to study how different treatment regimens and interventions may be deployed to mitigate AMR persistence.},
}
@article {pmid39986751,
year = {2025},
author = {Wang, C and Zhao, J and Zhao, W and Xue, L and Chen, Y and Tian, J and Wang, H and Ji, X and Tian, X and Zhang, J and Gu, Y},
title = {A comparative study of the composition of microorganisms and metabolites in different β-casein genetic types of dairy cows based on metagenomics and non-targeted metabolomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {204},
number = {},
pages = {115859},
doi = {10.1016/j.foodres.2025.115859},
pmid = {39986751},
issn = {1873-7145},
mesh = {Animals ; Cattle ; *Caseins/metabolism ; *Metabolomics ; *Metagenomics ; Female ; Rumen/microbiology/metabolism ; Gastrointestinal Microbiome ; Milk/microbiology ; Bacteria/metabolism/classification/genetics ; Genotype ; },
abstract = {β-Casein is the main component of cow's milk protein, with A1 and A2 β-casein being the most common. Of these, A1 β-casein hydrolysate produces BCM-7, which can cause lactose intolerance, while A2 β-casein milk is more gentle on the gut. However, there is limited research on the composition of rumen microbiota, metabolites, and host metabolites in different genotype cows using metagenomics and metabolomics. In this study, we used multi-omics analysis techniques to perform enrichment analysis of differential metabolites, identifying three key metabolic pathways in all three groups: Arachidonic acid metabolism and Tryptophan metabolism. The metabolites in these pathways exhibited unique metabolic characteristics within each group. We then used random forests and ROC to predict key metabolites in these pathways, identifying that the signature metabolites in the A2A2 group were predominantly anti-inflammatory substances, including 12-HETE, PGD2-4d, and Arachidonic Acid. The signature metabolites in the A1A2 group and A2A2 group were Indoleacetaldehyde. The AUC of these signature metabolites was greater than 0.85. Macrogenic linear discriminant analysis (LDA > 2.5) found that the microorganisms with greater contribution were concentrated in the A2A2 group. Compared with the other two groups, g_Bacteroides and g_Parabacteroides were mainly enriched in the A1A2 group. In group A2A2, g_Xanthomonas and g_Acetobacter are mainly enriched. Then, the key microorganisms in A1A2 group were identified by correlation analysis as g_Bacteroides and g_Parabacteroides. The key microorganisms in group A2A2 were g_Acetobacter, g_Xanthomonas and g_Mannheimia, which were consistent with the results of LEfSe analysis. These microorganisms mainly affect the degradation of fiber in the diet, host metabolism and the occurrence of inflammation. In conclusion, our results provide theoretical basis and data support for the study of dairy cows with different genotypes of β-casein, and help to determine the potential biological functions of different genotypes of casein in dairy products and their effects on human health.},
}
@article {pmid39986132,
year = {2025},
author = {Ren, L and Liu, Z and Wang, J and Su, Y},
title = {Mixed fungal infection of Actinomucor elegans and Aspergillus fumigatus in a person with severe fever with thrombocytopenia syndrome.},
journal = {Diagnostic microbiology and infectious disease},
volume = {112},
number = {1},
pages = {116750},
doi = {10.1016/j.diagmicrobio.2025.116750},
pmid = {39986132},
issn = {1879-0070},
abstract = {In this report, a 69-year-old man with fever, thrombocytopenia, and hepatic and renal dysfunction presented to our hospital. His disease progression was rapid, and he became unconscious. The patient was diagnosed with severe fever with thrombocytopenia syndrome (SFTS). However, his inflammation markers continued to rise until a mixed fungal infection was detected. Metagenomic next-generation sequencing of blood detected elevated sequence numbers for Actinomucor elegans and Aspergillus fumigatus. The culture of the bronchoalveolar lavage fluid were positive for Aspergillus fumigatus and Escherichia coli. Infection was controlled after adjusting the antifungal regimens against Actinomucor elegans. The patient's condition gradually improved. This patient was diagnosed with possible mucormycosis. Reports of Mucorales infection associated with SFTS are rare. We hope that this case report will draw the attention of physicians in the area where SFTS occurs to figure out if patients with SFTS are susceptible to mucormycosis.},
}
@article {pmid39986042,
year = {2025},
author = {Bacha, LF and Oliveira, MAP and Landuci, F and Vicente, AC and Paz, PH and Lima, M and Hilário, M and Campos, LS and Thompson, M and Chueke, C and Tschoeke, D and Ottoni, A and Teixera, LM and Cosenza, C and de Souza, W and de Rezende, C and Thompson, C and Thompson, F},
title = {Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil.},
journal = {The Science of the total environment},
volume = {968},
number = {},
pages = {178778},
doi = {10.1016/j.scitotenv.2025.178778},
pmid = {39986042},
issn = {1879-1026},
abstract = {Baia da Ilha Grande (BIG), Rio de Janeiro, Brazil, is one of the largest bays in the world. BIG is important because it serves as a route for the mining and oil industries and plays a vital role in mariculture activities. However, BIG has suffered significant impacts in recent years due to increased pollution and climate change, culminating in a local mariculture collapse. We examined the pollution levels of the bay. Biogeochemical, microbiological, and metagenomics analyses were conducted in ten rivers during the 2022 dry and rainy seasons. Combined data analyses showed that the bay's ten most significant rivers are polluted and classified into three decreasing levels of pollution groups (P1-P3). The P1 group (Centro, Japuíba, Jacuecanga) had the worst-case scenario for all pollution types, and the highest number of the nearby populations, nautical workshops and hospitals. Whereas the P2 (Jacarei, Perequeaçu and Taquari) and P3 (Frade, Bracuí, Mambucaba, São Roque) had relatively reduced pollution, as shown mainly by fecal bacteria. Metals, such as Al (>0.3 mg/L), Fe (>1.4 mg/L), Pb (>0.15 mg/L), and resistance genes (∼2 % metagenomic profile) were also more abundant in P1. High levels of metals and antibiotic resistance genes were a strong indication of pollution. The results from this study shed light on the health status of BIG rivers for further conservation programs and public policies to prevent rivers and marine biodiversity losses, and they serves as a warning on the urgent need to treat effluents in the region.},
}
@article {pmid39986631,
year = {2025},
author = {Trueba-Santiso, A and Wimmer, R and Eskildsen, M and Cubero-Cardoso, J and Lema, JM and Nielsen, JL},
title = {Reliable methodology to determine biotransformation of PBAT in anaerobic conditions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132242},
doi = {10.1016/j.biortech.2025.132242},
pmid = {39986631},
issn = {1873-2976},
abstract = {Biodegradable plastics can enhance food waste utilization in anaerobic digestion (AD) units, but their fate under thermophilic conditions remains unclear. Previous studies using methane production, calorimetry, or spectroscopic analyses often report inconsistent results. This study tracks the biotransformation of polybutylene adipate co-terephthalate (PBAT) in thermophilic AD (55 °C) using [1]H NMR to quantify monomers. While 1,4-butanediol degraded quickly, adipic (AA) and terephthalic acid (TPA) accumulated over time. Monomer analysis estimated PBAT biotransformation at 11.1 ± 1.9 % (TPA) and 10.1 ± 2.3 % (AA). The core microbial community remained stable, indicating intrinsic hydrolytic capacities, which were stable despite TPA and AA accumulation. This workflow provides a robust methodology to evaluate the biotransformation of plastics.},
}
@article {pmid39986099,
year = {2025},
author = {Li, M and Wang, Z and Feng, Z and Lu, J and Chen, D and Chen, C and He, H and Zhang, Q and Chen, X and Morel, JL and Baker, AJM and Chao, Y and Tang, Y and Jiang, F and Qiu, R and Wang, S},
title = {New insights into efficient iron sulfide oxidation for arsenic immobilization by microaerophilic and acidophilic Fe(II)-oxidizing bacteria under micro-oxygen and acidic conditions.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137695},
doi = {10.1016/j.jhazmat.2025.137695},
pmid = {39986099},
issn = {1873-3336},
abstract = {Microbial-mediated FeS oxidation to Fe(Ⅲ) minerals via chemolithoautotrophic Fe(Ⅱ) oxidizers under pH/O2 limitations engages As immobilization. However, this process is constrained under the dual stress of micro-oxygen and acidic conditions due to the critically diminished Fe(Ⅱ) oxidation capacity. Therefore, the interplay between Fe(Ⅱ) oxidation, carbon metabolism, and As immobilization in Fe(Ⅱ)-oxidizing bacteria under micro-oxygen and acidic conditions remains unclear. This study presents the first successful enrichment of microaerophilic and acidophilic Fe(II)-oxidizing bacteria (MAFeOB). These bacteria are capable of oxidizing FeS to Fe(III) minerals and immobilizing up to 27,835 mg/kg of As(Ⅴ) under micro-oxygen content (below 3.2 mg/L) and acidic pH (4.5-6.2). Through comprehensive metagenomic analysis, it was speculated that MAFeOB harbor a suite of genes potentially participating in critical processes, including carbon fixation, Fe(II) oxidation, and arsenic detoxification. Notably, a potential electron transfer pathway from Cyc2_repCluster2 to Cytochrome cbb3-type oxidases facilitates Fe(II) oxidation. Furthermore, As(Ⅲ) efflux pump (arsA, arsB, acr3) and As(Ⅲ) oxidase (aioA) genes indicate MAFeOB's potential for As immobilization. Our findings underscore the pivotal role of MAFeOB in overcoming limitations associated with Fe(III) mineral formation, thereby enhancing arsenic immobilization under micro-oxygen and acidic water.},
}
@article {pmid39985994,
year = {2025},
author = {Song, C and Wang, S and Zhang, Q and Li, M and Zhang, B},
title = {Natural mackinawite-based elimination of vanadium and ammonium from wastewater in autotrophic biosystem.},
journal = {Water research},
volume = {277},
number = {},
pages = {123333},
doi = {10.1016/j.watres.2025.123333},
pmid = {39985994},
issn = {1879-2448},
abstract = {Vanadium (V) production results in significant amounts of wastewater, which often co-contains considerable ammonium (NH4[+]) after being used as precipitants. Both pentavalent V [V(V)] and NH4[+] can be removed independently through biological process. However, internal interactive biotechnology for one-step elimination of V(V) and NH4[+] remains an enigma. In this study, we proposed biologically removing V(V) and NH4[+] simultaneously with natural mineral mackinawite as electron donor and its oxidation products as electron acceptors. Our bioreactor achieved a V(V) removal efficiency of 99.5 ± 0.22 % and an NH4[+]-N removal capacity of 49.5 ± 0.40 g/m[3]·d. V(V) was reduced to tetravalent V precipitates, while mackinawite was bio-oxidized to Fe(III) and sulfate. Metagenomic binning analysis indicated Sulfurivermis sp. mediated mackinawite oxidation and V(V) reduction. Putative Pseudomonas sp. conducted NH4[+] assimilation, anaerobic ammonium oxidation coupled to Fe(III) reduction (Feammox), and denitrification, achieving complete NH4[+]-N removal. Real-time qPCR validated the upregulation of functional genes involved in V(V) reduction and nitrogen metabolisms, with improved functional enzyme activities. Cytochrome c, nicotinamide adenine dinucleotide, and extracellular polymeric substances promoted electron transfer, facilitating the elimination of both V(V) and NH4[+]-N from wastewater. This study offers a novel and sustainable biological strategy for one-step treating V industrial wastewater.},
}
@article {pmid39985639,
year = {2025},
author = {Zhang, N and Tran, S and Moskatel, LS},
title = {The Gut Microbiome and Migraine: Updates in Understanding.},
journal = {Current neurology and neuroscience reports},
volume = {25},
number = {1},
pages = {20},
pmid = {39985639},
issn = {1534-6293},
mesh = {Humans ; *Migraine Disorders/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; },
abstract = {PURPOSE OF REVIEW: We provide an overview of the field of microbiome research, the current understanding of the microbiome-gut-brain axis, and the most recent updates on the interplay between migraine and the gut microbiome.<br><br>RECENT FINDINGS: Pre-clinical studies suggest that gut microbiota is required for normal pain sensation. There is also evidence in rodent models that there is potential application of food, herbal medicines, probiotics, and short chain fatty acids (SCFAs) as novel therapies for migraine. Evidence from human cohorts suggests that there is altered gut microbiota in people with migraine, and that the microbiome dysbiosis is from both compositional and functional aspects. Recent metagenome-wide association studies (MWAS) that employ Mendelian Randomization support the causal association between gut microbiota and migraine. The connection between migraine and the gut microbiome remains underexplored, but recent preclinical and clinical studies support the association between gut microbiota and the development of migraine.},
}
@article {pmid39985228,
year = {2025},
author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ},
title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70010},
doi = {10.1002/ajb2.70010},
pmid = {39985228},
issn = {1537-2197},
support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; },
abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.<br><br>METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.<br><br>RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.<br><br>CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.},
}
@article {pmid39984459,
year = {2025},
author = {Maharramov, E and Czikkely, MS and Szili, P and Farkas, Z and Grézal, G and Daruka, L and Kurkó, E and Mészáros, L and Daraba, A and Kovács, T and Bognár, B and Juhász, S and Papp, B and Lázár, V and Pál, C},
title = {Exploring the principles behind antibiotics with limited resistance.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1842},
pmid = {39984459},
issn = {2041-1723},
mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; Drug Resistance, Bacterial/genetics/drug effects ; Mutation ; Microbial Sensitivity Tests ; Bacteria/drug effects/genetics ; Acinetobacter baumannii/drug effects/genetics ; Pseudomonas aeruginosa/drug effects/genetics ; Metagenomics/methods ; Escherichia coli/drug effects/genetics ; Klebsiella pneumoniae/drug effects/genetics ; },
abstract = {Antibiotics that target multiple cellular functions are anticipated to be less prone to bacterial resistance. Here we hypothesize that while dual targeting is crucial, it is not sufficient in preventing resistance. Only those antibiotics that simultaneously target membrane integrity and block another cellular pathway display reduced resistance development. To test the hypothesis, we focus on three antibiotic candidates, POL7306, Tridecaptin M152-P3 and SCH79797, all of which fulfill the above criteria. Here we show that resistance evolution against these antibiotics is limited in ESKAPE pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, while dual-target topoisomerase antibiotics are prone to resistance. We discover several mechanisms restricting resistance. First, de novo mutations result in only a limited elevation in resistance, including those affecting the molecular targets and efflux pumps. Second, resistance is inaccessible through gene amplification. Third, functional metagenomics reveal that mobile resistance genes are rare in human gut, soil and clinical microbiomes. Finally, we detect rapid eradication of bacterial populations upon toxic exposure to membrane targeting antibiotics. We conclude that resistance mechanisms commonly found in natural bacterial pathogens provide only limited protection to these antibiotics. Our work provides guidelines for the future development of antibiotics.},
}
@article {pmid39983710,
year = {2025},
author = {Chiu, CY and Godasi, RR and Hughes, HR and Servellita, V and Foresythe, K and Tubati, A and Zorn, K and Sidhu, S and Wilson, MR and Bethina, SV and Abenroth, D and Cheng, Y and Grams, R and Reese, C and Isada, C and Thottempudi, N},
title = {Two Human Cases of Fatal Meningoencephalitis Associated with Potosi and Lone Star Virus Infections, United States, 2020-2023.},
journal = {Emerging infectious diseases},
volume = {31},
number = {2},
pages = {215-221},
doi = {10.3201/eid3102.240831},
pmid = {39983710},
issn = {1080-6059},
mesh = {Humans ; *Meningoencephalitis/virology/diagnosis/epidemiology ; United States/epidemiology ; Fatal Outcome ; Male ; Animals ; Female ; Middle Aged ; Phylogeny ; Bunyaviridae Infections/virology/epidemiology/diagnosis ; Immunocompromised Host ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Aged ; History, 21st Century ; },
abstract = {We used clinical metagenomic next-generation sequencing of cerebrospinal fluid to investigate bunyavirus infections in 2 immunocompromised patients in the United States who had fatal meningoencephalitis. Potosi virus has been isolated from mosquito vectors and Lone Star virus from tick vectors. These findings highlight the power of metagenomic next-generation sequencing in broad-based, agnostic detection of emerging viral infections that test negative using conventional targeted diagnostic methods.},
}
@article {pmid39983689,
year = {2025},
author = {Parry, RH and Yamada, KYH and Hood, WR and Zhao, Y and Lu, JY and Seluanov, A and Gorbunova, V and Modhiran, N and Watterson, D and Isaacs, A},
title = {Henipavirus in Northern Short-Tailed Shrew, Alabama, USA.},
journal = {Emerging infectious diseases},
volume = {31},
number = {2},
pages = {392-394},
doi = {10.3201/eid3102.241155},
pmid = {39983689},
issn = {1080-6059},
mesh = {Animals ; Alabama/epidemiology ; *Phylogeny ; *Shrews/virology ; *Henipavirus/genetics/classification ; Genome, Viral ; Metagenomics/methods ; Paramyxoviridae Infections/epidemiology/virology/veterinary ; },
abstract = {RNA metagenomic analysis of tissues from 4 wild-caught northern short-tailed shrews in Alabama, USA, revealed a novel henipavirus (family Paramyxoviridae). Phylogenetic analysis supported the placement of the virus within the shrew henipavirus clade, related to human-infecting shrewborne henipaviruses. Our study results highlight the presence of henipavirus infections in North America.},
}
@article {pmid39983413,
year = {2025},
author = {Li, Q and Li, H and Tian, L and Wang, Y and Ouyang, Z and Li, L and Mao, Y},
title = {Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene.},
journal = {Environment international},
volume = {197},
number = {},
pages = {109334},
doi = {10.1016/j.envint.2025.109334},
pmid = {39983413},
issn = {1873-6750},
abstract = {In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.},
}
@article {pmid39984934,
year = {2025},
author = {Chen, X and Wei, J and Zhang, L and Wang, H and Zhang, Y and Li, Z and Wang, X and Liu, L and Zhang, Y and Zhang, T},
title = {Association between plasma short-chain fatty acids and inflammation in human immunodeficiency virus-associated neurocognitive disorder: a pilot study.},
journal = {Lipids in health and disease},
volume = {24},
number = {1},
pages = {66},
pmid = {39984934},
issn = {1476-511X},
support = {7222091//Natural Science Foundation of Beijing Municipality/ ; 81873761//National Natural Science Foundation of China/ ; 82241072, 82072271//National Natural Science Foundation of China/ ; 7222095//Beijing Natural Science Foundation/ ; },
abstract = {BACKGROUND AND AIMS: Short-chain fatty acids (SCFAs), key metabolites produced by gut microbiota, have neuroprotective effects in neurodegenerative diseases by modulating immune responses. However, their role in human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remains largely unexplored.<br><br>METHODS: We recruited HAND patients, HIV Control, and healthy controls (HC). Plasma SCFAs and SCFA-producing gut microbiota were quantified via gas chromatography-mass spectrometry and fecal metagenomic analysis. Inflammatory cytokine levels were measured using liquid chromatography. Receiver operating characteristic (ROC) curves were generated to evaluate the predictive accuracy of SCFAs for HAND.<br><br>RESULTS: Plasma SCFAs were significantly reduced in HAND patients, correlating with a decrease in SCFA-producing gut bacteria, such as Prevotella and its related species. Reduced SCFAs were positively correlated with pro-inflammatory cytokines and cognitive impairment, while being negatively correlated with anti-inflammatory cytokines. ROC curve analysis demonstrated that several SCFAs exhibited strong predictive accuracy for HAND status.<br><br>CONCLUSIONS: SCFAs may influence cognitive function by modulating inflammatory responses, and identifies plasma SCFAs as potential biomarkers and therapeutic targets for HAND. Further investigation is needed to delineate the mechanisms that SCFAs influence HAND pathology.},
}
@article {pmid39984857,
year = {2025},
author = {Zhang, L and Hu, J and Xin, Y and Cheng, H and Yan, Y and Wang, Q},
title = {Capnocytophaga ochracea detected in cerebrospinal fluid of a meningioma patient: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {249},
pmid = {39984857},
issn = {1471-2334},
support = {81972349//National Natural Science Foundation of China/ ; },
abstract = {Capnocytophaga ochracea (C. ochracea) is a species of Gram-negative and facultative anaerobic bacterium. It was first reported in 1979 and isolated from both healthy and diseased sites in the oral flora. The bacteria can cause septicemia, endocarditis, endometritis, blepharoconjunctivitis and other infections. Herein, we present the first cerebrospinal fluid (CSF) infection case caused by C. ochracea in humans. Gram-negative fusiform, non-spore forming rods were detected in an anaerobic bottle of CSF culture obtained from a 50-year-old man who had been hospitalized for meningioma in Tianjin Huanhu Hospital. Although the organism could not be identified using a conventional method, it was finally identified as C. ochracea based on the results of metagenomics next generation sequencing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16 S rDNA sequencing analysis. Subsequently, Streptococcus oralis was also detected in the CSF of the patient. The patient was treated with meropenem and vancomycin, and the infection was well controlled. The clinically rare C. ochracea can be pathogenic in central nervous system of humans.},
}
@article {pmid39984074,
year = {2025},
author = {OuYang, M and Liu, C and Shengping, and Qiu, Q and OuYang, K and Li, Y and Zang, Y and Zhao, X},
title = {Characterization of acidophilic cellulase with β-glucanase and xylanase activity from the rumen metagenome and in vitro evaluation of barley digestibility.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141141},
doi = {10.1016/j.ijbiomac.2025.141141},
pmid = {39984074},
issn = {1879-0003},
abstract = {In this study, RuCel143, an acidophilic GH5 cellulase endowed with β-glucanase and xylanase activity was identified from the rumen metagenome. Its hydrolytic efficacy was evaluated using barley in an in vitro simulation of monogastric digestion. Optimal activity for RuCel143's cellulase was observed at pH 3.5 and 40 °C, while for xylanase it was pH 4.0 and 50 °C. The cellulase exhibited strong pH tolerance, retaining 94.3 % of its initial activity after 4 h at pH 2.5. In contrast, xylanase activity increased by 80.7 % after 4 h at pH 8.0. RuCel143 exhibited good resistance to various ions and common inhibitors, with Cu[2+] and Mn[2+] enhancing the cellulase activity by 26.9 % and 95.6 % at 1 mM concentration, respectively. Mutation analysis involving Tyr162Ala, His235Ala, and Glu285Ala showed reduced activities to 67.4 %, 29.3 %, and 19.5 % of the wild type, respectively. Hydrolysis product analysis revealed that RuCel143 primarily produced cellobiose and xylopentaose from carboxymethyl cellulose sodium and wheat straw xylan. Comparative tests on barley, wheat, and wheat bran demonstrated RuCel143's superior performance on barley. Simulation results of in vitro monogastric digestion indicated that RuCel143 can increase the digestibility of barley from 52.6 % to 60.8 % and reduce the viscosity coefficient from 1.41 to 1.38. In summary, RuCel143 is an exceptionally acid-tolerant cellulase with both β-glucanase and xylanase activities, demonstrating unique enzymatic properties that could potentially be leveraged to improve the degradation of barley in monogastric animals.},
}
@article {pmid39983954,
year = {2025},
author = {Guo, J and Guan, A and Chen, M and Chen, Y and Qi, W and Cao, X and Peng, J and Liu, H and Qu, J and Jia, Z and Hu, H},
title = {Spatial Distribution of Potential Nitrogen Reduction Rates and Associated Microbial Communities Revealed by Metagenomic Analysis in Yangtze River Sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121170},
doi = {10.1016/j.envres.2025.121170},
pmid = {39983954},
issn = {1096-0953},
abstract = {Understanding the intricacies of nitrogen reduction processes and the composition of associated microbial communities is crucial for illuminating the reactions of ecosystems and their functions to persistent nitrogen inputs. To enhance research on the nitrogen reduction process, we determined the potential rates, quantified the relevant genes, and analyzed the macro factors in the sediments of the Yangtze River. The results showed that dissimilatory reduction of nitrate to ammonium (DNRA) dominated the N-reduction processes in the Yangtze River sediment, with average rates of 0.89±0.71 nmol N g[-1]·h[-1]. Meanwhile, denitrification and anammox rates were 0.73±0.74 and 0.07±0.07 nmol N g[-1]·h[-1], respectively. The Three Gorges Dam (TGD) caused higher potential rates (nmol N g[-1]·h[-1]) of denitrification (1.38), anammox (0.12), DNRA (1.48), and N2O depletion (1.49 nmol g[-1]·h[-1]) in the Three Gorges Reservoir (TGR) compared to other river reaches. The average copy numbers (copies·g[-1]) of nrfA (2.96×10[6]), narG (8.17×10[5]), nirS (6.10×10[6]), nosZ (2.77×10[6]), and hzsB (3.68×10[5]) in TGR sediments were higher than those in the other reaches. The TGD's interception of fine sediments and nutrients enhanced microbial gene abundance, thereby favoring N-reduction processes and resulting in N2O depletion in reservoir sediments. Moreover, the TGD caused a decreased contribution gap between DNRA and denitrification in the TGR (2%) compared with the upper (35%) and lower (18%) reaches, while causing predominant anammox (50%) in the middle reach. Metagenomic results suggested that sediment particle size, along with organic carbon and inorganic nitrogen concentrations, influenced N reduction rates by affecting narG, norB and C, nrfA and H, and hzsB and C. This study reveals the spatial pattern of the N-reduction rate in the Yangtze River sediments and quantitatively defines the intensity of dam effects on sediment N-reduction rate.},
}
@article {pmid39983731,
year = {2025},
author = {Saha, S and Kalathera, J and Sumi, TS and Mane, V and Zimmermann, S and Waschina, S and Pande, S},
title = {Mass lysis of predatory bacteria drives the enrichment of antibiotic resistance in soil microbial communities.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.01.068},
pmid = {39983731},
issn = {1879-0445},
abstract = {Numerous studies have investigated the effects of antibiotics on the evolution and maintenance of antimicrobial resistance (AMR). However, the impact of microbial interactions in antibiotic-free environments on resistance within complex communities remains unclear. We investigated whether the predatory bacterium M. xanthus, which can produce antimicrobials and employ various contact-dependent and -independent prey-killing mechanisms, influences the abundance of antibiotic-resistant bacteria in its local environment simply through its presence, regardless of active predation. We observed an association between the presence of M. xanthus in soil and the frequency of antibiotic-resistant bacteria. Additionally, culture-based and metagenomic analysis showed that coculturing M. xanthus with soil-derived communities in liquid cultures enriched AMR among non-myxobacterial isolates. This is because the lysis of M. xanthus, triggered during the starvation phase of the coculture experiments, releases diffusible growth-inhibitory compounds that enrich pre-existing resistant bacteria. Furthermore, our results show that death during multicellular fruiting body formation-a starvation-induced stress response in M. xanthus that results in over 90% cell death-also releases growth-inhibitory molecules that enrich resistant bacteria. Hence, the higher abundance of resistant bacteria in soil communities, where M. xanthus can be detected, was because of the diffusible growth-inhibitory substances that were released due to the death of M. xanthus cells during fruiting body formation. Together, our findings demonstrate how the death of M. xanthus, an important aspect of its life cycle, can impact antibiotic resistomes in natural soil communities without the anthropogenic influx of antibiotics.},
}
@article {pmid39983489,
year = {2025},
author = {Karlsson, M and Jönsson, HL and Hultberg, M},
title = {Inclusion of biochar in mushroom substrate influences microbial community composition of the substrate and elemental composition of the fruiting bodies.},
journal = {The Science of the total environment},
volume = {968},
number = {},
pages = {178914},
doi = {10.1016/j.scitotenv.2025.178914},
pmid = {39983489},
issn = {1879-1026},
abstract = {Due to its structure, biochar makes the soil porous and oxygen-rich, enhancing the water-holding capacity and increasing the cation exchange capacity for a longer duration. These aspects could also be favourable for mushroom production. However, biochar has been considerably less investigated within this context. This study investigated the impact of biochar on mushroom production, quality, and the microbial communities of the substrates. Two different biochar's produced from local feedstocks, plant- or sludge based, were evaluated in the production of oyster mushrooms (Pleurotus ostreatus) at two different concentrations (5 % and 10 %). The results showed that inclusion of biochar in the substrate negatively impacted fruiting body production. The elemental composition of the fruiting body was also affected by inclusion of biochar and partly reflected the elemental composition of the biochar. The metagenomics revealed that inclusion of biochar in the substrate altered the microbial community structure. The bacterial diversity based on Shannon indices was higher in the substrate wherein no biochar was added. Bacterial community richness (Chao 1) was higher in samples with biochar compared to the control with no added biochar. Fungal community richness based on Chao 1 indices displayed an increase in samples with an inclusion of biochar. Overall, this study provides novel insights into the impact of biochar in mushroom production regarding its concentration and the effect of the origin material of the biochar.},
}
@article {pmid39983259,
year = {2025},
author = {Lyte, JM and Jia, X and Caputi, V and Zhang, D and Daniels, KM and Phillips, GJ and Lyte, M},
title = {Heat stress in chickens induces temporal changes in the cecal microbiome concomitant with host enteric serotonin responses.},
journal = {Poultry science},
volume = {104},
number = {3},
pages = {104886},
doi = {10.1016/j.psj.2025.104886},
pmid = {39983259},
issn = {1525-3171},
abstract = {Heat stress is a potent modulator of the avian neuroendocrine system with concomitant impact on the gut microbiome. As an interkingdom signaling molecule, serotonin is largely derived from the gut and found in large concentrations in the avian gut lumen. Despite the role of serotonin in animal stress physiology and related host-microbe interactions, whether heat stress alters avian enteric concentrations of serotonin is unknown. As such, the present study sought to determine whether acute or chronic exposure to moderate heat stress alters both enteric serotonin concentrations and the microbiome in the chicken gut. Chickens were, or were not, subjected to an acute (1 day), repeated acute (2 days) or chronic (6 days) moderate ambient cyclic heat stress (12h per day, 31°C). Enteric concentrations of serotonin were significantly decreased in the acute heat stress group (P < 0.05), and rebounded to become elevated in the chronic heat stress group (P < 0.05). Shotgun metagenomic sequencing revealed heat stress caused both functional and taxonomic changes in the cecal microbiome. Abundances of bacterial taxa that are known to interact with the host via the serotonergic system, including Lactobacillus spp., and Bifidobacterium spp., were significantly (P < 0.05) altered by heat stress. As these findings demonstrate that heat stress can alter serotonin concentrations in the chicken intestinal tract, with distinct outcomes depending on duration of the stressor, serotonergic signaling may serve as potential leverageable point of intervention in host-microbe interactions including foodborne pathogen colonization in the chicken gut. In addition, this study provides novel insight into the impact of acute and chronic heat stress on the avian microbiome, and its relationship to stress-driven changes in the enteric serotonergic system.},
}
@article {pmid39983257,
year = {2025},
author = {Wang, Y and Cao, J and Liu, Q and Huang, J and Zhang, P and Zhang, Z and Li, B and Liu, Y and Xiao, B and Song, X and De Clercq, E and Li, G and Zheng, F},
title = {Association between respiratory pathogens and severe clinical outcomes in people living with HIV-1 and pulmonary infections: A 180-day longitudinal cohort study.},
journal = {Journal of infection and public health},
volume = {18},
number = {4},
pages = {102694},
doi = {10.1016/j.jiph.2025.102694},
pmid = {39983257},
issn = {1876-035X},
abstract = {BACKGROUND: Many respiratory pathogens have been identified in people living with HIV-1 and pulmonary infection, but their impact on clinical outcomes remains largely unclear.<br><br>METHODS: Metagenomic sequencing and traditional laboratory diagnostics were applied to identify bacterial, viral, and fungal respiratory pathogens. Clinical outcomes were assessed by (i) mortality or ICU transfer during hospitalization, and (ii) 30-day re-hospitalization and 180-day mortality after hospital discharge.<br><br>RESULTS: Microbiological analyses of bacterial, viral and fungal pathogens in 237 in-patients with HIV-1 and pulmonary infections revealed Pneumocystis jirovecii (58&#x202f;%) as the most prevalent respiratory pathogen, followed by Cytomegalovirus (39&#x202f;%), Mycobacterium tuberculosis (22&#x202f;%), Talaromyces marneffei (17&#x202f;%), and Epstein-Barr virus (16&#x202f;%). Fifty-six patients (24&#x202f;%) were coinfected with bacterial, viral and fungal pathogens, referred to as bacterial+fungal+viral coinfections. Risk factors for bacterial+fungal+viral coinfections (RR=8.41, 95&#x202f;%CI: 4.2-14.3), severe pneumonia (RR=13.6, 95&#x202f;%CI: 8.14-19.3), and elevated C-reactive protein levels (RR=6.42, 95&#x202f;%CI: 1.58-10.13) were significantly associated with mortality or ICU transfer during hospitalization. After hospital discharge, 38 patients (16&#x202f;%) were rehospitalized within 30 days. Antiretroviral therapy reduced the risk of 30-day rehospitalization (HR=0.21, p&#x202f;=&#x202f;0.01). During the 180-day follow-up, 13 patients (5.5&#x202f;%) died. Survival analyses identified severe pneumonia and age &#x2265;&#x202f;60 years as risk factors for 180-day mortality.<br><br>CONCLUSIONS: Multiple pulmonary coinfections are associated with severe outcomes in in-patients with HIV-1 infection. Effective management of both HIV-1 and pulmonary infections is crucial to reduce hospitalization rates and mortality risk.},
}
@article {pmid39982899,
year = {2025},
author = {Gittrich, MR and Sanderson, CM and Wainaina, JM and Noel, CM and Leopold, JE and Babusci, E and Selbes, SC and Farinas, OR and Caine, J and Davis Ii, J and Mutalik, VK and Hyman, P and Sullivan, MB},
title = {Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0313947},
doi = {10.1371/journal.pone.0313947},
pmid = {39982899},
issn = {1932-6203},
mesh = {*Klebsiella/virology/genetics ; *Bacteriophages/genetics/isolation &amp; purification/physiology ; *Genome, Viral ; Rhizosphere ; Phylogeny ; Plant Development ; Soil Microbiology ; Host Specificity ; },
abstract = {Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.},
}
@article {pmid39982611,
year = {2025},
author = {Wang, X and Liu, Q and Wu, B and Zhao, H and Hu, J and Li, N},
title = {Successful treatment of carbapenem-resistant Acinetobacter baumannii meningitis and purulent ventriculitis using cefiderocol combination therapy: a case report and literature review.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39982611},
issn = {1435-4373},
abstract = {The application of cefiderocol in treating carbapenem-resistant Acinetobacter baumannii (CRAB) central nervous system (CNS) infections is rarely reported. Here we presented the case of a 66-year-old man with CRAB meningitis and purulent ventriculitis successfully treated with a combination antibiotic therapy including cefiderocol. Cerebrospinal fluid (CSF) analysis revealed normalization of glucose, chloride, protein, and lactate levels. CRAB cultures turned negative by Day 7, and metagenomics next generation sequencing (mNGS) results were negative by Day 25. The cefiderocol-contained regimen was continued for 41 days, with no recurrence of CRAB infection and no cefiderocol-associated adverse effects were observed. This case highlighted the potential of cefiderocol as a promising therapeutic option in treating CRAB CNS infections.},
}
@article {pmid39982015,
year = {2025},
author = {Cao, X and Ma, H and Li, SA and Huang, H and Cui, F and Tanentzap, AJ},
title = {Enhanced Release and Reactivity of Soil Water-Extractable Organic Matter Following Wildfire in a Subtropical Forest.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13557},
pmid = {39982015},
issn = {1520-5851},
abstract = {Climate-driven increases in wildfire frequency may disrupt soil carbon dynamics, potentially creating positive feedback within global carbon cycle. However, the release and lability of soil carbon following wildfire remain unclear, limiting our ability to predict fire impacts on carbon cycling. Here, we investigated chemical alterations in soil water-extractable organic matter (WEOM) following a subtropical forest wildfire by comparing burned soils to an adjacent unburned site. The consensus is that fire-altered DOM is aromatic and less reactive. However, we found that 10 months postfire, burned soils contained nearly three times more water-extractable organic carbon (WEOC) than the control site. Reactomics analysis further revealed an overall 8-fold increase in potential reactivity of this carbon, identified by higher abundances of molecular formulas involved in identified microbial reaction pathways. Specifically, burned soils exhibited elevated potential oxidative enzyme reactions, linked to a higher nominal oxidation state of carbon (NOSC) in WEOM. Metagenomic analysis revealed an enrichment of microbial taxa specialized in degrading aromatic compounds in burned areas, supporting the occurrence of potential microbial reaction pathways acting on WEOM in postfire soils. These findings highlight that wildfires may accelerate soil carbon loss through reactive WEOM mobilization and microbial response, with implications for long-term carbon-climate projections.},
}
@article {pmid39981802,
year = {2025},
author = {Bartlett, A and Blakeley-Ruiz, JA and Richie, T and Theriot, CM and Kleiner, M},
title = {Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202400149},
doi = {10.1002/pmic.202400149},
pmid = {39981802},
issn = {1615-9861},
support = {593607//Foundation for Food and Agriculture Research/ ; R35GM138362//National Institute of General Medical Sciences of the National Institutes of Health/ ; },
abstract = {Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Defined diets frequently use purified casein as the protein source. Previous work indicated that casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and found that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.},
}
@article {pmid39981377,
year = {2025},
author = {Zhao, R and He, G and Xiang, L and Ji, M and He, R and Wei, X},
title = {Metagenomic next-generation sequencing assists in the diagnosis of visceral leishmaniasis in non-endemic areas of China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1517046},
pmid = {39981377},
issn = {2235-2988},
mesh = {*Leishmaniasis, Visceral/diagnosis/parasitology ; Humans ; China ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Molecular Diagnostic Techniques/methods ; Leishmania/genetics/isolation &amp; purification/classification ; Female ; Adult ; DNA, Protozoan/genetics ; },
abstract = {INTRODUCTION: Leishmaniasis, a protozoan disease caused by infection by Leishmania, is a critical issue in Asia, South America, East Africa, and North Africa. With 12 million cases globally, leishmaniasis is one of the most serious neglected tropical diseases worldwide. Direct identification of infected tissues is currently the primary method of diagnosis; however, the low sensitivity and inconvenience of microscopic examination in detecting amastigotes, parasitic manifestations of Leishmania, leads to the possibility of misdiagnosis, delayed diagnosis, and underdiagnosis.<br><br>METHODS: With the development of metagenomic nextgeneration sequencing (mNGS) technology for pathogen identification, it is possible to detect specific nucleic acid sequences characteristic of Leishmania parasites, which opens new avenues for the more accurate diagnosis of leishmaniasis. In this study, we report two cases of leishmaniasis from Henan Province, China, in which Leishmania parasites were identified using mNGS technology, massively expediting diagnosis and treatment.<br><br>RESULTS: Our report demonstrates that the mNGS method is applicable to peripheral blood samples (PB), which are far more readily available in clinical settings, in addition to bone marrow aspirate samples (BM), which are traditionally used for diagnosis of visceral leishmaniasis.<br><br>CONCLUSION: Our report validates the efficacy of mNGS technology as a rapid and accurate method of diagnosis for leishmaniasis.},
}
@article {pmid39980208,
year = {2025},
author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K},
title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14086},
doi = {10.1111/1755-0998.14086},
pmid = {39980208},
issn = {1755-0998},
support = {856488//H2020 European Research Council/ ; },
abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.},
}
@article {pmid39979617,
year = {2025},
author = {Ohlsson, C and Lawenius, L and Jiang, Y and Horkeby, K and Wu, J and Nilsson, KH and Koskela, A and Tuukkanen, J and Movérare-Skrtic, S and Henning, P and Sjögren, K},
title = {The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6182},
doi = {10.1038/s41598-025-91056-2},
pmid = {39979617},
issn = {2045-2322},
mesh = {Animals ; Female ; *Probiotics/pharmacology/administration &amp; dosage ; Mice ; *Bone Density/drug effects ; Diet, High-Fat/adverse effects ; Bone and Bones/drug effects ; Mice, Inbred C57BL ; Ovariectomy ; Gastrointestinal Microbiome/drug effects ; Diet ; },
abstract = {Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p ≤ 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.},
}
@article {pmid39979545,
year = {2025},
author = {Thompson, S and Wang, J and Schott, T and Nissinen, R and Haapalainen, M},
title = {Genomes of the Bacterial Endosymbionts of Carrot Psyllid Trioza apicalis Suggest Complementary Biosynthetic Capabilities.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {145},
pmid = {39979545},
issn = {1432-0991},
mesh = {Animals ; *Hemiptera/microbiology ; *Symbiosis ; *Genome, Bacterial ; *Daucus carota/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Metagenome ; },
abstract = {Carrot psyllid Trioza apicalis is a serious pest of cultivated carrot and also a vector of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso). To find out whether T. apicalis harbours other species of bacteria that might affect the Lso infection rate, the bacterial communities and metagenome in T. apicalis were studied. Lso haplotype C was detected in a third of the psyllids sampled, at different relative amounts. Surprisingly, T. apicalis was found to harbour only one secondary endosymbiont, a previously unknown species of gamma proteobacterium endosymbiont (Gpe), beside the primary endosymbiont 'Candidatus Carsonella ruddii' (CCr). The relative abundancies of these two endosymbionts were approximately equal. The genomes of CCr, Gpe and Lso were assembled from a T. apicalis metagenome sample. Based on the 16S rRNA gene, the closest relative of Gpe of T. apicalis could be a secondary endosymbiont of Trioza magnoliae. The 253.171 kb Gpe genome contains all the tRNA and rRNA genes and most of the protein-coding genes required for DNA replication, transcription and translation, but it lacks most of the genes for amino acid biosynthesis. Gpe has no genes encoding cell wall peptidoglycan synthesis, suggesting it has no cell wall, and could thus live as an intracellular endosymbiont. Like the CCr of other psyllids, CCr of T. apicalis retains a broad amino acid biosynthetic capacity, whilst lacking many genes required for DNA replication and repair and for transcription and translation. These findings suggest that these two endosymbionts of T. apicalis are complementary in their biosynthetic capabilities.},
}
@article {pmid39979340,
year = {2025},
author = {Di Costanzo, F and Di Marsico, M and Orefice, I and Kristoffersen, JB and Kasapidis, P and Chaumier, T and Ambrosino, L and Miralto, M and Aiese Cigliano, R and Verret, F and Tirichine, L and Trindade, M and Van Zyl, L and Di Dato, V and Romano, G},
title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida).},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {310},
pmid = {39979340},
issn = {2052-4463},
mesh = {*Diatoms/genetics ; Genome ; Molecular Sequence Annotation ; DNA Methylation ; Transcriptome ; DNA Transposable Elements ; Metagenome ; },
abstract = {Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.},
}
@article {pmid39978635,
year = {2025},
author = {Esse, J and Träger, J and Steininger, P and Bihlmaier, K and Fürst, J and Bardonicsek-Depnering, Z and Naumann-Bartsch, N and Morhart, P and Castellanos, I and Krause, SW and Herbst, L and Strauß, R and Chada, M and Korn, K and Valenza, G and Teschner, D and Bogdan, C and Held, J},
title = {Metagenomic analysis of microbial cell-free DNA from plasma of patients with suspected infections: performance and therapeutic impact in clinical routine.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.02.016},
pmid = {39978635},
issn = {1469-0691},
abstract = {OBJECTIVES: The sensitivity of blood cultures (BC) is limited, especially when antimicrobial therapy already has been administered or when non-culturable pathogens are causing the disease. Metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) from plasma has the potential to compensate for the disadvantages of BC diagnostics.<br><br>METHODS: We conducted a retrospective study in patients with suspected infections over a period of 3&#xa0;months. cfDNA from plasma was analysed by mNGS (Illumina NextSeq, 25 million reads per sample, read length 75 base pairs) and sequences were analysed with DISQVER&#xae;, a CE-IVDD-labelled software algorithm and curated database. The data were compared to findings obtained with simultaneously taken BC and other microbiological results (+/- 7&#xa0;days).<br><br>RESULTS: DISQVER&#xae; analysis was performed on 190 samples from 147 patients (124 adult, 23 pediatric). The median time-to-result including transport was two days (IQR 2-3; range 2-8). DISQVER&#xae; detected 158 pathogens (103 bacteria, 49 viruses, four fungi, one parasite) in 80 plasma samples (positivity rate 42.1%). The median number of pathogens per positive sample was one (IQR 1-2; range 1-10). The most common bacteria were Enterobacterales (30.1%; 31/103), anaerobic bacteria (18.4%; 19/103) and Enterococcus spp. (15.5%; 16/103), the most frequent viruses were Epstein-Barr virus (28.6%; 14/49), human herpesvirus 6B (18.4%; 9/49) and human cytomegalovirus (18.4%; 9/49). Mycobacterium avium, Legionella pneumophila, Tropheryma whipplei, Rhizomucor pusillus and Leishmania infantum were detected in one sample each. Simultaneous BC were positive in only 10.2% (18/176) of the samples, but were mostly (68.2%; 120/176) collected under antibiotic therapy. DISQVER&#xae; analysis resulted in 24 treatment changes in 20 patients (13.6%; 20/147; 9 start/escalation, 10 stop/de-escalation, 2 catheter replacements, 3 other).<br><br>CONCLUSIONS: DISQVER&#xae; significantly increased the detection rate of pathogens, led to the diagnosis of serious infections that otherwise would have been missed, and possibly improved the treatment of more than 10% of patients.},
}
@article {pmid39978335,
year = {2025},
author = {Wang, Z and Tian, L and Jiang, Y and Ning, L and Zhu, X and Chen, X and Xuan, B and Zhou, Y and Ding, J and Ma, Y and Zhao, Y and Huang, X and Hu, M and Fang, JY and Shen, N and Cao, Z and Chen, H and Wang, X and Hong, J},
title = {Synergistic role of gut-microbial L-ornithine in enhancing ustekinumab efficacy for Crohn's disease.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.01.007},
pmid = {39978335},
issn = {1932-7420},
abstract = {The role of the intestinal microbiome in Crohn's disease (CD) treatment remains poorly understood. This study investigates microbe-host interactions in CD patients undergoing ustekinumab (UST) therapy. Fecal metagenome, metabolome, and host transcriptome data from 85 CD patients were analyzed using multi-omics integration and mediation analysis. Our findings reveal significant microbiome-metabolite-host interactions. Specifically, Faecalibacterium prausnitzii was linked to altered L-ornithine biosynthesis, resulting in higher L-ornithine levels in patients before UST therapy. In vivo and in vitro studies demonstrated that microbiome-derived L-ornithine enhances UST treatment sensitivity in CD by disrupting the host IL-23 receptor signaling and inhibiting Th17 cell stabilization through the IL-12RB1/TYK2/STAT3 axis. L-ornithine significantly enhances the therapeutic efficacy of UST in CD patients, as demonstrated in a prospective clinical trial. These findings suggest that targeting specific microbe-host metabolic pathways may improve the efficacy of inflammatory bowel disease (IBD) treatments.},
}
@article {pmid39978123,
year = {2025},
author = {Jin, G and Wang, X and Cui, R and Yuan, S and Wang, M and Chen, Z},
title = {Comprehensive assessment of antibiotic impacts and risk thresholds on aquatic microbiomes and resistomes.},
journal = {Water research},
volume = {276},
number = {},
pages = {123262},
doi = {10.1016/j.watres.2025.123262},
pmid = {39978123},
issn = {1879-2448},
abstract = {Understanding the impacts of environmentally relevant low-level antibiotics on aquatic microbiomes and resistomes is crucial for risk assessment of anthropogenic antibiotic contamination. Here, we investigated the effects of seven subinhibitory concentrations of trimethoprim and lincomycin (10 ng/L to 10 mg/L), individually and in combination, on surface water microcosms over 1 and 7 days, using unspiked samples as controls. Metagenomic sequencing revealed a decrease in bacterial community α-diversity and an increase in resistome α-diversity with rising antibiotic concentrations upon 7 days of exposure. Notably, the β-diversity of both bacterial communities and resistomes exhibited a biphasic response, decreasing and then increasing with breakpoint concentrations of 2.73 µg/L and 0.68 µg/L, respectively. We also observed concentration-dependent increases in certain metagenome-assembled antibiotic-resistant bacteria (MAARB) and antibiotic resistance genes (ARGs), with minimum selective concentrations (MSCs) of 2.28 µg/L for trimethoprim targeting OXA-21 and 32.4 µg/L for lincomycin targeting erm(F). Among various metrics for identifying risk thresholds that induce significant changes in microbial taxa, resistomes, individual ARGs, and MAARB, the breakpoint concentration derived from resistome β-diversity was the most conservative. We propose integrating this metric into environmental risk assessment frameworks for antibiotics. Our study provides a systematic evaluation of antibiotic impacts on aquatic microbiomes and resistomes, offering key insights for refining risk assessments of antibiotic contamination in aquatic environments.},
}
@article {pmid39978085,
year = {2025},
author = {Mu, X and Chen, S and He, C and Li, H and Huang, Z},
title = {Bartonella henselae and Aspergillus flavus coinfection in an immunocompromised patient.},
journal = {Diagnostic microbiology and infectious disease},
volume = {112},
number = {1},
pages = {116708},
doi = {10.1016/j.diagmicrobio.2025.116708},
pmid = {39978085},
issn = {1879-0070},
abstract = {OBJECTIVE: This clinical study reports a case of atypical cat scratch disease in a patient undergoing immunosuppressive treatment, who contracted COVID-19 during the treatment period. Despite pharmacological and surgical interventions, Bartonella henselae was not completely cleared, leading to the recurrence of symptoms. The study highlights the challenges of management and the need for thorough immune assessment and precise diagnosis.<br><br>METHODS: A case report provides a detailed description of the treatment process for a young female patient with cat scratch disease (CSD), who had been treated with immunosuppressive agents (adalimumab and baricitinib) for ankylosing spondylitis and developed a concurrent COVID-19 infection during the treatment of CSD.The diagnosis was confirmed through macrogenomic second-generation sequencing. Pharmacological and surgical interventions were administered, and clinical outcomes were monitored.<br><br>RESULTS: When a patient is infected with Bartonella henselae and remains in a prolonged immunocompromised state, pharmacological or surgical treatment may still fail to completely clear the pathogen, leading to the recurrence of symptoms.<br><br>CONCLUSION: This case emphasizes the recurrence of symptoms in a patient undergoing long-term immunosuppressive treatment who contracted COVID-19 during Bartonella henselae infection. It suggests a potential interaction between immunosuppression and infection. It highlights the importance of immune assessment, accurate diagnosis, and vigilant management. Appropriate therapeutic strategies should be considered for patients with prolonged illness and impaired self-healing capability. Further research is warranted to clarify the mechanisms behind these interactions and to optimize management strategies for similar cases.},
}
@article {pmid39978531,
year = {2025},
author = {Perrotta, BG and Kidd, KA and Marcarelli, AM and Paterson, G and Walters, DM},
title = {Effects of chronic metal exposure and metamorphosis on the microbiomes of larval and adult insects, and riparian spiders through the aquatic-riparian food web.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125867},
doi = {10.1016/j.envpol.2025.125867},
pmid = {39978531},
issn = {1873-6424},
abstract = {The macroinvertebrate microbiome controls various aspects of the host's physiology, from regulation of environmental contaminants to reproductive output. Aquatic insects provide critical nutritional subsidies linking aquatic and riparian food webs while simultaneously serving as a contaminant pathway for riparian insectivores in polluted ecosystems. Previous studies have characterized the transport and transfer of contaminants from aquatic to riparian ecosystems through insect metamorphosis, but both contaminant exposure and metamorphosis are energetically intensive processes that may cause host microbiomes to undergo radical transformation in structure and function, potentially affecting the host's physiology. We collected arthropods from three sites within Torch Lake, a historical copper mine in the Keweenaw Peninsula, Michigan, USA, and three sites within a nearby reference lake. Our objectives were to: 1) characterize the variation in microbiome communities and predicted metagenomic functions with legacy copper mining activity across space, among host types and family-level host taxonomy, 2) characterize how insect metamorphosis alters the microbiome community, including the degree of endosymbiotic infection, and predicted metagenomic function. We field-collected organisms, extracted their DNA, and sequenced the 16S region of the rRNA gene to characterize microbiome communities, then predicted metagenomic function. Site, lake, and host taxonomy affected the host microbiome community composition. Copper exposure increased the abundance of xenobiotic and lipid metabolism pathways in the Araneidae spider microbiome. Metamorphosis reduced the alpha diversity, altered the community composition, and predicted metagenomic function. We observed a bioconcentration of endosymbiotic bacteria in adult insects, especially holometabolous insects. Through metamorphosis, we observed a transition in function from xenobiotic degradation pathways to carbohydrate metabolism. Overall, contaminant exposure alters the microbiome composition in aquatic insects and riparian spiders and alters the function of the microbiome across the aquatic-riparian interface. Furthermore, metamorphosis is a critical element in shaping the aquatic insect microbiome across its life history.},
}
@article {pmid39975892,
year = {2025},
author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O},
title = {The effects of dietary fat on gut microbial composition and function in ovarian cancer.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5904007/v1},
pmid = {39975892},
issn = {2693-5015},
abstract = {Objectives : The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC). Methods : Thirty female C57BL/6J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function. Results : Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides , Lachnospiracae bacterium , Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides . Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice. Conclusions These results highlight the intricate relationship between diet, the gut microbiome, and tumor metabolism. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.},
}
@article {pmid39975683,
year = {2025},
author = {Fang, J and Wang, Z and Shen, Y and Wu, X and Fang, H and Sun, X and Yu, T and Zhang, Q},
title = {Case report: The value of early application of mNGS technology in the diagnosis and treatment of severe Legionnaires' disease: reports of two cases with different outcomes.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1501192},
pmid = {39975683},
issn = {2296-858X},
abstract = {BACKGROUND: Legionnaires' disease has a high clinical mortality rate, and early diagnosis and treatment are critical. Increasing evidence shows that metagenomic next-generation sequencing (mNGS) has excellent potential for the early identification of pathogens. To help clinicians better recognize Legionnaires' disease in its early stage and to illustrate the diagnostic value of mNGS technology, we reviewed and summarized two cases of severe Legionnaires' disease.<br><br>METHODS AND ANALYSIS: We selected two patients with severe Legionnaires' disease who were admitted to our department in recent years. We discuss experience with them and the shortcomings in their treatment by summarizing their medical history, disease evolution, tests, and diagnostic and therapeutic processes.<br><br>RESULTS: In both patients, the diagnosis of Legionnaires' disease was confirmed through analysis of the bronchoalveolar lavage fluid (BALF). The middle-aged male patient was cured and discharged due to early detection and diagnosis. The elderly immunocompromised patient died due to a delay in diagnosis.<br><br>CONCLUSION: This study highlights the importance of the early recognition and diagnosis of severe Legionnaires' disease and the advantages of mNGS in identifying the pathogen.},
}
@article {pmid39975405,
year = {2025},
author = {Zhou, Z and Riley, R and Kautsar, S and Wu, W and Egan, R and Hofmeyr, S and Goldhaber-Gordon, S and Yu, M and Ho, H and Liu, F and Chen, F and Morgan-Kiss, R and Shi, L and Liu, H and Wang, Z},
title = {GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.30.635558},
pmid = {39975405},
issn = {2692-8205},
abstract = {Genome foundation models hold transformative potential for precision medicine, drug discovery, and understanding complex biological systems. However, existing models are often inefficient, constrained by suboptimal tokenization and architectural design, and biased toward reference genomes, limiting their representation of low-abundance, uncultured microbes in the rare biosphere. To address these challenges, we developed GenomeOcean , a 4-billion-parameter generative genome foundation model trained on over 600 Gbp of high-quality contigs derived from 220 TB of metagenomic datasets collected from diverse habitats across Earth's ecosystems. A key innovation of GenomeOcean is training directly on large-scale co-assemblies of metagenomic samples, enabling enhanced representation of rare microbial species and improving generalizability beyond genome-centric approaches. We implemented a byte-pair encoding (BPE) tokenization strategy for genome sequence generation, alongside architectural optimizations, achieving up to 150× faster sequence generation while maintaining high biological fidelity. GenomeOcean excels in representing microbial species and generating protein-coding genes constrained by evolutionary principles. Additionally, its fine-tuned model demonstrates the ability to discover novel biosynthetic gene clusters (BGCs) in natural genomes and perform zero-shot synthesis of biochemically plausible, complete BGCs. GenomeOcean sets a new benchmark for metagenomic research, natural product discovery, and synthetic biology, offering a robust foundation for advancing these fields.},
}
@article {pmid39975011,
year = {2025},
author = {Ziemski, M and Gehret, L and Simard, A and Dau, SC and Risch, V and Grabocka, D and Matzoros, C and Wood, C and Cabrera, PM and Hernández-Velázquez, R and Herman, C and Evans, K and Robeson, MS and Bolyen, E and Caporaso, JG and Bokulich, NA},
title = {MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.27.635007},
pmid = {39975011},
issn = {2692-8205},
abstract = {Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.},
}
@article {pmid39974997,
year = {2025},
author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, D and Lieberman, TD},
title = {Intraspecies associations from strain-rich metagenome samples.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.07.636498},
pmid = {39974997},
issn = {2692-8205},
abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based, framework to accurately quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we uncover previously undetected clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will propel new mechanistic insights from accumulating metagenomic data.},
}
@article {pmid39974142,
year = {2025},
author = {Dravillas, C and Williams, N and Husain, M and Hoyd, R and Hussein, A and Meara, A and Lynn, M and Bibi, A and Conrad, B and Lepola, N and Gray, S and Bodnar, M and Arya, N and Roberts, S and Hoang, P and Apparicio, J and Merrill, D and Wu, R and Verschraegen, C and Burd, CE and Kendra, K and Spakowicz, D},
title = {The Association of the Microbiome with Melanoma Tumor Response to Immune Checkpoint Inhibitor Treatment and Immune-Related Adverse Events (NCT05102773).},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.30.25321413},
pmid = {39974142},
abstract = {Improved understanding of the factors that underlie immune checkpoint inhibitor (ICI) response and toxicity are needed as only half of patients with metastatic melanoma respond, and 10-40% experience immune-related adverse events (irAEs). Modifying the gut microbiome could positively affect response to ICIs and reduce toxicities. Here, we sought to determine if the pre-treatment gut microbiome predicts ICI response or toxicity in the setting of metastatic melanoma. Melanoma patients (n=88) over 18 years of age, planning to receive ICI therapy enrolled in a prospective observational cohort study at The Ohio State University Comprehensive Cancer Center Skin Cancer Clinic. Patients taking corticosteroids for indications other than adrenal physiologic replacement were excluded. Stools were collected at baseline, within 10 days of an irAE as determined by CTCAE v 5.0 criteria, and at 12 weeks. ICI response and progression-free survival (PFS) were evaluated q12 weeks using Response Evaluation Criteria in Solid Tumors (RECIST v1.1). Metagenomic whole-genome shotgun sequencing of the microbiome was classified using MetaPhlAn4/HUMAnN3 and differential abundance analyzed with ANCOM-BC2. Of the 88 patients enrolled, 41 had metastatic disease and complete data. There were 25 participants classified as responders, defined as having complete response or partial response according to RECIST criteria, or stable disease with 6-month PFS. Grade ≥ 1 irAEs were observed in 15/41 participants. The abundance of Intestinimonas butyriciproducens (q-value = 0.002) and Longicatena caecimuris (q-value = 0.003) were enriched in responders, Tenericutes (q-value= 0.001) and Lachnospira sp. NSJ 43 (q-value =0.002) in non-responders. Blautia luti , as well as several other Lachnospiraceae , were associated with response and no irAE (response q-value = 0.02, no irAE q-value = 0.02). The association of response to ICIs with several taxa in the family Lachnospiraceae , a prevalent microbial family in the gut, is consistent with prior research, which has found that this family may influence treatment outcomes through various mechanisms, such as immune regulation, metabolism, and pathogen exclusion. While no statistical relationship was observed between response and irAEs in this cohort, the microbes associated with both could serve as biomarkers. Future studies to assign causal roles for (specific microbes) in response and toxicity could identify mechanisms to improve patient outcomes.},
}
@article {pmid39973225,
year = {2025},
author = {Chen, C and Yu, Y and Zhu Ma, LZ and Nin, J and Zhang, D and Nong, W and Pan, X},
title = {Visceral leishmaniasis related secondary haemophagocytic syndrome: A case report.},
journal = {The Journal of international medical research},
volume = {53},
number = {2},
pages = {3000605251318204},
doi = {10.1177/03000605251318204},
pmid = {39973225},
issn = {1473-2300},
mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/parasitology/complications ; *Leishmaniasis, Visceral/diagnosis/complications ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Bone Marrow/pathology/parasitology ; },
abstract = {Visceral leishmaniasis (VL) is a parasitic disease that can trigger haemophagocytic syndrome (HPS), making its prompt diagnosis crucial. The application of metagenome next-generation sequencing (mNGS) provides a rapid diagnostic approach, particularly for patients with negative bone marrow aspiration results. We present here, a case of a male patient in his early 50s who presented with fever and abdominal pain. Routine examinations failed to identify its specific cause. However, diagnosis through mNGS helped prevent a potentially fatal outcome.},
}
@article {pmid39578945,
year = {2025},
author = {Li, D and Zhi, J and Ye, J and Yue, W and Yang, Y},
title = {Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis.},
journal = {Environmental entomology},
volume = {54},
number = {1},
pages = {119-129},
doi = {10.1093/ee/nvae117},
pmid = {39578945},
issn = {1938-2936},
support = {[2016] 5802//Guizhou International Science and Technology Cooperation Base/ ; },
mesh = {Diet ; Gastrointestinal Microbiome ; Metagenome ; Phaseolus ; Rosa ; Sequence Analysis, DNA ; *Thysanoptera/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.},
}
@article {pmid39970645,
year = {2025},
author = {Wang, W and Tao, J and Pang, R and Zhang, L and Zhang, Y and Su, Y and Li, W and Hong, S and Kim, H and Zhan, M and Xie, B},
title = {Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137644},
doi = {10.1016/j.jhazmat.2025.137644},
pmid = {39970645},
issn = {1873-3336},
abstract = {Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.},
}
@article {pmid39971118,
year = {2025},
author = {Kong, F and Wang, W and Wang, X and Yang, H and Tang, J and Li, Y and Shi, J and Wang, S},
title = {Performance and mechanism of nano Fe-Al bimetallic oxide enhanced constructed wetlands for the treatment of Cr(VI)-contaminated wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121154},
doi = {10.1016/j.envres.2025.121154},
pmid = {39971118},
issn = {1096-0953},
abstract = {Enhancing the synergistic interactions between substrates and microorganisms in constructed wetlands (CWs) represents a promising approach for treating heavy metal-contaminated wastewater. Multifunctional nanomaterials may play a significant role in this process. However, their impacts and mechanisms in this context remain unclear. In this study, artificial zeolite spheres loaded with Fe-Al double metal oxide (Fe-Al-NBMO) were synthesized and utilized in the CW to treat Cr(VI)-contaminated wastewater. Adsorption experiments demonstrated that the adsorption capacity of Fe-Al-NBMO loaded substrate for Cr(VI) was 988.43 mg/kg at an initial concentration of 30 mg/L, 361, and 37 times higher than that of gravel and carrier, respectively. The CW experiment indicated that the Cr(VI) effluent concentration in CW-ZL with Fe-Al-NBMO substrate did not exceed the integrated wastewater discharge standard (GB8978-1996) (0.5 mg/L) at an influent concentration of 50 mg/L. The introduction of the Fe-Al-NBMO substrate promoted microbial growth and increase the Extracellular Polymeric Substances (EPS) and other metabolite contents, thereby enhancing the microbial adsorption of Cr(VI). Furthermore, the removal performance of Cr(VI) was enhanced by the increase in resistant microorganisms (Hyphomicrobium and Rhodopseudomonas) and functional genes. Notably, metaproteomic analysis revealed that the elevated abundance of NADH-quinone oxidoreductase (nuoB, nuoC, nuoD, nuoE, nuoF, and nuoG), reductive coenzymes (fbp, ALDO, mcrA, and cdhC), metabolic pathways of sulfur (Cysp), and glutathione transferase (GsiB, frmA, and gfa) contributed to Cr(VI) removal. Our results provide a robust strategy for treating Cr(VI)-contaminated wastewater by CWs with Fe-Al-NBMO loaded substrate.},
}
@article {pmid39970657,
year = {2025},
author = {Feng, W and Zhang, Q and Li, J and Liu, J and Duan, C and Peng, Y and Peng, Y},
title = {Facilitating multiple nitrite for anammox process directly treating municipal wastewater: Optimized organics utilization and microbial composition.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124460},
doi = {10.1016/j.jenvman.2025.124460},
pmid = {39970657},
issn = {1095-8630},
abstract = {While direct anammox implementation is attractive when treating wastewater, nitrite (NO2[-]-N) availability and excess organic matter significantly limit its practical application. This study proposed partial nitrification and endogenous partial denitrification/anammox (PN/A-EPD/A) for the treatment of real municipal wastewater (COD/N ratio: 2.8) within a single-stage reactor under anaerobic/aerobic/anoxic mode. Interestingly, with reducing dissolved oxygen concentration (5.0 ± 1.0 → 1.0 ± 0.5 mg-O2/L) during aerobic phase, Comammox Nitrospira clade A became dominated and introduced vast nitrate (NO3[-]-N) into the subsequent anoxic stage. Both in-situ and ex-situ tests confirmed that sufficient NO3[-]-N as electron acceptors were in favor of the EPD/A occurrence with endogenous organics utilization, which was obtained by anaerobic endogenous transformation. Metagenomic results confirmed the role of Thauera in facilitating NO3[-]-N→NO2[-]-N process, and further supporting AnAOB. As a result, Ca. Brocadia gradually enriched on granules (from 0.08% to 3.51%) and contributed up to 51.5 % to total inorganic nitrogen removal through the PN/A-EPD/A process. Optimized carbon utilization pathway promoted the re-cooperative balance of microorganisms and this process achieved efficient nitrogen removal (93.5%) and desirable quality of effluent (3.2 mg-N/L) when treating real municipal wastewater.},
}
@article {pmid39970096,
year = {2024},
author = {Begmatov, SA and Beletsky, AV and Rakitin, AL and Lukina, AP and Sokolyanskaya, LO and Rakitin, AV and Glukhova, LB and Mardanov, AV and Karnachuk, OV and Ravin, NV},
title = {[Antibiotic Resistance Genes in Cattle Gut Microbiota: Influence of Housing Conditions].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {6},
pages = {996-1006},
pmid = {39970096},
issn = {0026-8984},
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Housing, Animal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics/drug effects ; beta-Lactams/pharmacology ; beta-Lactamases/genetics ; },
abstract = {Resistance to antimicrobial drugs is an urgent problem not only in public health, but also in animal husbandry. The widespread use of antimicrobials in feed additives is one of the main reasons for the rapid spread of antibiotic resistance in the microbiota of the gastrointestinal tract of farm animals. To characterize antibiotic resistance genes (resistome), we performed metagenomic analysis of the feces of 24 cattle from different regions of Russia, including cows of different breeds and yaks. Animals differed in the type of housing: year-round on pastures or in barns of conventional farms, with consumption of feed additives. Although genes of resistance to aminoglycosides, β-lactams, glycopeptides, MLS antibiotics (macrolides, lincosamides, and streptogramins), phenicols, and tetracyclines were detected in samples from both groups of animals, the content of the resistome in the fecal microbiome of stall-bred cattle was about ten times higher than in animals kept on pastures. The resistome of stall cattle was dominated by β-lactamases and tetracycline resistance genes, the content of which in the microbiome was 24 and 60 times higher, respectively, than in animals kept on pastures. Apparently, the spread of resistance to β-lactams and tetracyclines in stall cattle reflects the active use of these antibiotics in livestock production. Metagenomic analysis of livestock feces can be used to quantify antibiotic resistance genes for the purpose of monitoring antimicrobial drugs used in animal husbandry.},
}
@article {pmid39969428,
year = {2025},
author = {Bloom, PP and Bassis, CM and Crossette, E and Silber, JL and Norman, JM and Young, VB and Lok, ASF},
title = {Safety and efficacy of a defined bacterial consortium, VE303, to treat HE.},
journal = {Hepatology communications},
volume = {9},
number = {3},
pages = {},
doi = {10.1097/HC9.0000000000000650},
pmid = {39969428},
issn = {2471-254X},
mesh = {Humans ; Male ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects ; *Hepatic Encephalopathy/drug therapy ; Aged ; Treatment Outcome ; Vancomycin/therapeutic use/adverse effects ; Anti-Bacterial Agents/therapeutic use/adverse effects/administration &amp; dosage ; Feces/microbiology/chemistry ; Lactulose/therapeutic use ; Rifaximin/therapeutic use ; Adult ; },
abstract = {BACKGROUND: Novel therapies are needed to treat HE, and microbiome modulation is a promising target. VE303 is a defined consortium of 8 purified, clonal bacterial strains, known to produce metabolites that may be beneficial in HE. We evaluated the safety and efficacy of VE303 to treat HE.<br><br>METHODS: We performed a single-center, randomized, placebo-controlled trial of VE303 in adult patients with a history of overt HE (NCT04899115). Eligible patients were taking lactulose and rifaximin, had no recent systemic antibiotics, and had MELD &#x2264;20. All patients received 5 days of oral vancomycin followed by randomization to 14 days of VE303 or placebo (2:1). The primary endpoints were incidence of serious adverse events and change in psychometric HE score (PHES) from baseline to 4 weeks after treatment. Stool samples underwent metagenomic sequencing and metabolite quantification.<br><br>RESULTS: Eighteen patients completed the trial, 56% men, with a mean age of 59 years and a mean MELD of 11. Patients who received VE303 had a mean change in PHES of +1.5 versus -1.0 in those who received a placebo (p=0.20). Two of the 12 patients who received VE303 had at least 1 serious adverse event (all overt HE hospitalizations), compared with 0/6 patients who received a placebo. In the patients who received VE303, 2 of 8 strains engrafted in >50% of patients. Both VE303 strain engraftment and increased stool butyrate production had a trend toward improved PHES.<br><br>CONCLUSIONS: VE303 was well tolerated in patients with cirrhosis and a history of overt HE, leading to the engraftment of certain VE303 strains and a higher percentage of patients with improved PHES.},
}
@article {pmid39969320,
year = {2024},
author = {Liu, K and Yang, Z and Xie, W and Wang, S and Hu, S},
title = {Revision after knee arthroplasty due to Mycoplasma hominis infection: A case report and literature review.},
journal = {Medicine},
volume = {103},
number = {52},
pages = {e41174},
doi = {10.1097/MD.0000000000041174},
pmid = {39969320},
issn = {1536-5964},
support = {2021MS10//Research on the mechanism of PRMT3 regulating trabecular bone chromatin remodeling and participating in ONFH/ ; 2024RS-CXTD-86//Shaanxi Province Innovation Capacity Support Program/ ; },
mesh = {Humans ; Male ; *Mycoplasma Infections/diagnosis/drug therapy ; Aged ; *Arthroplasty, Replacement, Knee/adverse effects ; *Reoperation ; *Mycoplasma hominis/isolation &amp; purification ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Prosthesis-Related Infections/diagnosis/microbiology/drug therapy ; Osteoarthritis, Knee/surgery ; },
abstract = {RATIONALE: Mycoplasma hominis is an opportunistic pathogen commonly found in the human genitourinary system. However, infections caused by Mycoplasma hominis following knee arthroplasty are relatively rare.<br><br>PATIENT CONCERNS: A 68-year-old male patient underwent bilateral total knee arthroplasty 2 years ago due to osteoarthritis. Over the past 3 months, he developed persistent swelling and pain in both knees, along with the formation of a mass in the left knee. The patient also has a history of type 2 diabetes and hypoalbuminemia.<br><br>DIAGNOSES: Joint fluid samples from both knees were collected for metagenomic sequencing (mNGS), which detected Mycoplasma hominis infection. Histopathological examination confirmed chronic infection.<br><br>INTERVENTIONS: The patient underwent 1-stage revision surgery for the left knee, followed by intravenous doxycycline (100&#x2009;mg, q12h) and intra-articular injections of vancomycin (0.5&#x2009;g/d) and meropenem (0.5&#x2009;g/d) for 2 weeks. Afterward, the patient was switched to oral rifampin (450&#x2009;mg daily) and moxifloxacin (400&#x2009;mg daily) for six weeks. Following improvement in the left knee symptoms, 1-stage revision surgery was performed on the right knee. The same antibiotic regimen was used postoperatively.<br><br>OUTCOMES: The patient experienced significant postoperative improvement, with marked pain relief and no signs of recurrent infection. The knee remained stable, and functional recovery was observed. To date, there have been no signs of infection recurrence during follow-up.<br><br>LESSONS: After joint arthroplasty, if a patient has persistent infection symptoms, does not respond to beta-lactam antibiotics, and has negative blood cultures, Mycoplasma infection should be considered. In this instance, the use of mNGS proved highly effective in diagnosing this atypical pathogen. The patient improved significantly after 1-stage revision surgery and targeted antibiotic therapy, though longer follow-up is needed to confirm long-term outcomes. Additionally, limited access to mNGS in some regions may delay diagnosis and treatment.},
}
@article {pmid39969192,
year = {2025},
author = {Haro-Moreno, JM and López-Pérez, M and Molina-Pardines, C and Rodriguez-Valera, F},
title = {Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.},
journal = {mBio},
volume = {},
number = {},
pages = {e0345524},
doi = {10.1128/mbio.03455-24},
pmid = {39969192},
issn = {2150-7511},
abstract = {Genomic diversity in prokaryotic species is largely due to the existence of extensive pangenomes, allowing different gene complements to be drawn depending on the strain. Here, we have studied the diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order as a proxy to measure such genetic diversity in a single population. The study of single-amplified genomes (SAGs) from the whole order found a pattern similar to that of other well-studied microbes, such as the Enterobacteriales or Alteromonas, where distinct OBCs represent strains containing different gene pools. We found that most of the OBC sharing happened among individuals of the same clonal frame (>99% average nucleotide identity). Moreover, given the parsimonious way this cluster changes, the diversity of the OBCs can be extrapolated to the size of the population's pangenome. This assumes that different OBCs correspond to lineages containing unique flexible gene pools, as seen in the aforementioned microbes. Through long-read metagenomics, we could detect 380 different OBCs at a single Mediterranean sampling site. Within a single population (single species and sample) of the endemic Ia.3/VII (gMED) genomospecies, we identified 158 OBCs, of which 130 were unique. These findings suggest that the gene pool within a single population might be substantial (several thousands). While this figure is large, it aligns with the complexity of the dissolved organic matter that these organisms can potentially degrade.IMPORTANCEDifferent strains of the same bacterial species contain very different gene pools. This has been long known by epidemiologists. However, it is unknown what gene pool is present in a single set of environmental conditions, i.e., the same time and place in free-living bacteria. Here, we have leveraged information from SAGs to analyze the diversity of the gene cluster coding for the O-chain polysaccharide, a typical component of the flexible gene pool classically used as a tool to differentiate strains in clinical microbiology. It evolves at a similar rate to the rest of the genome and does not seem to be affected by an arms race with phages. One single species of Pelagibacteriales (gMED) revealed an astounding diversity in one sample studied by long-read metagenomics. Our results point to a large gene pool (local pangenome) present in a single population, which is critical to interpreting the biological meaning of the pangenome, i.e., it provides intrapopulation diversity rather than characterizing strains with different distribution in time and/or space.},
}
@article {pmid39968394,
year = {2025},
author = {Zhao, N and Bai, J and Li, X and Xu, G and Fu, X and Li, J and Niu, L and Yao, J and Zhou, X},
title = {Correlation study on gut microbiota and myosteatosis in patients with liver cirrhosis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1513973},
pmid = {39968394},
issn = {2296-861X},
abstract = {OBJECTIVE: To investigate the features of gut microbiota in cirrhotic patients with myosteatosis and identify specific bacterial species that may be involved in the pathogenesis of myosteatosis.<br><br>METHODS: 80 patients with liver cirrhosis were categorized into the myosteatosis group (n&#x202f;=&#x202f;44) and the non-myosteatosis group (n&#x202f;=&#x202f;36). Metagenomic sequencing was used to analyze the differences in gut microbiota composition between the two groups. Subsequently, the value of meaningful gut microbiota in the diagnosis of myosteatosis in patients with liver cirrhosis was analyzed.<br><br>RESULTS: At the species level, however, 15 bacterial species exhibited significant differences in relative abundance between these two groups. The relative abundance of Roseburia hominis and Subdoligranulum unclassified was inversely associated with mean muscle attenuation density at the L3 level (p&#x202f;<&#x202f;0.05). Assessement of the diagnostic potential of Roseburia hominis and Subdoligranulum unclassified for the development of myosteatosis showed that the areas under the ROC curves (AUCs) was 0.869 [95% confidence interval (CI): 0.709-1.029; p&#x202f;<&#x202f;0.05] for Roseburia hominis and 0.828 (95% CI: 0.6472-1.009; p&#x202f;<&#x202f;0.05) for Subdoligranulum unclassified.<br><br>CONCLUSION: Our study establishes compositional alterations of gut microbiota in patients with liver cirrhosis combined with myosteatosis and suggests the diagnostic potential for using gut microbiota as noninvasive biomarkers.},
}
@article {pmid39968350,
year = {2025},
author = {Lee, CZ and Worsley, SF and Davies, CS and Silan, E and Burke, T and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS},
title = {Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf008},
pmid = {39968350},
issn = {2730-6151},
abstract = {Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.},
}
@article {pmid39968349,
year = {2025},
author = {Bhandari, R and Robbins, CJ and Arora, AK and Chaston, JM and Kang, DS},
title = {Motility genes are associated with the occurrence of Drosophila melanogaster-associated gut microbes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf013},
pmid = {39968349},
issn = {2730-6151},
abstract = {Recent work highlighted the role of motility genes in dispersing fly-associated microbes and their spread between hosts. We investigated whether bacterial genes encoding motility are associated with the occurrence of bacteria above passive dispersal levels in the gut of wild Drosophila melanogaster. We revisited 16S amplicon and shotgun metagenome data of wild flies and correlated four genera of bacteria (Commensalibacter, Gluconobacter, Lactobacillus, and Tatumella) with motility genes. We plotted the microbes against neutral models of ecological drift and passive dispersal. Microbes with positive correlations to motility were exclusively found at or above neutral model predictions, suggesting motility genes are crucial for fly microbiota spread and colonization. This information is crucial for understanding how specific gene functions contribute to microbial community dispersal and colonization within the fly host. Moreover, this study's findings serve as a proof of concept for using the neutral model to predict microbial functions essential for survival and dissemination in diverse hosts.},
}
@article {pmid39968048,
year = {2024},
author = {Nene, M and Kunene, NW and Pierneef, R and Hadebe, K},
title = {Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1487595},
pmid = {39968048},
issn = {1664-302X},
abstract = {INTRODUCTION: The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.<br><br>METHODS: Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.<br><br>RESULTS: Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration.<br><br>DISCUSSION: The detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.},
}
@article {pmid39968047,
year = {2024},
author = {Ling, M and Szarvas, J and Kurmauskaitė, V and Kiseliovas, V and Žilionis, R and Avot, B and Munk, P and Aarestrup, FM},
title = {High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1516656},
pmid = {39968047},
issn = {1664-302X},
abstract = {Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics to study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling high-throughput sequencing of genetic material from thousands of singular bacterial cells in parallel. Here, we validated the use of microfluidics and semi-permeable capsules (SPCs) technology (Atrandi) to isolate individual bacterial cells from sewage and pig fecal samples. Our method involves extracting and amplifying single bacterial DNA within individual SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding and short-read sequencing. We tested two different sequencing approaches with different numbers of SPCs from the same sample for each sequencing run. Using a deep sequencing approach, we detected 1,796 and 1,220 SAGs, of which 576 and 599 were used for further analysis from one sewage and one fecal sample, respectively. In shallow sequencing data, we aimed for 10-times more cells and detected 12,731 and 17,909 SAGs, of which we used 2,456 and 1,599 for further analysis for sewage and fecal samples, respectively. Additionally, we identified the top 10 antimicrobial resistance genes (ARGs) in both sewage and feces samples and linked them to their individual host bacterial species.},
}
@article {pmid39967836,
year = {2025},
author = {Álvarez-Narváez, S and Harrell, TL and Nour, I and Mohanty, SK and Conrad, SJ},
title = {Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1498921},
pmid = {39967836},
issn = {2673-7647},
abstract = {Since viruses are obligate intracellular pathogens, sequencing their genomes results in metagenomic data from both the virus and the host. Virology researchers are constantly seeking new, cost-effective strategies and bioinformatic pipelines for the retrieval of complete viral genomes from these metagenomic samples. Avian orthoreoviruses (ARVs) pose a significant and growing threat to the poultry industry and frequently cause economic losses associated with disease in production birds. Currently available commercial vaccines are ineffective against new ARV variants and ARV outbreaks are increasing worldwide, requiring whole genome sequencing (WGS) to characterize strains that evade vaccines. This study compares the effectiveness of long-read and short-read sequencing technologies for obtaining ARV complete genomes. We used eight clinical isolates of ARV, each previously processed using our published viral genome enrichment protocol. Additionally, we evaluate three assembly methods to determine which provided the most complete and reliable whole genomes: De novo, reference-guided or hybrid. The results suggest that our ARV genome enrichment protocol caused some fragmentation of the viral cDNA that impacted the length of the long reads (but not the short reads) and, as a result, caused a failure to produce complete genomes via de novo assembly. Overall, we observed that regardless of the sequencing technology, the best quality assemblies were generated by mapping quality-trimmed reads to a custom reference genome. The custom reference genomes were in turn constructed with the publicly available ARV genomic segments that shared the highest sequence similarity with the contigs from short-read de novo assemblies. Hence, we conclude that short-read sequencing is the most suitable technology to combine with our ARV genome enrichment protocol.},
}
@article {pmid39967182,
year = {2025},
author = {Mu, Y and Yao, S and Huang, Y and Zhu, Z and Li, D and Song, Y and Liu, Z and Zhang, C and Yu, S},
title = {Unveiling the metabolic heterogeneity and formation mechanism in Chinese typical Daqu based on Qu-omics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {202},
number = {},
pages = {115735},
doi = {10.1016/j.foodres.2025.115735},
pmid = {39967182},
issn = {1873-7145},
mesh = {*Metabolomics ; Alcoholic Beverages/analysis ; Volatile Organic Compounds/analysis/metabolism ; Odorants/analysis ; Taste ; Bacteria/classification/metabolism/genetics ; Pyrazines/metabolism/analysis ; Metabolome ; Humans ; China ; East Asian People ; },
abstract = {The metabolic characteristics of Daqu are crucial factors affecting the sensory attributes of Baijiu. However, the mechanisms underlying the development of Daqu's metabolic profile, particularly the relationship with functional species, remain insufficiently understood. Therefore, we employed Qu-omics to comprehensively analyze the metabolic profiles of the three typical types of Daqu, namely high-, medium-, and low-temperature Daqu (HTD, MTD, and LTD). Flavoromics and metabolomics analyses revealed that the concentrations of both volatile and non-volatile compounds were highest in MTD, followed by those in LTD, which were characterized by elevated levels of esters, alcohols, and organic acids. In contrast, HTD exhibited a distinct metabolic profile, with a significantly higher abundance of aldehydes, ketones, pyrazines, amino acids, and small peptides. Additionally, 47 volatiles and 26 non-volatiles were identified as differential markers among three types of Daqu, including aroma-active compounds such as 2,5-dimethylpyrazine and phenethyl alcohol. The metabolic pathways associated with these metabolites were reconstructed by integrating metagenomic datasets, which highlighted the potential role of functional bacteria in shaping Daqu's metabolic profiles. Specifically, Staphylococcus gallinarum, Brevibacterium intestinavium, and Kroppenstedtia eburnean may play essential roles in HTD, while Bacillus velezensis/Weissella cibaria and Kosakonia cowanii/Pantoea agglomerans in MTD and LTD, respectively. These findings enhance our understanding of the metabolic diversity of Chinese Daqu and provide valuable insights for flavor regulation.},
}
@article {pmid39967175,
year = {2025},
author = {Aragão, MOP and Lima, FR and Passamani, FRF and Santos, MAA and Rezende, JP and Batista, LR},
title = {Fungal and bacterial diversity present on the rind and core of Natural Bloomy Rind Artisanal Minas Cheese from the Canastra region, Brazil.},
journal = {Food research international (Ottawa, Ont.)},
volume = {202},
number = {},
pages = {115724},
doi = {10.1016/j.foodres.2025.115724},
pmid = {39967175},
issn = {1873-7145},
mesh = {*Cheese/microbiology ; Brazil ; *Food Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; Animals ; Microbiota/genetics ; Geotrichum/genetics ; Milk/microbiology ; Biodiversity ; Cattle ; Lactococcus/genetics/isolation &amp; purification/classification ; },
abstract = {Globally recognized for its unique sensory attributes, Natural Bloomy Rind Artisanal Minas Cheese (NBRAMC) from the Canastra microregion is made from raw cow's milk using a natural starter culture derived from the local environment. During ripening process, microorganisms, predominantly Geotrichum candidum, develop on the surface, with the microbial community playing a crucial role in shaping the cheese's distinctive characteristics. This study aimed to characterize the microbial community, including filamentous fungi, yeasts, and bacteria, present in the rind and core of NBRAMC. Amplicon sequencing of the ITS and 16S rRNA gene regions was performed on rind and core samples from cheeses produced at six distinct producers. Results indicated that G. candidum and Diutina catenulata were the most prevalent fungal species, and Candida intermedia being more abundant exclusively in the interior of the cheeses. The bacterial community displayed greater diversity in the rind, with genera such as Lactococcus, Brevibacterium, and Corynebacterium variabile, while Lactococcus and Streptococcus dominated the core. An inverse relationship between D. catenulata and G. candidum abundance was noted. Significant variations in microbial community profiles were found among producers, despite their geographical proximity. While low levels of undesirable fungi were detected, some samples showed a notable presence of undesirable bacteria, indicating potential hygiene issues during cheese handling. These findings provide valuable insights into the microbial dynamics of NBRAMC, supporting the implementation of strategies that can enhance the quality and safety of the product.},
}
@article {pmid39967137,
year = {2025},
author = {Espí-Malillos, A and López-Almela, I and Ruiz-García, P and López-Mendoza, MC and Carrón, N and González-Torres, P and Quereda, JJ},
title = {Raw milk at refrigeration temperature displays an independent microbiota dynamic regardless Listeria monocytogenes contamination.},
journal = {Food research international (Ottawa, Ont.)},
volume = {202},
number = {},
pages = {115637},
doi = {10.1016/j.foodres.2024.115637},
pmid = {39967137},
issn = {1873-7145},
mesh = {*Listeria monocytogenes/growth &amp; development/genetics/isolation &amp; purification ; *Milk/microbiology ; Animals ; *Refrigeration ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; Cold Temperature ; },
abstract = {Dairy products made of raw milk are associated with hypervirulent L. monocytogenes clonal complexes (CCs) CC1, CC4, and CC6, and cause half of the reported listeriosis outbreaks in Europe. However, it is currently unknown whether the overrepresentation of L. monocytogenes hypervirulent clones in dairy products made of raw milk is conditioned by an alteration in the native raw milk microbiota growth and/or composition. In this study, the lag phase, maximal growth rate, and the final maximal concentration of mesophilic aerobic bacteria from native raw milk bacteria were measured at refrigerated temperature (4 °C) in the presence and absence of L. monocytogenes contamination. The raw milk microbiota composition and dynamics were evaluated in the presence and absence of L. monocytogenes hypervirulent (CC1, CC4, CC6), and hypovirulent (CC9 and CC121) clones at 4 °C by using 16S rRNA high-throughput sequencing. Our results showed that the growth and composition of the microbial communities naturally present in raw milk are independent of the contamination with hyper- or hypovirulent L. monocytogenes CCs at refrigeration temperature. Pseudomonas was the most abundant genus in raw milk on days 11 and 21, while Carnobacterium was the second most abundant genus regardless of the contaminant L. monocytogenes CCs. Altogether these results suggest that the overrepresentation of hypervirulent L. monocytogenes CC1, CC4, and CC6 in dairy products is not the consequence of a differential alteration in the native composition of the raw milk microbiota.},
}
@article {pmid39967058,
year = {2025},
author = {Zhang, L and Zhong, Y and Fan, Q and Li, S and Zhu, J and Ma, X and Zhu, Y and Wu, R and Zhang, Z and Zhou, F and Wu, Y and Cai, M and Ma, Y},
title = {Coupled Physical-Biogeochemical Dynamics of Polycyclic Aromatic Compounds in the East China Sea.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11906},
pmid = {39967058},
issn = {1520-5851},
abstract = {Polycyclic aromatic compounds (PACs), including harmful polycyclic aromatic hydrocarbons (PAHs) and more toxic derivatives, are continuously released contaminants. Their provenance and dynamics in coastal oceans remain poorly understood. This study presents the first comprehensive assessment of PACs in coastal oceans by combining their presence with key hydrological and biogeochemical indicators, and potential microbial degradation. High concentrations of Σ92PACs (48-660 ng/L) were observed in the East China Sea, influenced vertically by upwelling and related sediment resuspension during winter. Spatial heterogeneity reveals distinct distribution patterns: PAHs and alkyl-PAHs were mainly influenced by riverine inputs, horizontal transport via coastal currents, and fronts acting as barriers, in contrast, oxygen-PAHs and nitro-PAHs were primarily shaped by secondary transformations within warm water masses rich in nutrients. The relationship between dissolved PACs and chlorophyll a underscores the dominance of biodegradation over the marginal biological pump effect during wintertime low primary productivity. Metagenomic analysis further highlights microbial degradation as a crucial PAC removal pathway, with enhanced microbial diversity driven by terrigenous advection and upwelling. The methodologies and findings of this research provide valuable insights into PAC cycling in coastal oceans.},
}
@article {pmid39966722,
year = {2025},
author = {Wang, J and Song, M and Yao, L and Li, P and Si, E and Li, B and Meng, Y and Ma, X and Yang, K and Zhang, H and Shang, X and Wang, H},
title = {Metagenomic analysis reveal the phytoremediation effects of monocropping and intercropping of halophytes Halogeton glomeratus and Suaeda glauca in saline soil of Northwestern China.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {213},
pmid = {39966722},
issn = {1471-2229},
support = {32001514//National Natural Science Foundation of China/ ; 31960072//National Natural Science Foundation of China/ ; 20JR10RA507//Key Projects of Natural Science Foundation of Gansu Province/ ; 22JR5RA880//Key Projects of Natural Science Foundation of Gansu Province/ ; Ganfx-03Y06//Fuxi Talent Project of Gansu Agricultural University/ ; GAUfx-04Y011//Fuxi Talent Project of Gansu Agricultural University/ ; 2021CYZC-12//Industrial Support Project of Colleges and Universities in Gansu Province/ ; Grant CARS-05-04B-2//China Agriculture Research System/ ; },
abstract = {AIMS: Planting halophytes is a widely used method of phytoremediation for saline soils. The succulent halophytes Halogeton glomeratus and Suaeda glauca are widely used for remediation of saline soil in the arid region of Northwestern China. However, whether intercropping of H. glomeratus and S. glauca can increase the improvement effect for saline soil is yet to be proved.<br><br>MATERIALS AND METHODS: Therefore, this study analyzed three phytoremediation planting modes: monocropping of H. glomeratus (Hg), monocropping of S. glauca (Sg), and H. glomeratus and S. glauca intercropping (Hg||Sg). These were applied in field experiments, with biomass and soil physicochemical properties measured for each treatment, and the mechanism was analyzed using macrogenomics.<br><br>RESULTS: After harvesting the halophytes after one season, the Hg treatment had the highest dry biomass and soil total dissolved salt content was reduced; correspondingly, soil pH were decreased and soil organic matter content were increased. The results showed that Actinobacteria, Acidobacteria and Proteobacteria were the dominant phylum under the four treatments. This suggests that Hg treatment was more capable of producing microorganisms favorable to saline soil remediation.<br><br>CONCLUSIONS: Thus, H. glomeratus monocropping is a more effective phytoremediation strategy for saline soil in the dry zone of Northwestern China.},
}
@article {pmid39966439,
year = {2025},
author = {Chen, X and Yin, X and Xu, X and Zhang, T},
title = {Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1744},
pmid = {39966439},
issn = {2041-1723},
support = {T21-705/20-N//University Grants Committee (UGC)/ ; },
mesh = {*Metagenome/genetics ; Humans ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Primates/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.},
}
@article {pmid39965710,
year = {2025},
author = {Qiu, H and Zhao, W and Qin, Y and Wang, Y and Bai, M and Su, S and Wang, C and Zhao, Z},
title = {Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132248},
doi = {10.1016/j.biortech.2025.132248},
pmid = {39965710},
issn = {1873-2976},
abstract = {Ammonia-oxidizing activity of different ammonia-oxidizing microorganisms (AOMs), such as ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammoxs), were investigated by adding the inhibitors such as 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide, octyne, and KCLO3 in biofilm systems with different salinities. It was found that the ammonia-oxidizing activity of all AOMs gradually decreased with increasing salinity. The ammonia-oxidizing activity of AOB was consistently higher than those of AOA and comammox at different salinities. Moreover, nitrite-oxidizing bacteria (NOB) were more sensitive to changes in salinity than AOMs. Metagenomic analysis revealed that nitrifiers were detected at high level, with the AOB Nitrosomonas sp. comprising 24.9 % and the NOB Nitrospira sp. comprising 47.2% of all nitrifiers. The main functional genes involved in the nitrification reaction were amoABC, hao, and nxrAB. This study demonstrates that higher abundance of functional microorganisms and genes is related to the ammonia-oxidizing activity and ammonia removal contribution rate.},
}
@article {pmid39965343,
year = {2025},
author = {Šaula, T and Cigić, B and Jamnik, P and Kralj Cigić, I and Poklar Ulrih, N and Požrl, T and Marolt, G},
title = {Enrichment of the nutritional value of pea flour milling fractions through fermentation.},
journal = {Food chemistry},
volume = {476},
number = {},
pages = {143303},
doi = {10.1016/j.foodchem.2025.143303},
pmid = {39965343},
issn = {1873-7072},
abstract = {In this work, pea flour and two milling fractions obtained by industrial-scale air classification were characterized and fermented by Lactiplantibacillus plantarum to increase their nutritional value. Scanning electron microscopy and chemical analysis revealed major differences in the morphology and composition of the flours. Protein-rich (43.7 %) fraction exhibits a few-fold higher mineral, spermidine (290 μg/g), but also a higher phytate (20.4 mg/g) content compared to starch-rich fraction. Flour type and inoculum majorly influenced the composition of the fermented product. In spontaneously fermented flours, biogenic amines accumulated up to 6.6 mg/g, which was the main drawback besides the large variations between batches, as confirmed by metagenomic analysis. Higher contents of lactic acid, free amino groups formed by proteolysis and gamma-aminobutyric acid were determined in inoculated fermentations of protein rich fraction, whereas a higher relative bioavailability of minerals was found in the inoculated starch-rich fraction, as the phytate content was reduced by 42 %.},
}
@article {pmid39966546,
year = {2025},
author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M},
title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {39966546},
issn = {1530-0447},
abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.<br><br>METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N&#x2009;=&#x2009;41&#x2009;+&#x2009;41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.<br><br>RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.<br><br>CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.<br><br>IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.},
}
@article {pmid39966520,
year = {2025},
author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM},
title = {Metagenomic estimation of dietary intake from human stool.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {39966520},
issn = {2522-5812},
support = {R01DK133468//U.S. Department of Health &amp; Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; },
abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.},
}
@article {pmid39966419,
year = {2025},
author = {Heidrich, V and Fackelmann, G and Malesevic, M and Armanini, F and Dey, H and Mengoni, C and Stanisavljevic, N and Vukotic, G and Segata, N},
title = {Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {30},
pmid = {39966419},
issn = {2055-5008},
abstract = {Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.},
}
@article {pmid39965493,
year = {2025},
author = {Zhang, H and Pan, F and Wen, Z and Chen, W and Zhou, C},
title = {Impacts of successive Chinese fir plantations on soil carbon and nitrogen dynamics: Conclusive insights from metagenomic analysis.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124510},
doi = {10.1016/j.jenvman.2025.124510},
pmid = {39965493},
issn = {1095-8630},
abstract = {Chinese fir forests play a significant role both economically and ecologically, contributing to soil and water conservation while also serving as an efficient timber-producing species that brings economic benefits. However, the issue of soil degradation due to continuous Chinese fir planting cannot be overlooked. Continuous planting leads to a decrease in soil nutrients, a reduction in microbial diversity, and changes in microbial community composition, which in turn affect the abundance of carbon and nitrogen cycle functional genes in Chinese fir forest soils. We utilized metagenomic sequencing technology to investigate the dynamics of microbial community composition and carbon and nitrogen-related functional genes in the soils of Chinese fir forests across different plantation generations, exploring their relationship with soil carbon and nitrogen nutrients. We found that the relative abundance of bacterial communities is dominant in both phylum and genus levels within microbial communities. The partial least squares path models (PLS-PM) indicated that planting generations had a negative effect on dissolved organic carbon (DOC), nitrate nitrogen (NO3[-]-N), and microbial biomass nitrogen (MBN), with a significant negative impact on microbial residual carbon (MRC). Easily utilizable carbon nutrient (DOC) in Chinese fir forest soil showed a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.91, p < 0.01), and on the abundance of methane metabolism functional genes (direct effect = 1.27, p < 0.01). Nitrogen nutrients (NO3[-]-N, MBN) in the soil also had a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.90, p < 0.01). Bacterial communities (Acidobacteria and Verrucomicrobia) had significant negative effects on carbon and nitrogen cycling processes. The abundance of nasA and nirA genes generally showed a decreasing trend with increasing plantation generations. The decrease in available nitrogen nutrients with increased plantation generations was influenced by Assimilatory nitrogen reduction to ammonia (ANRA), an energy-consuming process. In summary, the continuous planting of Chinese fir had significant impacts on the carbon and nitrogen nutrient cycling processes, and it influenced the composition of microbial communities and the spatial distribution of functional genes. Clarifying the changes in carbon and nitrogen nutrient cycling processes in Chinese fir continuous planting provides a reference for maintaining the productivity of Chinese fir plantations.},
}
@article {pmid39965412,
year = {2025},
author = {Secomandi, E and De Gregorio, MA and Garcia-Perez, P and Vaccari, F and Puglisi, E and Lucini, L},
title = {Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.},
journal = {Plant physiology and biochemistry : PPB},
volume = {221},
number = {},
pages = {109646},
doi = {10.1016/j.plaphy.2025.109646},
pmid = {39965412},
issn = {1873-2690},
abstract = {Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.},
}
@article {pmid39965334,
year = {2025},
author = {Zhang, J and Lei, H and Huang, J and Wong, JWC and Li, B},
title = {Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137559},
doi = {10.1016/j.jhazmat.2025.137559},
pmid = {39965334},
issn = {1873-3336},
abstract = {The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&amp;MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&amp;MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&amp;MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&amp;MRGs), Cupriavidus (2 ARGs, 10 BRGs&amp;MRGs), and Bacillus (14 ARGs, 21 BRGs&amp;MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&amp;MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.},
}
@article {pmid39964655,
year = {2025},
author = {Pitt, A and Lienbacher, S and Schmidt, J and Neumann-Schaal, M and Wolf, J and Wenng, H and Oren, A and Huber, Z and Hahn, MW},
title = {Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39964655},
issn = {1618-1905},
abstract = {During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3[T] was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186B[T] and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65% for comparison of strain 1-SAACH[T] with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186B[T] and 2-AUSEE-184A6 revealed 95.76%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3[T] (= DSM 117800[ T] = JCM 37097[ T]) and Aquirufa novilacunae sp. nov. with type strain BAHN-186B[T] (= DSM 118143[ T] = JCM 37099[ T]). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.},
}
@article {pmid39964161,
year = {2025},
author = {Babalola, OO and Adedayo, AA and Akinola, SA},
title = {Microbiome insights from a South African cultural and natural landmark cave using metagenomics next-generation sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0118324},
doi = {10.1128/mra.01183-24},
pmid = {39964161},
issn = {2576-098X},
abstract = {The microbiome study of Sterkfontein Cave (a natural and cultural cave) revealed fascinating insights into its metagenome study and functional annotation. The largely unexplored cave soil microbiota showcases intricate survival adaptations with promising potential for various human applications. Here, we report the microbial diversity and functions associated with Sterkfontein Cave soil.},
}
@article {pmid39963501,
year = {2024},
author = {Nelson, AR and Rhoades, CC and Fegel, TS and Roth, HK and Caiafa, MV and Glassman, SI and Borch, T and Wilkins, MJ},
title = {Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae108},
pmid = {39963501},
issn = {2730-6151},
abstract = {Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.},
}
@article {pmid39963497,
year = {2025},
author = {Van Laere, Y and Fraiture, MA and Gobbo, A and De Keersmaecker, SCJ and Marchal, K and Roosens, NHC and Vanneste, K},
title = {Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1532788},
pmid = {39963497},
issn = {1664-302X},
abstract = {Biopesticides, biological agents for pest control in plants, are becoming increasingly prevalent in agricultural practices. However, no established methodology currently exists to assess their quality, and there are currently no publicly available authenticity and purity evaluations of commercial products. This lack of data may represent risks because of their widespread dispersal in the environment. We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. Four commercially available bioinsecticidal products containing Bacillus thuringiensis serovar kurstaki strain HD-1 were collected from the European market as a case study. Two sequencing approaches were employed: WGS of isolates and metagenomics sequencing of all genetic material in a product. To assess authenticity, isolate WGS data were compared against the publicly available reference genome of the expected strain. Antimicrobial resistance gene content, insecticidal gene content, and single nucleotide polymorphism differences were characterized to evaluate similarity to the reference genome. To assess purity, metagenomic sequencing data were analyzed using read classification and strain differentiation methods. Additionally, long- and short-read data were used to assess potential large-scale structural variations. Our results confirmed all investigated products to be authentic and pure. With the increasing usage of biopesticides, it is crucial to have adequate quality control methods. Our proposed approach could be adapted for other biopesticides, and similar products, providing a standardized and robust approach to contribute to biopesticide safety.},
}
@article {pmid39963423,
year = {2024},
author = {Kelliher, JM and Xu, Y and Flynn, MC and Babinski, M and Canon, S and Cavanna, E and Clum, A and Corilo, YE and Fujimoto, G and Giberson, C and Johnson, LYD and Li, KJ and Li, PE and Li, V and Lo, CC and Lynch, W and Piehowski, P and Prime, K and Purvine, S and Rodriguez, F and Roux, S and Shakya, M and Smith, M and Sarrafan, S and Cholia, S and McCue, LA and Mungall, C and Hu, B and Eloe-Fadrosh, EA and Chain, PSG},
title = {Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {3575-3583},
pmid = {39963423},
issn = {2001-0370},
abstract = {Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.},
}
@article {pmid39962786,
year = {2025},
author = {Li, Y and Zhou, XH and Wang, XD and Wang, CJ and Cao, K and Liu, SX},
title = {[Diagnosis of mucormycosis in three children following hematopoietic stem cell transplantation using metagenomic next-generation sequencing].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {27},
number = {2},
pages = {219-224},
pmid = {39962786},
issn = {1008-8830},
mesh = {Humans ; *Mucormycosis/diagnosis/etiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; *High-Throughput Nucleotide Sequencing ; Female ; Child ; Child, Preschool ; Metagenomics/methods ; },
abstract = {This article reports the clinical characteristics and treatment processes of three cases of mucormycosis occurring after hematopoietic stem cell transplantation in children, along with a review of relevant literature. All three patients presented with chest pain as the initial symptom, and metagenomic next-generation sequencing (mNGS) confirmed the mucycete infection early in all cases. Two patients recovered after treatment, while one succumbed to disseminated infection. mNGS has facilitated early diagnosis and treatment, reducing mortality rates. Additionally, surgical intervention is an important strategy for improving the prognosis of this condition.},
}
@article {pmid39962733,
year = {2025},
author = {Chen, N and Liu, L and Wang, J and Mao, D and Lu, H and Shishido, TK and Zhi, S and Chen, H and He, S},
title = {Novel Gene Clusters for Secondary Metabolite Synthesis in Mesophotic Sponge-Associated Bacteria.},
journal = {Microbial biotechnology},
volume = {18},
number = {2},
pages = {e70107},
doi = {10.1111/1751-7915.70107},
pmid = {39962733},
issn = {1751-7915},
support = {422010882//Startup Foundation of Ningbo University/ ; 422110473//Startup Foundation of Ningbo University/ ; 422207513//Startup Foundation of Ningbo University/ ; 31600016//National Natural Science Foundation of China/ ; 41776168//National Natural Science Foundation of China/ ; 2021Z04//Ningbo Natural Science Foundation/ ; D16013//National 111 Project of China/ ; NNF22OC0080109//Novo Nordisk Fonden/ ; },
mesh = {*Multigene Family ; *Porifera/microbiology ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism/classification ; Animals ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Metagenome ; Peptide Synthases/genetics/metabolism ; Terpenes/metabolism ; Phylogeny ; },
abstract = {Mesophotic coral ecosystems (MCEs) host a diverse array of sponge species, which represent a promising source of bioactive compounds. Increasing evidence suggests that sponge-associated bacteria may be the primary producers of these compounds. However, cultivating these bacteria under laboratory conditions remains a significant challenge. To investigate the rich resource of bioactive compounds synthesised by mesophotic sponge-associated bacteria, we retrieved 429 metagenome-assembled genomes (MAGs) from 15 mesophotic sponges, revealing a strong correlation between bacterial diversity and sponge species. Furthermore, we identified 1637 secondary metabolite biosynthetic gene clusters (BGCs) within these MAGs. Among the identified BGCs, terpenes were the most abundant (495), followed by 369 polyketide synthases (PKSs), 293 ribosomally synthesised and post-translationally modified peptides (RiPPs) and 135 nonribosomal peptide synthetases (NRPSs). The BGCs were classified into 1086 gene cluster families (GCFs) based on sequence similarity. Notably, only five GCFs included experimentally validated reference BGCs from the Minimum Information about a Biosynthetic Gene cluster database (MIBiG). Additionally, an unusual abundance of BGCs was detected in Entotheonella sp. (s191209.Bin93) from the Tectomicrobia phylum. In contrast, members of Proteobacteria and Acidobacteriota harboured fewer BGCs (6-7 on average), yet their high abundance in MCE sponges suggests a potentially rich reservoir of BGCs. Analysis of the BGC distribution patterns revealed that a subset of BGCs, including terpene GCFs (FAM_00447 and FAM_01046), PKS GCF (FAM_00235), and RiPPs GCF (FAM_01143), were widespread across mesophotic sponges. Furthermore, 32 GCFs were consistently present in the same MAGs across different sponges, highlighting their potential key biological roles and capacity to yield novel bioactive compounds. This study not only underscores the untapped potential of mesophotic sponge-associated bacteria as a source of bioactive compounds but also provides valuable insights into the intricate interactions between sponges and their symbiotic microbial communities.},
}
@article {pmid39962698,
year = {2025},
author = {Ye, Y and Guo, XW and Yang, MQ and Min, W and Guo, HJ},
title = {[Microbial Community Structure and Functional Genes of Phosphorus Cycling in Cotton Field Soil Under Long-term Saline Drip Irrigation].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {2},
pages = {1225-1235},
doi = {10.13227/j.hjkx.202402036},
pmid = {39962698},
issn = {0250-3301},
mesh = {*Phosphorus/metabolism ; *Gossypium/growth &amp; development/genetics ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Salinity ; Saline Waters ; Bacteria/genetics/classification/metabolism/growth &amp; development ; },
abstract = {Freshwater resources are scarce in arid regions, and the rational use of brackish water resources can alleviate local freshwater shortages, but long-term brackish drip irrigation increases the risk of soil salinization, which in turn affects soil nutrient transformation and microbial diversity. Soil phosphorus availability is critical for crop growth, yet it is unclear how long-term brackish drip irrigation will affect soil phosphorus transformation. Therefore, to investigate the effects of long-term brackish drip irrigation on soil phosphorus-transforming microorganisms and their functional genes in cotton fields, the experiment was set up with two irrigation water salinities, freshwater （0.35 dS·m[-1], FW） and brackish water （8.04 dS·m[-1], SW）. The results showed that long-term brackish drip irrigation significantly decreased cotton dry matter weight, phosphorus uptake, yield, soil pH, and Ca2-P and Ca10-P contents but significantly increased cotton phosphorus content and soil water content； electrical conductivity； quick phosphorus； and Ca8-P, Al-P, Fe-P, and O-P contents. The dominant species in each treatment at the phylum level were Ascomycetes, Actinobacteria, Acidobacteria, Bacillus, and Greenscapes； and at the phylum level, the dominant species were α-Ascomycetes, Actinobacteria, β-Ascomycetes, Oleococcus thermophilus, and γ-Ascomycetes. including Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi. Select dominant species at the class level included Alphaproteobacteria, Actinomycetia, Betaproteobacteria, Thermoleophilia, and Gammaproteobacteria. Long-term saline drip irrigation significantly reduced the relative abundance of Actinobacteria, Acidobacteria, and Nitrospirae but significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes and significantly reduced the expression levels of the organic phosphorus mineralization gene phnA, transport gene pit, and polyphosphate synthesis gene ppaC. Moreover, it significantly increased the expression levels of the polyphosphate degradation gene HDDC3； organic phosphorus mineralization genes phnG, phoA, phnH, phnL, phnM, phnN, phnP, and phnW； transport genes phnK, phnE, phnC, and phnD； and the regulatory gene phoB. Correlation analysis showed that soil phosphorus-cycling microorganisms and functional genes were closely related to soil physicochemical properties and soil inorganic phosphorus content. Therefore, long-term saline drip irrigation changes the composition of soil phosphorus-cycling microorganisms by affecting soil physical and chemical properties and inorganic phosphorus content, which in turn drives the expression of phosphorus-cycling-related functional genes to regulate and adapt to salt stress.},
}
@article {pmid39962619,
year = {2025},
author = {Foucault, P and Halary, S and Duval, C and Goto, M and Marie, B and Hamlaoui, S and Jardillier, L and Lamy, D and Lance, E and Raimbault, E and Allouti, F and Troussellier, M and Bernard, C and Leloup, J and Duperron, S},
title = {A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {24},
pmid = {39962619},
issn = {2524-6372},
support = {COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; },
abstract = {With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.},
}
@article {pmid39962548,
year = {2025},
author = {Yuan, J and Ma, L and Du, J and Sun, H and Li, S and Zhou, G and Rao, G and Sun, F and Chen, W and Miao, H and Tian, D and Cheng, C and Wang, Y and Li, L and Li, L and Pang, Y},
title = {Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {13},
pmid = {39962548},
issn = {1476-0711},
support = {2024-4-1042//Capital's Funds for Health Improvement and Research/ ; 2024-1-1041//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sensitivity and Specificity ; DNA, Bacterial/genetics ; Male ; Female ; Adult ; Middle Aged ; Nanopore Sequencing/methods ; Genome, Bacterial ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.},
}
@article {pmid39961991,
year = {2025},
author = {Booth, ME and Wood, HM and Travis, MA and , and Quirke, P and Grabsch, HI},
title = {The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {},
number = {},
pages = {},
pmid = {39961991},
issn = {1436-3305},
abstract = {BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.<br><br>METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.<br><br>RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth&#xa0;of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth&#xa0;of invasion&#xa0;were associated with microbiome composition in the TCGA cohort.<br><br>CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.},
}
@article {pmid39961944,
year = {2025},
author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A},
title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39961944},
issn = {1559-0291},
support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.},
}
@article {pmid39961017,
year = {2025},
author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES},
title = {Microbial ecology of Serpentinite-hosted ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf029},
pmid = {39961017},
issn = {1751-7370},
abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.},
}
@article {pmid39960952,
year = {2025},
author = {Liu, H and Li, Q and Ouyang, X and Li, Q and Min, Y and Dai, L},
title = {Diagnosis of early neurobrucellosis using metagenomic next-generation sequencing of the cerebrospinal fluid in nonepidemic zone: Case report and lecture review.},
journal = {Medicine},
volume = {104},
number = {7},
pages = {e41481},
doi = {10.1097/MD.0000000000041481},
pmid = {39960952},
issn = {1536-5964},
mesh = {Humans ; *Brucellosis/diagnosis/cerebrospinal fluid/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; Female ; Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/drug therapy/microbiology ; Doxycycline/therapeutic use ; Male ; Early Diagnosis ; Brucella/isolation &amp; purification ; Adult ; },
abstract = {RATIONALE: Brucella neuropathy is a rare clinical condition, particularly in nonendemic areas, where it often presents with nonspecific symptoms such as fever and headaches, leading to frequent misdiagnoses. In these regions, Brucella antibodies are not routinely tested, and the positive rate of blood cultures is relatively low during the early stage of the disease. In addition, the low culture-positive rate of cerebrospinal fluid (CSF) means that many neurobrucellosis diagnoses rely on peripheral blood cultures or Brucella antibodies, which is not rigorous. This is problematic because the treatment of central nervous system brucellosis differs significantly from that of other types of brucellosis. The purpose of this study is to provide a method for the early diagnosis of Brucella neuropathy in nonendemic areas. We present a case of early-stage neurobrucellosis diagnosed using metagenomic next-generation sequencing (mNGS) of CSF. This approach helps avoid delaying diagnosis in the early stage in nonepidemic areas, potentially reducing the duration before diagnosis, which is of great significance for timely and appropriate treatment.<br><br>PATIENT CONCERNS: The patient had fever, mild headache, and a slight increase in CSF leukocytes.<br><br>DIAGNOSES: CSF mNGS detected Brucella, which was later confirmed by serum Brucella antibody testing.<br><br>INTERVENTIONS: The patient was treated with rifampicin, doxycycline, and ceftriaxone.<br><br>OUTCOMES: The patient experienced significant relief from the headache, and the fever did not recur. Subsequent examinations revealed no abnormalities in the CSF leukocytes or mNGS results.<br><br>LESSONS: We reviewed 10 articles on brucellosis diagnosed using mNGS, including 7 articles on neurobrucellosis (10 cases). Our review highlights the sensitivity of mNGS as a powerful tool for early detection of neurobrucellosis in the CSF. The common symptoms include fever and headache, with brain magnetic resonance imaging detecting lesions in most cases. CSF mNGS results varied, with only a few positive Brucella cultures or antibody tests.},
}
@article {pmid39960906,
year = {2025},
author = {Dong, H and Feng, J and Wu, S and Liang, F and Li, H and Liang, X and Liao, W and Pan, Y and Tang, G and Li, D and Zhou, W and Cao, Z and Wang, W and Hu, J},
title = {First case report of long-term latent infection paracoccidioidomycosis in China.},
journal = {Medicine},
volume = {104},
number = {7},
pages = {e41409},
doi = {10.1097/MD.0000000000041409},
pmid = {39960906},
issn = {1536-5964},
support = {2021-2023//Guangzhou Medical Key Discipline/ ; 202002030152, 202201010744 and 2023A03J0539//Science and Technology Program of Guangzhou/ ; 2023A03J0539//Science and Technology Program of Guangzhou/ ; B2021038//Medical Science Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Paracoccidioidomycosis/diagnosis/drug therapy/epidemiology ; Male ; China/epidemiology ; *Antifungal Agents/therapeutic use ; *Paracoccidioides/isolation &amp; purification ; *Latent Infection/diagnosis/drug therapy ; Voriconazole/therapeutic use/administration &amp; dosage ; Middle Aged ; },
abstract = {RATIONALE: Although paracoccidioidomycosis is one of the most prevalent endemic mycoses in Latin American countries, where at least 10 million people are infected, the prevalence of paracoccidioidomycosis in China remains unknown because no related case has been reported, and its diagnosis is extremely challenging for local clinicians because of the complexity of disease progression and lack of specific evidence.<br><br>PATIENT CONCERNS: Here, we report the first case of PCM in a male patient with a long-term latent infection in China.<br><br>DIAGNOSIS: The results of special staining, immunohistochemistry, lymph node biopsy pathology, and metagenomic second-generation sequencing indicated that the patient was infected with Paracoccidioides brasiliensis.<br><br>INTERVENTIONS: In this case, the patient was administered voriconazole 200&#x2009;mg twice daily.<br><br>OUTCOMES: After continuous treatment for 6 months, the patient's symptoms improved significantly, and the medication was discontinued. The outpatient follow-up revealed no discomfort.<br><br>LESSONS: This case is of great value for the early diagnosis, treatment, and prevention of the spread of this emerging infectious disease in China.},
}
@article {pmid39960726,
year = {2025},
author = {Kenyon, AL and Solomon, IH},
title = {What every neuropathologist needs to know: Update on neuro infectious disease workups and consultation resources.},
journal = {Journal of neuropathology and experimental neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jnen/nlaf009},
pmid = {39960726},
issn = {1554-6578},
abstract = {Efficient histopathological diagnosis of central nervous system infections can be challenging but is critical for therapeutic decision making in cases for which less invasive blood or cerebrospinal fluid testing has been unrevealing. A wide variety of bacteria, fungi, viruses, and parasites can cause infections, particularly in immunocompromised individuals. Histological findings may be nonspecific or overlap with noninfectious inflammatory conditions. To minimize wasted tissue and time, a systematic approach is recommended in which: (1) relevant patient history (eg, comorbidities, travel and other exposures, and immune status) and radiological findings are reviewed, (2) a preliminary differential diagnosis based on this information and on inflammatory patterns and visualization of potential microorganisms on hematoxylin and eosin stains is generated, (3) special stains, immunohistochemistry, in situ hybridization, or molecular testing (pathogen-specific or broad-spectrum) are used for confirmation and further classification, and (4) correlation with culture results and other laboratory testing is performed to arrive at a final integrated diagnosis. Discrepancies between molecular and histological findings are often due to contamination and require careful evaluation to avoid treatment of false positives. Consultation with infectious disease pathologists or public health reference laboratories may be needed to confirm diagnoses of unusual organisms or when specialized testing is required.},
}
@article {pmid39958980,
year = {2025},
author = {Huang, X and Qiu, J and Pan, L and Wang, C and Tang, C},
title = {Acute Necrotizing Fasciitis Caused by Rhizopus Infection in a Patient with Diabetes and Pulmonary Tuberculosis: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {775-782},
pmid = {39958980},
issn = {1178-6973},
abstract = {BACKGROUND: Zygomycosis, also termed mucormycosis, is a rare yet highly fatal fungal infection caused by Mucorales species, notably Rhizopus spp.<br><br>CASE PRESENTATION: This case study details a 72-year-old man with diabetes, pulmonary tuberculosis, and nephrotic syndrome who developed acute necrotizing fasciitis attributable to R. oryzae. Despite initial empirical antibiotic therapy, the infection progressed rapidly. Metagenomic next-generation sequencing (mNGS) facilitated a swift diagnosis, identifying R. oryzae in blood and drainage samples. The treatment included amphotericin B and isavuconazole, along with aggressive surgical debridement. The patient exhibited substantial improvement, and he was discharged after stabilization.<br><br>CONCLUSION: This case highlights the critical role of early diagnosis through mNGS and the need for a multidisciplinary approach to manage severe mucormycosis in immunocompromised patients.},
}
@article {pmid39958933,
year = {2025},
author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P},
title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1511625},
pmid = {39958933},
issn = {2235-2988},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; },
abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.<br><br>METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.<br><br>RESULTS: The &#x3b1;-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.<br><br>DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.},
}
@article {pmid39957783,
year = {2024},
author = {Chattaraj, S and Mitra, D and Chattaraj, M and Ganguly, A and Thatoi, H and Mohapatra, PKD},
title = {Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100286},
pmid = {39957783},
issn = {2666-5174},
abstract = {A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.},
}
@article {pmid39956110,
year = {2025},
author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU},
title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70056},
doi = {10.1111/1462-2920.70056},
pmid = {39956110},
issn = {1462-2920},
support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; },
abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.},
}
@article {pmid39956369,
year = {2025},
author = {Abe, M and Sekizuka, T and Miyazaki, Y},
title = {Gastrointestinal anaerobes and Enterococcus faecalis promote Candida glabrata gastrointestinal colonization and organ dissemination.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102658},
doi = {10.1016/j.jiac.2025.102658},
pmid = {39956369},
issn = {1437-7780},
abstract = {BACKGROUND: Candida glabrata is a common causative pathogen of endogenous candidiasis. It is assumed that the gastrointestinal flora affects C. glabrata gastrointestinal colonization and organ dissemination in the gastrointestinal tract (GIT). However, no reports have yet described the relationships between C. glabrata and bacteria in the GIT. This study aimed to clarify these relationships using a mouse endogenous candidiasis model with cortisone acetate immunosuppression.<br><br>METHODS: Dysbiosis was induced in the GIT by several antibiotic combinations, and then C. glabrata gastrointestinal colonization and organ dissemination were evaluated. Next, metagenomic sequencing analysis of the gastrointestinal flora was performed to identify bacteria associated with C. glabrata organ dissemination. Finally, coinfection experiments were performed using bacteria isolated from the mouse GIT.<br><br>RESULTS: C. glabrata organ dissemination was significantly promoted using specific antibiotics regardless of the amount of colonization in the GIT. Metagenomic sequencing analysis of the gastrointestinal flora showed that Enterococcus species and anaerobes were significantly associated with enhanced organ dissemination, whereas Enterobacterales, such as Escherichia species and Klebsiella species, were associated with the suppression of organ dissemination. In coinfection experiments, Enterococcus faecalis and Faecalibaculum rodentium inoculation, but not either of them, increased C. glabrata organ dissemination without affecting gastrointestinal colonization.<br><br>CONCLUSIONS: Coinfection with gastrointestinal bacteria promoted C. glabrata organ dissemination, which would indicate that gastrointestinal flora could affect C. glabrata dissemination. Therefore, the gastrointestinal flora could be a target for intervention or treatment in clinical settings. Insights from this study would lead to better control of endogenous candidiasis focusing on the gastrointestinal flora.},
}
@article {pmid39955324,
year = {2025},
author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO},
title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5619},
pmid = {39955324},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation &amp; purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; },
abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.},
}
@article {pmid39954816,
year = {2025},
author = {Ladyhina, V and Rajala, E and Sternberg-Lewerin, S and Nazirzadeh, L and Bongcam-Rudloff, E and Dicksved, J},
title = {Methodological aspects of investigating the resistome in pig farm environments.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107103},
doi = {10.1016/j.mimet.2025.107103},
pmid = {39954816},
issn = {1872-8359},
abstract = {A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.},
}
@article {pmid39954461,
year = {2025},
author = {Schacksen, PS and Macêdo, WV and Rellegadla, S and Vergeynst, L and Nielsen, JL},
title = {Dynamics of nitrogen-transforming microbial populations in wastewater treatment during recirculation of hydrothermal liquefaction process-water.},
journal = {Water research},
volume = {276},
number = {},
pages = {123254},
doi = {10.1016/j.watres.2025.123254},
pmid = {39954461},
issn = {1879-2448},
abstract = {The global reliance on non-renewable fossil fuels highlights the urgent need for sustainable alternative energy sources. Hydrothermal liquefaction (HTL) offers a promising solution by converting biomass, such as sewage sludge, into biocrude oil. However, the integration of excess HTL-process water (HTL-PW), a by-product of this process, into conventional wastewater treatment requires careful evaluation. This study investigates the effects of recirculating HTL-PW in sequencing batch reactors (SBRs) using synthetic wastewater. Two SBRs were operated in parallel: one fed 0.15 % (v/v) HTL-PW and the other with only synthetic feed. The reactor receiving HTL-PW demonstrated superior stability, effective nitrification, and consistent denitrification with no adverse effects on nitrogen species turnover. A comprehensive approach combining 16S rRNA gene amplicon sequencing for relative abundance and metagenomic analysis, for enhanced resolution of nitrogen-transforming populations, revealed the genetic repertoire and potential of 58±4 % and 65±4 % of the genus-level annotations from the HTL-PW and control reactors, respectively. The HTL-PW-fed reactor maintained robust performance, with microbial community analysis revealing a strong association between nitrogen transformations and specific microbial taxa, thereby explaining the observed reactor stability and efficiency in nitrogen conversion. These findings demonstrate the feasibility of integrating HTL-PW into wastewater treatment systems, showing that recirculating HTL-PW at the tested concentrations does not adversely affect nitrogen transformations, supports stable nitrification and denitrification, ensures complete ammonium utilisation, and promotes diverse and dynamic microbial communities similar to those in full-scale wastewater treatment plants.},
}
@article {pmid39954395,
year = {2025},
author = {Xiao, H and Zhou, C and Xiao, Z and Cai, F and Zhang, S and Sheng, S and Jin, C and Fu, Y},
title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples offers diagnostic utility in bacteriologically negative pulmonary tuberculosis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {4},
pages = {116725},
doi = {10.1016/j.diagmicrobio.2025.116725},
pmid = {39954395},
issn = {1879-0070},
abstract = {Rapid diagnosing Mycobacterium tuberculosis (M. tb) in patients with pulmonary tuberculosis (PTB) cases is critical, particularly in cases without bacteriologically confirmed disease, as it enables timely treatment initiation and can thus interrupt further disease transmission. In this study, the utility of metagenomic next-generation sequencing (mNGS) as a diagnostic tool was evaluated using samples of bronchoalveolar lavage fluid (BALF) samples from 300 bacteriologically negative PTB (BN-PTB) patients hospitalized from January 2020 through December 2023. The diagnostic performance of mNGS was compared to that of acid-fast staining (AFS), conventional Roche culture, and the Xpert method among these BN-PTB patients, using clinical diagnosis as the gold standard. The final analyses enrolled 112 PTB patients and 188 non-PTB cases. These analyses revealed that mNGS-based M. tb detection yields a sensitivity of 94.64 % (106/112), a specificity of 98.94 % (186/188), a positive predictive value (PPV) of 98.15 % (106/108), and a negative predictive value (NPV) of 96.88 % (186/192). This mNGS approach outperformed the AFS, Roche culture, and Xpert methods in terms of sensitivity, specificity, PPV, and NPV (p < 0.05). The superior diagnostic performance of this approach was further supported by its area under the curve and corresponding confidence intervals. Together, these data demonstrate that mNGS can improve the detection of M. tb in BALF samples from BN-PTB patients with high levels of speed, sensitivity, and specificity. This mNGS approach may thus be a valuable diagnostic tool for the rapid detection of M. tb in BN-PTB, providing a foundation for the precision diagnosis and treatment of PTB in the future.},
}
@article {pmid39954350,
year = {2025},
author = {Dong, Y and Liu, H and Habimana, O},
title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.},
journal = {International journal of food microbiology},
volume = {432},
number = {},
pages = {111098},
doi = {10.1016/j.ijfoodmicro.2025.111098},
pmid = {39954350},
issn = {1879-3460},
abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.},
}
@article {pmid39954080,
year = {2025},
author = {Liang, Y and Zhao, Y and Yin, Z and Zeng, X and Han, X and Wen, M},
title = {Functional and structural insights into α-L-Rhamnosidase: cloning, characterization, and decoding evolutionary constraints through structural motif.},
journal = {Archives of microbiology},
volume = {207},
number = {3},
pages = {61},
pmid = {39954080},
issn = {1432-072X},
support = {2023KF005//Yunnan University/ ; 2023KF005//Yunnan University/ ; },
mesh = {*Glycoside Hydrolases/genetics/chemistry/metabolism ; *Cloning, Molecular ; Catalytic Domain ; Substrate Specificity ; Amino Acid Sequence ; Amino Acid Motifs ; Evolution, Molecular ; Bacterial Proteins/genetics/chemistry/metabolism ; Binding Sites ; Phylogeny ; Models, Molecular ; Bacteria/enzymology/genetics ; },
abstract = {α-L-rhamnosidase [E.C. 3.2.1.40] is important in various industrial and biotechnological applications. However, limited knowledge of the structural features of its active site residues and their local geometric arrangements during substrate interaction hinders further application development. In this study, we examined functionally characterized microbial α-L-rhamnosidases. Despite considerable differences in their global structures, the local structures of the substrate-binding sites and key residues were highly conserved. Using the local structural motif, we characterized α-L-rhamnosidase genes from metagenomic samples of traditional fermentation starters. To comprehensively understand the distribution of α-L-rhamnosidases with this motif in the AlphaFold database, we screened 26,858 α-L-rhamnosidase structures. Our findings showed that only 5678 out of 26,858 structures contain the specific conserved motifs, emphasizing their potential significance in mining enzyme function. Moreover, the analysis of structural diversity among representative enzymes demonstrated variation in the number and types of domains within this enzyme family. Further investigation of representative α-L-rhamnosidase sequences with this structural motif confirmed the evolutionary constraints of 15 key residues, indicating strong selective pressures to maintain these elements essential for enzyme functionality. These residues were consistently present across ancestral sequences, underscoring their importance throughout the enzyme's evolutionary history. This study suggests that structure-guided approaches are valuable for discovering functional enzymes. Identifying conserved motif across diverse microbial taxa not only aids in predicting enzyme functionality but also offers opportunities for enzyme engineering and biotechnological applications.},
}
@article {pmid39955557,
year = {2025},
author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A},
title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {15},
pmid = {39955557},
issn = {2524-4671},
support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.},
}
@article {pmid39954481,
year = {2025},
author = {El Houari, A and Carpenter, M and Chaplin, D and Golyshin, P and McDonald, JE},
title = {Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {2},
pages = {126590},
doi = {10.1016/j.syapm.2025.126590},
pmid = {39954481},
issn = {1618-0984},
abstract = {Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5[T], was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5-1 g.L[-1], 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5[T] was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5[T] grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112[T] (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5[T] belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5[T] is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5[T] (= DSM 112743[T] = ATCC TSD-267[T]) being the type of strain. This study highlights the biotechnological potential of strain m5[T], specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.},
}
@article {pmid39954460,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Ren, J and Qi, J and Zhu, M and Feng, Y and Li, M and Wang, B and Li, X and Song, C},
title = {Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China.},
journal = {Water research},
volume = {276},
number = {},
pages = {123285},
doi = {10.1016/j.watres.2025.123285},
pmid = {39954460},
issn = {1879-2448},
abstract = {Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.},
}
@article {pmid39953827,
year = {2025},
author = {Reed, GM and Strickland, AK and Mutchler, CT and Ochoa, AR and Asin, SN and Blackburn, AN},
title = {Evaluating Nanopore Sequencing as a Respiratory Virus Diagnostic Tool for the Prehospital Setting.},
journal = {Military medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/milmed/usaf046},
pmid = {39953827},
issn = {1930-613X},
support = {DS21RES11//Defense Health Agency/ ; DS21RES11//Defense Health Agency/ ; },
abstract = {INTRODUCTION: Upper respiratory tract infections are a strain on military that results in lost duty days and an overall reduced readiness of the force. Improved diagnostic testing would enable better force health protection measures and earlier treatment of illness. Lightweight portable devices are preferred for diagnostic testing in austere environments where they are sometimes needed during military deployment. Current diagnostic testing is targeted to specific pathogens despite multiple pathogens that present with similar symptoms. In practice the pathogens that cause upper respiratory tract infections often go unidentified, which could be improved using agnostic or semi-agnostic diagnostic testing. Here, we performed an evaluation of shotgun metagenomic sequencing using the Oxford Nanopore Technologies (ONT) Rapid Sequencing Kit as a method for diagnostic testing of upper respiratory tract infections. This sequencing library preparation kit was chosen because of its ease of use and compatibility with the ONT MinION, a lightweight portable sequencer.<br><br>MATERIALS AND METHODS: Samples from patients with symptoms of upper respiratory tract infections were collected at Wilford Hall Ambulatory Surgical Center under an approved IRB protocol. Nasal rinse samples from 59 study participants were tested using the BioFire FilmArray Respiratory 2.1 Panel as well as shotgun metagenomic sequencing using ONT Rapid Sequencing Kit and ONT R9.4.1 flow cells.<br><br>RESULTS: A mixture of various viral pathogens was present among the 59 samples used in this study. We observed high specificity and modest sensitivity to detect the identified pathogens using shotgun metagenomic sequencing. Shotgun metagenomic sequencing detected additional pathogens that were missed by the BioFire FilmArray Respiratory 2.1 Panel, which are discussed. Lastly, we observe modest evidence of nonuniformity of the proportion of reads belonging to the pathogen during the duration of sequencing runs, which has implications for improving sensitivity by increasing the amount of sequencing performed.<br><br>CONCLUSIONS: Overall, ONT Rapid Sequencing Kit combined with alignment to a known panel of pathogens has shown great potential utility in our hands for quickly and accurately identifying viral respiratory pathogens. This, combined with its ease of use and portability, makes it a great candidate for further research and development toward a deployable agnostic diagnostic testing platform.},
}
@article {pmid39953749,
year = {2025},
author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A},
title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17695},
doi = {10.1111/mec.17695},
pmid = {39953749},
issn = {1365-294X},
support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.},
}
@article {pmid39953591,
year = {2025},
author = {Chen, H and Yao, X and Yang, C and Zhang, Y and Dong, H and Zhai, J and Fan, D and Zhou, Q},
title = {Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {186},
pmid = {39953591},
issn = {1479-5876},
support = {YCZYPT [2018]06//National Human Genetic Resource Sharing Service Platform/ ; },
mesh = {Humans ; *Lung Neoplasms/blood/microbiology/genetics ; *Metagenomics/methods ; *Biomarkers, Tumor/blood ; Female ; Male ; Middle Aged ; Metagenome/genetics ; Aged ; Case-Control Studies ; ROC Curve ; },
abstract = {Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.},
}
@article {pmid39953490,
year = {2025},
author = {Zhan, X and Tian, X and Zhang, C and Ye, J},
title = {A case of explosive community-acquired pneumonia and septic shock caused by Acinetobacter pittii.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {80},
doi = {10.1186/s12890-024-03457-0},
pmid = {39953490},
issn = {1471-2466},
mesh = {Humans ; *Shock, Septic/microbiology ; *Community-Acquired Infections/microbiology ; *Acinetobacter Infections/diagnosis/drug therapy/microbiology/complications ; *Acinetobacter/isolation &amp; purification ; *Anti-Bacterial Agents/therapeutic use ; Male ; Pneumonia, Bacterial/microbiology/complications/diagnosis ; Middle Aged ; Female ; Aged ; Retrospective Studies ; },
abstract = {BACKGROUND: Acinetobacter pittii, belongs to the genus Acinetobacter, has a special pathogenesis and is commonly known as nosocomial pathogen; community infections are rare.<br><br>OBJECTIVE: To present a case study of community-acquired pneumonia and septic shock resulting from infection with Acinetobacter pittii and to investigate the diagnosis, clinical features and treatment of Acinetobacter pittii infection.<br><br>METHODS: The clinical features and prognosis of patients with Acinetobacter pittii, infection were analyzed retrospectively.<br><br>RESULTS: The sepsis caused by Acinetobacter pittii, was improved after treatment.<br><br>DISCUSSION AND CONCLUSION: Pneumonia caused by fully sensitive hypervirulent Acinetobacter pittii is rare, usually with acute course, severe illness and high mortality. It is necessary to identify the infectious agent as soon as possible, and early treatment can improve the success rate of treatment.},
}
@article {pmid39952920,
year = {2025},
author = {Jiang, Q and Cao, L and Han, Y and Li, S and Zhao, R and Zhang, X and Ruff, SE and Zhao, Z and Peng, J and Liao, J and Zhu, B and Wang, M and Lin, X and Dong, X},
title = {Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1646},
pmid = {39952920},
issn = {2041-1723},
mesh = {*Geologic Sediments/microbiology ; *Nitrogen/metabolism ; *Bacteria/genetics/metabolism/classification ; Seawater/microbiology ; Cold Temperature ; Metagenomics/methods ; Nitrogen Cycle/genetics ; Metagenome/genetics ; Ammonium Compounds/metabolism ; Phylogeny ; Oceans and Seas ; },
abstract = {Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, [15]N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96-7.63 Tg N yr[-1] (1.65-2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.},
}
@article {pmid39952771,
year = {2025},
author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E},
title = {Exploring viral diversity in fermented vegetables through viral metagenomics.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104733},
doi = {10.1016/j.fm.2025.104733},
pmid = {39952771},
issn = {1095-9998},
mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation &amp; purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation &amp; purification/classification/genetics ; Enterobacteriaceae/isolation &amp; purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation &amp; purification/genetics/classification ; },
abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.},
}
@article {pmid39952762,
year = {2025},
author = {Li, Z and Liao, Y and Huang, C and Liu, J and Kong, X and Li, L and Li, Z and Gui, Y},
title = {Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104718},
doi = {10.1016/j.fm.2024.104718},
pmid = {39952762},
issn = {1095-9998},
mesh = {*Fermentation ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Flavoring Agents/metabolism/chemistry ; *Fungi/classification/metabolism/genetics/isolation &amp; purification ; China ; Gas Chromatography-Mass Spectrometry ; Amino Acids/metabolism/analysis ; Solid Phase Microextraction ; Food Microbiology ; Mycobiome ; Chromatography, High Pressure Liquid ; Condiments/microbiology/analysis ; },
abstract = {Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.},
}
@article {pmid39952751,
year = {2025},
author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F},
title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104734},
doi = {10.1016/j.fm.2025.104734},
pmid = {39952751},
issn = {1095-9998},
mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; },
abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.},
}
@article {pmid39952592,
year = {2025},
author = {Sun, T and Delaplace, P and Li, G and James, A and Pan, J and Zhang, J},
title = {Novel insights into the effect of arbuscular mycorrhizal fungi inoculation in soils under long-term biosolids application: emphasis on antibiotic and metal resistance genes, and mobile genetic elements.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125846},
doi = {10.1016/j.envpol.2025.125846},
pmid = {39952592},
issn = {1873-6424},
abstract = {The application of biosolids can improve soil fertility and crop productivity but also accompanies risks of heavy metals and antibiotics introduction. In the presence of heavy metals contamination, using arbuscular mycorrhizal fungi (AMF) is a promising strategy to enhance soil microbial community stability and plant tolerance resistance to heavy metals, and to reduce the spread of antibiotic resistance genes (ARGs). The present study investigated the impacts of AMF inoculation on soil and plant heavy metal contents, and soil microbial communities by pot experiments. The results showed that AMF inoculation significantly enhanced plant biomass, and reduced soil and plant heavy metals contents. While AMF inoculation did not alter bacterial and fungal community compositions, it increased bacterial diversity at higher biosolids concentrations. Notably, AMF inoculation enhanced microbial network complexity and increased keystone taxa abundance. Furthermore, several beneficial microorganisms with high resistance to heavy metals were enriched in AMF-inoculated soils. Metagenomic analysis revealed a reduction in the mobile genetic element (MGE) gene IS91 in AMF-inoculated soils and an increase in heavy metal resistance genes compared to soils without AMF. The possibility of reduction in MGE-mediated spread of ARGs is one of the key findings of this study. As a caution, this study also detected enrichment of few ARGs in high biosolids-amended soils with AMF inoculation. Overall, AMF inoculation could be a valuable strategy in agriculture for mitigating the environmental risks associated with biosolids, heavy metals and antibiotic resistance, thereby promoting sustainable soil management and health.},
}
@article {pmid39951448,
year = {2025},
author = {Li, Q and Wu, X and Niu, X and Yu, Z and Fang, S and Chu, X and Zhu, J and Song, Q and Hou, C and Wei, X},
title = {Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0317832},
doi = {10.1371/journal.pone.0317832},
pmid = {39951448},
issn = {1932-6203},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Female ; *Ovariectomy ; *Osteoporosis/drug therapy/metabolism ; *Metabolomics ; Rats ; *Flavonoids/pharmacology ; *Bone Density/drug effects ; *Polypodiaceae ; Metagenomics ; Rats, Sprague-Dawley ; Drugs, Chinese Herbal/pharmacology ; Rhizome ; },
abstract = {TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&amp;E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.},
}
@article {pmid39951402,
year = {2025},
author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M},
title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0306503},
doi = {10.1371/journal.pone.0306503},
pmid = {39951402},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; },
abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.},
}
@article {pmid39951352,
year = {2025},
author = {Li, Q and Tan, D and Xiong, S and Yu, K and Su, Y and Zhu, W},
title = {Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2467185},
doi = {10.1080/19490976.2025.2467185},
pmid = {39951352},
issn = {1949-0984},
mesh = {Animals ; *Glucagon-Like Peptide 1/metabolism/blood ; *Gastrointestinal Microbiome ; Swine ; *Tryptophan/metabolism ; *Lactobacillus/metabolism ; *Appetite/physiology ; Enteroendocrine Cells/metabolism ; Feeding Behavior ; Hypothalamus/metabolism ; },
abstract = {Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.},
}
@article {pmid39950859,
year = {2025},
author = {Ma, Y and Zhang, M and Wang, Z and Cao, L and Li, Y and Wan, Z and Kane, Y and Wang, G and Li, X and Zhang, C},
title = {Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection.},
journal = {Virulence},
volume = {},
number = {},
pages = {2467168},
doi = {10.1080/21505594.2025.2467168},
pmid = {39950859},
issn = {2150-5608},
abstract = {An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1, but had positive corrections with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effect of ART on virome and cytokine profile in HIV-1-infected individuals.},
}
@article {pmid39950834,
year = {2025},
author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS},
title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {3},
pages = {e70023},
doi = {10.1111/liv.70023},
pmid = {39950834},
issn = {1478-3231},
support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; },
abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.<br><br>METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline &#x2265;&#x2009;30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.<br><br>RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9&#x2009;years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p&#x2009;<&#x2009;0.001; Simpson index: p&#x2009;=&#x2009;0.001) and beta diversity (p&#x2009;=&#x2009;0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore&#x2009;=&#x2009;4.27), Lachnospira pectinoschiza (log10LDAscore&#x2009;=&#x2009;3.99), Anaerostipes hadrus (log10LDAscore&#x2009;=&#x2009;3.98), Roseburia faecis (log10LDAscore&#x2009;=&#x2009;3.97), Roseburia inulinivorans (log10LDAscore&#x2009;=&#x2009;3.58) and Agathobaculum butyriciproducens (log10LDAscore&#x2009;=&#x2009;2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p&#x2009;=&#x2009;0.015), A. hadrus (aOR:35.0; p&#x2009;=&#x2009;0.032) and A. butyriciproducens (aOR:22.3; p&#x2009;=&#x2009;0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).<br><br>CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.},
}
@article {pmid39950813,
year = {2025},
author = {Seguel Suazo, K and Nierychlo, M and Kondrotaite, Z and Petriglieri, F and Peces, M and Singleton, C and Dries, J and Nielsen, PH},
title = {Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148524},
doi = {10.1128/aem.01485-24},
pmid = {39950813},
issn = {1098-5336},
abstract = {Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.},
}
@article {pmid39950811,
year = {2025},
author = {Kwon, J and Tanner, W and Kong, Y and Wade, M and Bitler, C and Chiavegato, MB and Pettigrew, MM},
title = {Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0073824},
doi = {10.1128/msphere.00738-24},
pmid = {39950811},
issn = {2379-5042},
abstract = {Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M[2] = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.},
}
@article {pmid39950541,
year = {2025},
author = {Akter, MS and Punom, NJ and Eshik, MME and Ahmmed, S and Rabbane, MG and Rahman, MS},
title = {Investigation of Tilapia (Oreochromis niloticus) Mortality Events Targeting Tilapia Lake Virus Disease (TiLVD) in Bangladesh.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70262},
doi = {10.1002/vms3.70262},
pmid = {39950541},
issn = {2053-1095},
support = {//Grant for Advanced Research in Education (GARE)/ ; //Ministry of Education/ ; 37.20.0000.004.033.020.2016.673//Government of the People's Republic of Bangladesh/ ; },
mesh = {Animals ; Bangladesh/epidemiology ; *Fish Diseases/virology/mortality/epidemiology ; *Cichlids ; DNA Virus Infections/veterinary/virology/mortality/epidemiology ; Aquaculture ; },
abstract = {BACKGROUND: Tilapia lake virus (TiLV) is an emerging threat to the global tilapia industry. In early 2017, FAO declared that Bangladesh was in a high-risk zone of TiLV disease (TiLVD) spread.<br><br>OBJECTIVES: Considering the current scenario, the present work was designed to investigate the occurrence of TiLV in cultured Nile tilapia (Oreochromis niloticus) causing TiLVD in Bangladesh.<br><br>METHODS: In this study, several unusual tilapia mortality incidences were investigated. A total of 102 pooled organ samples of 102 tilapia fish were collected from 34 ponds of 25 farms in the regions of 12 Upazilas in Bangladesh from May to October 2019. As a part of the classical approach, histopathological analysis was performed. For molecular identification, both conventional and real-time PCR were used as diagnostic tools to identify TiLV in farm-raised Nile tilapia.<br><br>RESULTS: A total of 12 representative organ samples did not show any pathognomonic lesions related to TiLV infection in histopathological analysis. Conventional and real-time PCR assays yielded negative results for TiLV.<br><br>CONCLUSIONS: In our investigation, no trace of TiLV was detected in the studied samples. A large-scale study involving a broader range of samples collected across Bangladesh, along with the application of a viral metagenomics approach, could provide valuable insights into the unusual mortalities of tilapia in the country.},
}
@article {pmid39949721,
year = {2025},
author = {Neidhöfer, C and Klein, N and Yürüktümen, A and Hattenhauer, T and Mispelbaum, R and Bode, C and Holderried, TAW and Hoerauf, A and Parčina, M},
title = {Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1504262},
pmid = {39949721},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Bacteremia/diagnosis/microbiology ; Male ; Female ; *Cell-Free Nucleic Acids/blood ; *Metagenomics/methods ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; Sequence Analysis, DNA ; Young Adult ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Bloodstream infections are a critical challenge worldwide due to the slow turnaround time of conventional microbiological tests for detecting bacteremia in septic patients. Noscendo GmbH (Duisburg, Germany) has developed the CE/IVD pipeline DISQVER for clinical metagenomics testing based on cell-free DNA (cfDNA) from blood samples to address this issue.<br><br>METHODS: We conducted a retrospective study to evaluate the diagnostic utility of this methodological setup in improving treatment decisions since it was introduced into our clinical setting. Between January 2021 and June 2022, the first 300 cases in which DISQVER was applied at our university hospital were collected and analyzed. The results were compared with routine microbiology test results, clinical picture, associated treatment decisions, and clinical course.<br><br>RESULTS: Our findings demonstrate that DISQVER results where no pathogen was reported effectively ruled out bacterial bloodstream infections, whereas positive results varied in their usefulness. While the metagenomic approach proved highly valuable for detecting non-culturable and rare pathogens, its utility was limited in cases where detected microorganisms were commonly associated with the microbiota.<br><br>DISCUSSION: Performing on-site analysis might mitigate delays resulting from logistical challenges and might help optimizing antibiotic stewardship. Once prompt results can be obtained, the relevance of incorporating molecular resistograms will become more pronounced. Further, the specific patient subgroups that most benefit from this analysis must be worked out. Guiding clinicians in identifying the infection focus based on the detected bacteria would significantly improve patient care. Lastly, evidence of filamentous fungi must be diligently followed up.},
}
@article {pmid39948721,
year = {2025},
author = {Douillard, FP and Lanzoni, O and Duplouy, A and Lindström, M},
title = {Insects as Natural Hosts, Vectors and Reservoirs of Botulinum Neurotoxin-Producing Clostridia and Their Non-Toxinogenic Counterparts: Preliminary Evidence.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70053},
doi = {10.1111/1462-2920.70053},
pmid = {39948721},
issn = {1462-2920},
support = {328944//Academy of Finland/ ; 340705//Academy of Finland/ ; 683099/ERC_/European Research Council/International ; },
mesh = {Animals ; *Phylogeny ; *Clostridium/genetics/metabolism/classification ; *Botulinum Toxins/genetics/metabolism ; *Botulism/microbiology ; RNA, Ribosomal, 16S/genetics ; Insecta/microbiology ; Insect Vectors/microbiology ; Butterflies/microbiology ; },
abstract = {Insects play a significant role in the transmission and spread of bacterial pathogens that cause various diseases in humans and animals. The relationship among insects, bacterial pathogens and diseases is complex and depends on the specificity of the pathogens. Some clostridial species produce botulinum neurotoxin (BoNT), which is responsible for paralytic botulism. However, the ecology of these bacterial species and their non-toxinogenic phylogenetic counterparts remains unclear. This study specifically explored in silico evidence of the interconnection between BoNT-producing Clostridia and their non-toxinogenic counterparts with insects. Based on literature meta-analysis, the mining of 16S rRNA amplicon and metagenomic sequencing datasets and a pilot feeding experiment in the Glanville fritillary butterfly, Melitaea cinxia, we propose that BoNT-producing Clostridia and their non-toxinogenic phylogenetic counterparts are carried internally and/or externally in different insect orders. While previous case studies have indicated associations between Clostridia and insects, this work provides a more comprehensive view of their occurrence. It also highlights the need for further multidisciplinary investigations to characterise the natural ecology of BoNT-producing Clostridia and their non-toxinogenic counterparts in insects.},
}
@article {pmid39948426,
year = {2025},
author = {Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Li, Z and Tang, X},
title = {Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5400},
pmid = {39948426},
issn = {2045-2322},
support = {2021-I2M-1-068//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Child ; Goldenhar Syndrome/microbiology ; Dysbiosis/microbiology ; Adolescent ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Young Adult ; Metagenomics/methods ; Child, Preschool ; Case-Control Studies ; },
abstract = {Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.},
}
@article {pmid39948184,
year = {2025},
author = {Chen, A and Yu, Q and Zheng, L and Yi, J and Tang, Z and Ge, H and Ning, Y and Yin, N and Xie, Y and Chen, S and Shi, W and She, X and Xiang, J and Tang, J},
title = {Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {11},
pmid = {39948184},
issn = {1432-1831},
support = {81972198, 81773147//National Natural Science Foundation of China/ ; 2019SK2253//Key Research and Development Program of Hunan Province of China/ ; ZLXD2017004//Central South University/ ; ZLXD2017004//Central South University/ ; kq2208299//National Natural Science Foundation of Changsha/ ; },
mesh = {*Talaromyces ; Humans ; Animals ; *Macrophages/microbiology/immunology ; *Lung Neoplasms/microbiology ; Mice ; *Arginine/metabolism ; *Ornithine/metabolism/analogs &amp; derivatives/pharmacology ; Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; Cell Proliferation ; Macrophage Activation ; Female ; Male ; Metagenomics ; Disease Models, Animal ; Cell Line, Tumor ; Mycobiome ; Lung/microbiology/pathology ; },
abstract = {It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.},
}
@article {pmid39947845,
year = {2025},
author = {Jeon, Y and Struewing, I and Clauson, K and Reetz, N and Fairchild, N and Goeres-Priest, L and Dreher, TW and Labiosa, R and Carpenter, KD and Rosen, BH and Villegas, EN and Lu, J},
title = {Dominant Dolichospermum and microcystin production in Detroit Lake (Oregon, USA).},
journal = {Harmful algae},
volume = {142},
number = {},
pages = {102802},
doi = {10.1016/j.hal.2025.102802},
pmid = {39947845},
issn = {1878-1470},
mesh = {*Lakes/microbiology/chemistry ; *Microcystins/metabolism ; Cyanobacteria/metabolism/genetics ; Harmful Algal Bloom ; },
abstract = {The excessive growth of harmful cyanobacteria, including Dolichospermum (formerly known as Anabaena), in freshwater bodies has become a pressing global concern. However, detailed information about the role of Dolichospermum in shaping bloom dynamics and producing cyanotoxins is limited. In this study, a bloom event dominated by Dolichospermum spp. at Detroit Lake (Oregon, USA) was examined from 2019 to 2021. In 2019, early summer cyanobacterial community succession reached up to 8.7 % of total phytoplankton abundance. Dolichospermum was the major microcystin (MC)-producing genus, with peak MC levels of 7.34 μg L[-1]. The presence of MCs was strongly correlated with the abundance of Dolichospermum (r = 0.84, p < 0.05) and MC synthetase gene, mcyE-Ana (r = 0.63, p < 0.05). Metabolic analyses further showed that the presence of nif/pst genes linked to nitrogen and phosphorus metabolism was dominated by Dolichospermum from the bloom onset until September. In addition, the abundance of Dolichospermum was significantly correlated with the abundance of nitrogen-fixing nif-Ana gene (r = 0.62, p < 0.05). As the lake experienced a longer N and P scarcity period (May to September), the N2-fixing Dolichospermum was able to dominate over other non-fixing cyanobacteria present, including Microcystis and Planktothrix. Overall, our results facilitate a better understanding of the organism and will help working toward managing/predicting future blooms.},
}
@article {pmid39947314,
year = {2025},
author = {Zhang, X and Chen, Y and Xia, Y and Lin, S and Zhou, X and Pang, X and Yu, J and Sun, L},
title = {Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123462},
doi = {10.1016/j.lfs.2025.123462},
pmid = {39947314},
issn = {1879-0631},
abstract = {Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.},
}
@article {pmid39947201,
year = {2025},
author = {Yang, SNN and Kertesz, MA and Coleman, NV},
title = {Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70050},
doi = {10.1111/1462-2920.70050},
pmid = {39947201},
issn = {1462-2920},
support = {//University of Sydney/ ; },
mesh = {*Phylogeny ; *Mixed Function Oxygenases/genetics/metabolism/chemistry ; *Bacteria/enzymology/genetics/classification ; Biodegradation, Environmental ; Gene Transfer, Horizontal ; Substrate Specificity ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Iron/metabolism ; },
abstract = {Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.},
}
@article {pmid39947184,
year = {2025},
author = {Heinken, A and Hulshof, TO and Nap, B and Martinelli, F and Basile, A and O'Brolchain, A and O'Sullivan, NF and Gallagher, C and Magee, E and McDonagh, F and Lalor, I and Bergin, M and Evans, P and Daly, R and Farrell, R and Delaney, RM and Hill, S and McAuliffe, SR and Kilgannon, T and Fleming, RMT and Thinnes, CC and Thiele, I},
title = {A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101196},
doi = {10.1016/j.cels.2025.101196},
pmid = {39947184},
issn = {2405-4720},
abstract = {Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.},
}
@article {pmid39947133,
year = {2025},
author = {Elmassry, MM and Sugihara, K and Chankhamjon, P and Kim, Y and Camacho, FR and Wang, S and Sugimoto, Y and Chatterjee, S and Chen, LA and Kamada, N and Donia, MS},
title = {A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {2},
pages = {218-234.e12},
doi = {10.1016/j.chom.2025.01.002},
pmid = {39947133},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; Humans ; Mice ; Animals ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; Crohn Disease/microbiology ; Disease Models, Animal ; Multigene Family ; Colitis/microbiology ; Metagenomics ; Clostridium/genetics ; Mice, Inbred C57BL ; Female ; },
abstract = {Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.},
}
@article {pmid39946947,
year = {2025},
author = {Yu, J and Usman, M and Liu, F and Schäfer, F and Shen, Y and Zheng, Z and Cai, Y},
title = {CO2 agitation combined with magnetized biochar to alleviate "ammonia inhibited steady-state": Exploring the mechanism by combining metagenomics with macroscopic indicators.},
journal = {Water research},
volume = {276},
number = {},
pages = {123250},
doi = {10.1016/j.watres.2025.123250},
pmid = {39946947},
issn = {1879-2448},
abstract = {The "ammonia inhibited steady-state" phenomenon is frequently observed in the anaerobic digestion (AD) process of nitrogen-rich substrates. Reconfiguring microbial ecosystems has proven to be an effective strategy for mitigating ammonia inhibition. In the current study, biochars were screened and targeted for modification. CO2 agitation combined with magnetized biochar was used to aid the semi-continuous AD systems with "ammonia inhibited steady-state." The results indicated that coconut shell biochar had the best stimulating effect on AD performance. The content of oxygen-containing functional groups (OCFGs), which had a positive correlation with the electron donating capacity (EDC), was targeted to be regulated. This strategy significantly increased the CH4 yield by 31.7 % (from 344 to 278 mL/g VS) (p < 0.05). Isotope tracing and KEGG gene annotation indicated that this strategy stimulated the efficiency of the hydrogenotrophic pathway. Simultaneously, it accelerated the attachment of microorganisms, which made the DIET pathway between bacteria and archaea efficient. Under CO2 agitation, the attachment of functional microorganisms to the biochar accelerated. Biochar weakened the synthesis of bioelectronic carriers (Cyt-c and chemosensory pili), while the electroactivity of the AD system was enhanced. This means that biochar replaced bioelectronic carriers and improved the DIET efficiency. In addition, the strategy had a positive effect on the colonization of simultaneous nitrification-denitrifying bacteria (Georgenia), which led to a decrease in ammonia nitrogen concentrations. This study revealed the mechanism by which this strategy alleviates ammonia inhibition and provided a promising strategy for the efficient AD of nitrogen-rich substrates.},
}
@article {pmid39946886,
year = {2025},
author = {Shi, J and Zhang, Q and Sun, Y and Peng, Y and Wang, J and Wang, X},
title = {Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis.},
journal = {The Science of the total environment},
volume = {967},
number = {},
pages = {178825},
doi = {10.1016/j.scitotenv.2025.178825},
pmid = {39946886},
issn = {1879-1026},
abstract = {Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.},
}
@article {pmid39946873,
year = {2025},
author = {Feng, Y and Li, L and Ma, Q and Liu, S and Wang, P and Li, X and Ma, J},
title = {Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio).},
journal = {The Science of the total environment},
volume = {967},
number = {},
pages = {178838},
doi = {10.1016/j.scitotenv.2025.178838},
pmid = {39946873},
issn = {1879-1026},
abstract = {Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.},
}
@article {pmid39946816,
year = {2025},
author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Gonzalez-Peña, R and Adame-Gallegos, JR and Beristain-Ruiz, DM and Barajas-López, IN and Hargett, AM and Munderloh, UG and Blitvich, BJ},
title = {Detection of multiple novel viruses in argasid and ixodid ticks in Mexico.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {2},
pages = {102455},
doi = {10.1016/j.ttbdis.2025.102455},
pmid = {39946816},
issn = {1877-9603},
abstract = {We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.},
}
@article {pmid39946360,
year = {2025},
author = {Scaketti, M and Sujii, PS and Alves-Pereira, A and Schwarcz, KD and Francisconi, AF and Moro, MS and Moreno Martins, KK and de Jesus, TA and de Souza, GBF and Zucchi, MI},
title = {Sample Size Impact (SaSii): An R script for estimating optimal sample sizes in population genetics and population genomics studies.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0316634},
doi = {10.1371/journal.pone.0316634},
pmid = {39946360},
issn = {1932-6203},
mesh = {Sample Size ; *Genetics, Population ; *Polymorphism, Single Nucleotide ; Humans ; Genomics/methods ; Software ; Microsatellite Repeats/genetics ; Genotype ; Animals ; Metagenomics/methods ; },
abstract = {Obtaining large sample sizes for genetic studies can be challenging, time-consuming, and expensive, and small sample sizes may generate biased or imprecise results. Many studies have suggested the minimum sample size necessary to obtain robust and reliable results, but it is not possible to define one ideal minimum sample size that fits all studies. Here, we present SaSii (Sample Size Impact), an R script to help researchers define the minimum sample size. Based on empirical and simulated data analysis using SaSii, we present patterns and suggest minimum sample sizes for experiment design. The patterns were obtained by analyzing previously published genotype datasets with SaSii and can be used as a starting point for the sample design of population genetics and genomic studies. Our results showed that it is possible to estimate an adequate sample size that accurately represents the real population without requiring the scientist to write any program code, extract and sequence samples, or use population genetics programs, thus simplifying the process. We also confirmed that the minimum sample sizes for SNP (single-nucleotide polymorphism) analysis are usually smaller than for SSR (simple sequence repeat) analysis and discussed other patterns observed from empirical plant and animal datasets.},
}
@article {pmid39946339,
year = {2025},
author = {Long, C and Wang, P and Wu, J and Liu, J and Tan, Z and Li, W},
title = {Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0316456},
doi = {10.1371/journal.pone.0316456},
pmid = {39946339},
issn = {1932-6203},
mesh = {*Carps/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; Methane/metabolism ; Intestines/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Water Microbiology ; Methanosarcina/genetics/metabolism ; },
abstract = {The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.},
}
@article {pmid39945663,
year = {2025},
author = {Park, K and Shin, M and Natasha, A and Kim, J and Noh, J and Kim, SG and Kim, B and Park, J and Seo, YR and Cho, HK and Byun, KS and Kim, JH and Lee, YS and Shim, JO and Kim, WK and Song, JW},
title = {Novel human coronavirus in an infant patient with pneumonia, Republic of Korea.},
journal = {Emerging microbes &amp; infections},
volume = {},
number = {},
pages = {2466705},
doi = {10.1080/22221751.2025.2466705},
pmid = {39945663},
issn = {2222-1751},
abstract = {Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequently found among patients with respiratory infections. To date, limited attention has been directed towards alphacoronaviruses due to their low prevalence and fatality rates. Nasal swab and serum samples were collected from a paediatric patient, and an epidemiological survey was conducted. Retrospective surveillance investigated the molecular prevalence of CoV in 880 rodents collected in the Republic of Korea (ROK) from 2018 to 2022. Next-generation sequencing (NGS) and phylogenetic analyses characterised the novel HCoV and closely related CoVs harboured by Apodemus spp. On 15 December 2022, a 103-day-old infant was admitted with fever, cough, sputum production, and rhinorrhea, diagnosed with human parainfluenza virus 1 (HPIV-1) and rhinovirus co-infection. Elevated AST/ALT levels indicated transient liver dysfunction on the fourth day of hospitalisation. Metagenomic NGS (mNGS) identified a novel HCoV in nasal swab and serum samples. Retrospective rodent surveillance and phylogenetic analyses showed the novel HCoV was closely related to alphacoronaviruses carried by Apodemus spp. in the ROK and China. This case highlights the potential of mNGS to identify emerging pathogens and raises awareness of possible extra-respiratory manifestations, such as transient liver dysfunction, associated with novel HCoVs. While the liver injury in this case may be attributable to the novel HCoV, further research is necessary to elucidate its clinical significance, epidemiological prevalence, and zoonotic origins.},
}
@article {pmid39945545,
year = {2025},
author = {Verster, AJ and Salerno, P and Valls, R and Barrack, K and Price, CE and McClure, EA and Madan, JC and O'Toole, GA and Sanville, JL and Ross, BD},
title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0342024},
doi = {10.1128/mbio.03420-24},
pmid = {39945545},
issn = {2150-7511},
abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.},
}
@article {pmid39945541,
year = {2025},
author = {Lapid, R and Motro, Y and Craddock, H and Salah, I and King, R and Winner, K and Kahila Bar-Gal, G and Moran-Gilad, J},
title = {Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081924},
doi = {10.1128/msphere.00819-24},
pmid = {39945541},
issn = {2379-5042},
abstract = {UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.<br><br>IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.},
}
@article {pmid39945538,
year = {2025},
author = {Zhang, L and Zhang, T and Xu, Y-R and Sun, J-M and Pan, X-R and Gu, K-Z and Zhang, K-Q and Zhang, Z-G and Liang, L-M},
title = {Induction of conidial traps in the nematode-trapping fungus Drechslerella dactyloides by soil microbes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129124},
doi = {10.1128/msystems.01291-24},
pmid = {39945538},
issn = {2379-5077},
abstract = {UNLABELLED: Nematode-trapping fungi, renowned for their specialized predatory structures that ensnare nematodes, offer a promising biological approach to managing plant-parasitic nematodes. However, the efficacy of these fungi is frequently hampered by biotic and abiotic factors within the soil, which can significantly impede fungal germination (fungistasis). To counteract these environmental challenges, certain nematode-trapping fungi have evolved to produce traps from their conidia, referred to as conidial traps. This adaptation allows them to bypass the inhibitory effects of their surroundings, enhancing their predatory capabilities. In this study, we explored how soil affects conidial trap formation in Drechslerella dactyloides. Our findings revealed that Acinetobacter spp. and Pantoea spp. present in soil extracts play pivotal roles in triggering the development of these traps. Using metagenomic sequencing, we mapped the shifts in bacterial communities and their relative abundances before and after incubation for up to 24 hours to optimize soil induction effects. This analysis highlighted the enrichment of specific functional genes in soil microbes and provided insights into the mechanisms driving conidial trap formation, based on changes in soil characteristics. Furthermore, through bacterial isolation procedures, we successfully cultured and characterized the bacteria responsible for this phenomenon, confirming their potent ability to stimulate the production of conidial traps in nematode-trapping fungi. This study not only underscores the critical role of bacterial diversity in modulating the life cycle transitions of nematode-trapping fungi but also sets the stage for the development of more effective and sustainable strategies to harness these fungi in the battle against pathogenic nematodes.<br><br>IMPORTANCE: Predatory nematode-trapping fungi are important microbial antagonists of nematodes and can be developed into biocontrol agents. However, microbial biocontrol agents often suffer from inconsistent efficacy, primarily due to biotic and abiotic stresses in the rhizosphere soil. Drechslerella dactyloides, a nematode-trapping fungus, produces conidial traps in soil, serving as a survival strategy to overcome these stresses. In this study, we optimized soil suspensions to efficiently induce the formation of conidial traps. We found that bacteria in the soil directly trigger this formation. Metagenomic sequencing revealed bacterial enrichment during optimization, and we isolated and purified these bacteria with inducible activity. Our research deepens the understanding of this survival strategy of nematode-trapping fungi in nature, laying the foundation for enhancing the effectiveness of nematode biocontrol using this mechanism.},
}
@article {pmid39944722,
year = {2025},
author = {Saravanan, C and Gopinath, NK and Ganesan, R and Thirumurugan, D},
title = {Challenges and limitations in using bacterial metabolites as immunomodulators.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1535394},
doi = {10.3389/fcimb.2025.1535394},
pmid = {39944722},
issn = {2235-2988},
mesh = {Humans ; *Bacteria/metabolism ; *Immunologic Factors/metabolism ; *Gastrointestinal Microbiome ; Animals ; Metabolomics ; Immunomodulating Agents/metabolism ; Metagenomics ; },
abstract = {Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.},
}
@article {pmid39944653,
year = {2025},
author = {Ma, W and Zhao, Y and Liu, Y and Wang, Y and Yu, S and Huang, L},
title = {Bifidobacterium animalis subsp. lactis TG11 ameliorates loperamide-induced constipation in mice by modulating gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1525887},
doi = {10.3389/fmicb.2025.1525887},
pmid = {39944653},
issn = {1664-302X},
abstract = {INTRODUCTION: Constipation is a common gastrointestinal disorder that can affect quality of life. Probiotics have garnered substantial attention for their potential to alleviate constipation. This study investigates the preventive effects of Bifidobacterium animalis subsp. lactis TG11 on loperamide-induced constipation in mice.<br><br>METHODS: Mice were randomly assigned to normal control (NC), constipation model (CM), and low, medium, and high-dose TG11 treatment groups (LG, MG, HG). From days 1-14, LG, MG, and HG groups received 10[6], 10[7], and 10[8] CFU/mouse of TG11, respectively, while NC and CM groups received saline. On day 14, all groups except NC were administered loperamide (4 mg/kg) orally to induce constipation. Fecal samples were collected for short-chain fatty acid and gut microbiota analyses. Following a 16-hour fasting period, various parameters were assessed on day 15, including intestinal motility, fecal water content, defecation status, gut peptide levels in blood, and mRNA expression levels of SCF and c-kit in colonic tissue.<br><br>RESULTS: TG11 significantly enhanced intestinal motility and maintained fecal water content. It normalized blood levels of MTL, SP, SS, ET-1, Gas, and VIP in constipated mice, promoted short-chain fatty acid production, and improved microbial metabolism. TG11 markedly upregulated mRNA expression of SCF and c-kit in colonic tissue. Metagenomic sequencing revealed that TG11 modulated gut microbiota composition, increasing the abundance of beneficial bacteria, particularly Muribaculum_sp. and uncultured_Duncaniella.<br><br>DISCUSSION: Bifidobacterium animalis subsp. lactis TG11 demonstrates efficacy in ameliorating constipation, potentially through modulation of the gut microbiota composition.},
}
@article {pmid39944648,
year = {2025},
author = {Lu, J and Jiang, M and Chai, D and Sun, Y and Wu, L},
title = {Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1452423},
doi = {10.3389/fmicb.2025.1452423},
pmid = {39944648},
issn = {1664-302X},
abstract = {Attention Deficit Hyperactivity Disorder (ADHD) is a clinically common neurodevelopmental disorder of the brain. In addition to genetic factors, an imbalance in gut flora may also play a role in the development of ADHD. Currently, it is critical to investigate the function of gut flora and related metabolites, which may form the fundamental basis of bidirectional cross-linking between the brain and the gut, in addition to focusing on the changed gut flora in ADHD. This study aimed to investigate the possible relationship between changes in gut flora and metabolites and ADHD by analyzing metagenome and untargeted metabolomics of fecal samples from ADHD patients. Specifically, we attempted to identify key metabolites and the metabolic pathways they are involved in, as well as analyze in detail the structure and composition of the gut flora of ADHD patients. In order to further investigate the relationship between gut flora and ADHD symptoms, some behavioral studies were conducted following the transplantation of gut flora from ADHD patients into rats. The results of the metagenome analysis revealed several distinct strains, including Bacteroides cellulosilyticus, which could be important for diagnosing ADHD. Additionally, the ADHD group showed modifications in several metabolic pathways and metabolites, including the nicotinamide and nicotinic acid metabolic pathways and the metabolite nicotinamide in this pathway. The behavioral results demonstrated that rats with ADHD gut flora transplants displayed increased locomotor activity and interest, indicating that the onset of behaviors such as ADHD could be facilitated by the flora associated with ADHD. This research verified the alterations in gut flora and metabolism observed in ADHD patients and provided a list of metabolites and flora that were significantly altered in ADHD. Simultaneously, our findings revealed that modifications to the microbiome could potentially trigger behavioral changes in animals, providing an experimental basis for comprehending the function and influence of gut flora on ADHD. These results might provide new perspectives for the development of novel treatment strategies.},
}
@article {pmid39944638,
year = {2025},
author = {Sarsaiya, S and Jain, A and Singh, R and Gong, Q and Wu, Q and Chen, J and Shi, J},
title = {Unveiling the rhizosphere microbiome of Dendrobium: mechanisms, microbial interactions, and implications for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531900},
doi = {10.3389/fmicb.2025.1531900},
pmid = {39944638},
issn = {1664-302X},
abstract = {The rhizosphere microbiome plays a critical role in plant health and productivity by fostering beneficial microbial interactions that support nutrient cycling, stress tolerance, and disease suppression. In the context of Dendrobium, understanding its interactions is essential for optimizing cultivation and promoting sustainable agricultural practices. This review explores the rhizosphere microbiome of Dendrobium, focusing on the mechanisms and microbial interactions that contribute to plant health, stress tolerance, and growth and their implications for sustainable agriculture. This study highlights the diverse composition of microbial communities in the Dendrobium rhizosphere, including key bacteria (e.g., Pseudomonas fluorescens and Bacillus subtilis), fungi (e.g., Glomus spp.), and biocontrol agents (Trichoderma spp.), and discusses their roles in nutrient cycling, disease suppression, and plant growth promotion. This review emphasizes the significance of plant-microbe signaling, such as the production of flavonoids, phytohormones, and strigolactones, in shaping the microbial environment and enhancing plant resilience. Additionally, it addresses modern techniques for analyzing microbial communities, including metagenomics and next-generation sequencing, and their applications in advancing precision agriculture. Future research should focus on bridging knowledge gaps related to genotype-microbiome interactions, exploring emerging microbial consortia and enhancing the integration of microbiome management in precision agriculture systems to improve plant health and productivity.},
}
@article {pmid39944596,
year = {2025},
author = {Brizola Toscan, R and Lesiński, W and Stomma, P and Subramanian, B and Łabaj, PP and Rudnicki, WR},
title = {Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1460508},
doi = {10.3389/fgene.2025.1460508},
pmid = {39944596},
issn = {1664-8021},
abstract = {Antimicrobial resistance (AMR) is a growing global health concern, driven by urbanization and anthropogenic activities. This study investigated AMR distribution and dynamics across microbiomes from six U.S. cities, focusing on resistomes, viromes, and mobile genetic elements (MGEs). Using metagenomic data from the CAMDA 2023 challenge, we applied tools such as AMR++, Bowtie, AMRFinderPlus, and RGI for resistome profiling, along with clustering, normalization, and machine learning techniques to identify predictive markers. AMR++ and Bowtie outperformed other tools in detecting diverse AMR markers, with binary normalization improving classification accuracy. MGEs were found to play a critical role in AMR dissemination, with 394 genes shared across all cities. Removal of MGE-associated AMR genes altered resistome profiles and reduced model performance. The findings reveal a heterogeneous AMR landscape in urban microbiomes, particularly in New York City, which showed the highest resistome diversity. These results underscore the importance of MGEs in AMR profiling and provide valuable insights for designing targeted strategies to address AMR in urban settings.},
}
@article {pmid39944485,
year = {2025},
author = {Zhang, F and Wang, JL and Zhu, J and Si, S and Guo, H and Yue, X and Wen, W},
title = {When a sore throat turns into deadly multiple serous cavity effusions: the role of Prevotella oris in rapidly progressing infection-a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1517389},
doi = {10.3389/fmed.2025.1517389},
pmid = {39944485},
issn = {2296-858X},
abstract = {Severe infections that develop rapidly from ordinary symptoms not only increase patient misunderstandings but also lead to excessive detection of these symptoms by physicians. This case study describes a 19-year-old male individual who initially presented with a sore throat and subsequently developed multiple serous cavity effusions that lead to septic pulmonary embolism and septic shock. After multiple cultures of the patient's sputum yielded no identifiable pathogenic bacteria, the metagenomic next-generation sequencing (mNGS) revealed Prevotella oris as the predominant pathogen present in both the patient's peripheral blood and the pericardial drainage fluid. The subsequent antibiotic treatment, guided by the mNGS results, along with surgical drainage and mediastinal irrigation, effectively controlled and ultimately cured the patient's condition. This case is unique because it is the first to show that normally colonizing Prevotella can also cause fatal multiorgan infection as an opportunistic pathogen in a previously healthy young person with no immune-related diseases. The aim of this study is to expand clinical awareness of this common symptom and its potentially fatal outcome.},
}
@article {pmid39943872,
year = {2025},
author = {Büttner, KA and Bregy, V and Wegner, F and Purushothaman, S and Imkamp, F and Roloff Handschin, T and Puolakkainen, MH and Hiltunen-Back, E and Braun, D and Kisakesen, I and Schreiber, A and Entrocassi, AC and Gallo Vaulet, ML and López Aquino, D and Svidler López, L and La Rosa, L and Egli, A and Rodríguez Fermepin, M and Seth-Smith, HM and On Behalf Of The Escmid Study Group For Mycoplasma And Chlamydia Infections Esgmac, },
title = {Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs.},
journal = {Microbial genomics},
volume = {11},
number = {2},
pages = {},
doi = {10.1099/mgen.0.001353},
pmid = {39943872},
issn = {2057-5858},
mesh = {Humans ; *Chlamydia trachomatis/genetics/isolation &amp; purification ; *Whole Genome Sequencing/methods ; *Genome, Bacterial ; Neisseria gonorrhoeae/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; Treponema pallidum/genetics/isolation &amp; purification ; Sexually Transmitted Diseases, Bacterial/microbiology ; Switzerland ; DNA, Bacterial/genetics ; Mycoplasma genitalium/genetics/isolation &amp; purification ; Chlamydia Infections/microbiology ; },
abstract = {Rates of bacterial sexually transmitted infections (STIs) are rising, and accessing their genomes provides information on strain evolution, circulating strains and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasmoides (formerly Mycoplasma) genitalium (MG) is also a bacterial STI that is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole-genome sequences and evaluated four approaches using clinical samples from Argentina (39), and Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low-load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies, which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT-positive samples, from 36% of NG-positive samples and 60% of TP-positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. These data can be utilized to examine circulating strains and genotypic resistance and guide public health strategies.},
}
@article {pmid39943733,
year = {2025},
author = {Tizabi, D and Hill, RT and Bachvaroff, T},
title = {Nanopore Sequencing of Amoebophrya sp. Reveals Novel Collection of Bacteria Putatively Associated with Karlodinium veneficum.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf022},
pmid = {39943733},
issn = {1759-6653},
abstract = {The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate Karlodinium veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole genome sequencing of an Amoebophrya sp. ex Karlodinium veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes (MAG) were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, thirteen were identifiable at the generic level by BLAST (eight of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for < 2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of MAGs are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.},
}
@article {pmid39941991,
year = {2025},
author = {Wu, J and Zhao, N and Li, Q and Zhao, K and Tu, M and Li, J and Hu, K and Chen, S and Liu, S and Liu, A},
title = {Metagenomics and Metagenome-Assembled Genomes: Analysis of Cupei from Sichuan Baoning Vinegar, One of the Four Traditional Renowned Vinegars in China.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/foods14030398},
pmid = {39941991},
issn = {2304-8158},
abstract = {The microbial community in vinegar has primarily been investigated by analyzing short reads to determine operational taxonomic units, but it is also crucial to identify metagenome-assembled genomes (MAGs). In this study, the microbial diversity and functionality in Sichuan Baoning vinegar were examined through deep metagenomic sequencing and metagenomic binning. Results revealed that the most prevalent phylum was Firmicutes, followed by Proteobacteria and unclassified Bacteria. The most abundant bacterial species was Acetilactobacillus jinshanensis, while Saccharomyces cerevisiae was the most prevalent fungal species. The predominant viral species were Hopescreekvirus LfeInf, Myoviridae sp., and Siphoviridae sp. A total of 1395 MAGs were reconstructed, with 660 of them annotated. The majority of MAGs resolved at the species level were attributed to Firmicutes (n = 308), with Acetilactobacillus jinshanensis being the most abundant. According to the average nucleotide identity values, 223 out of the 660 MAGs might represent novel species. The recovered MAGs exhibited biomarker genes indicative of the genetic potential to encode several important secondary metabolites. This study helps to uncover the microbial composition and functional potential of microbial genomes in Sichuan Baoning vinegar.},
}
@article {pmid39941945,
year = {2025},
author = {Quek, JJW and Wong, JL and Tan, JL and Yeo, CC and Saw, SH},
title = {Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/foods14030352},
pmid = {39941945},
issn = {2304-8158},
support = {FRGS/1/2022/SKK06/UTAR/02/1//Ministry of Higher Education/ ; },
abstract = {Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.},
}
@article {pmid39941602,
year = {2025},
author = {Bessa, LJ and Egas, C and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Unveiling the Resistome Landscape in Peri-Implant Health and Disease.},
journal = {Journal of clinical medicine},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/jcm14030931},
pmid = {39941602},
issn = {2077-0383},
support = {2022.01430.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
abstract = {Background: The human oral microbiome is a critical reservoir for antibiotic resistance; however, subgingival peri-implant biofilms remain underexplored in this context. We aimed to explore the prevalence and distribution of antibiotic resistance genes (ARGs) in metagenomes derived from saliva and subgingival peri-implant biofilms. Methods: A total of 100 metagenome datasets from 40 individuals were retrieved from the Sequence Read Archive (SRA) database. Of these, 20 individuals had exclusively healthy implants and 20 had both healthy and affected implants with peri-implantitis. ARGs and their taxonomic assignments were identified using the ABRicate tool, and plasmid detection was performed with PlasmidFinder. Results: Four plasmid replicons were identified in 72 metagenomes, and 55 distinct ARGs from 13 antibiotic classes were detected in 89 metagenomes. ARGs conferring resistance to macrolides-lincosamides-streptogramins, tetracyclines, beta-lactams, and fluoroquinolones were the most prevalent. The msr(D) and mef(A) genes showed the highest prevalence, except in saliva samples from individuals with healthy implants, where mef(A) ranked fourth. A pairwise PERMANOVA of principal coordinate analysis based on Jaccard distances revealed that saliva samples exhibited significantly greater ARG diversity than subgingival biofilm samples (p < 0.05). However, no significant differences were observed between healthy and peri-implantitis-affected subgingival biofilm groups (p > 0.05). The taxonomic origins of ARGs were also analyzed to understand their distribution and potential impact on oral microbial communities. Conclusions: Resistome profiles associated with both peri-implant health and disease showed no significant differences and higher salivary abundance of ARGs compared to subgingival biofilm samples.},
}
@article {pmid39941194,
year = {2025},
author = {Bustos, IG and Martinez-Lemus, LF and Reyes, LF and Martin-Loeches, I},
title = {Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/diagnostics15030265},
pmid = {39941194},
issn = {2075-4418},
abstract = {Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance.},
}
@article {pmid39940952,
year = {2025},
author = {Parra, M and Izquierdo, K and Rubio, M and de la Fuente, A and Tello, M and Modak, B},
title = {Quercetin and Silybin Decrease Intracellular Replication of Piscirickettsia salmonis in SHK-1 Cell.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
doi = {10.3390/ijms26031184},
pmid = {39940952},
issn = {1422-0067},
support = {21212170//ANID/ ; 022341MC//DICYT/ ; },
mesh = {Animals ; *Quercetin/pharmacology ; *Silybin/pharmacology ; *Piscirickettsia/drug effects ; Cell Line ; Salmon/microbiology ; Fish Diseases/microbiology ; Oncorhynchus mykiss/microbiology ; Epithelial Cells/drug effects/microbiology/metabolism ; Piscirickettsiaceae Infections/microbiology ; Phagocytosis/drug effects ; Head Kidney/cytology ; },
abstract = {Piscirickettsia salmonis is the pathogen that has most affected the Chilean salmon industry for over 30 years. Considering the problems of excessive use of antibiotics, it is necessary to find new strategies to control this pathogen. Antivirulence therapy is an alternative to reduce the virulence of pathogens without affecting their growth. Polyphenolic compounds have been studied for their antiviral capacity. In this study, the capacity of quercetin and silybin to reduce the intracellular replication of P. salmonis in SHK-1 cells was evaluated. For this, three different infection protocols in Salmon Head Kidney-1(SHK-1) cells were used: co-incubation for 24 h, pre-incubation for 24 h prior to infection, and post-incubation for 24 h after infection. In addition, the effect of co-incubation in rainbow trout intestinal epithelial cells (RTgutGC) and the effect on the phagocytic capacity of SHK-1 cells were evaluated. The results obtained showed that quercetin and silybin decreased the intracellular replication of P. salmonis in SHK-1 cells when they were co-incubated for 24 h; however, they did not have the same effect in RTgutGC cells. On the other hand, both compounds decreased the phagocytosis of SHK-1 cells during co-incubation. These results are promising for the study of new treatments against P. salmonis.},
}
@article {pmid39940425,
year = {2025},
author = {Chen, E and Ajami, NJ and White, DL and Liu, Y and Gurwara, S and Hoffman, K and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L},
title = {Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.},
journal = {Nutrients},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/nu17030567},
pmid = {39940425},
issn = {2072-6643},
support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; DK56338/DK/NIDDK NIH HHS/United States ; 001//Gillson Longenbaugh Foundation/ ; 001//Gillson Longenbaugh Foundation/ ; CX001430//U.S. Department of Veterans Affairs/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Dairy Products/microbiology ; Middle Aged ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Aged ; Yogurt/microbiology ; },
abstract = {BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.<br><br>METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.<br><br>RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.<br><br>CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.},
}
@article {pmid39940254,
year = {2025},
author = {Barata, P and Oliveira, A and Soares, R and Fernandes, A},
title = {Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.},
journal = {Nutrients},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/nu17030395},
pmid = {39940254},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/radiation effects ; Female ; Middle Aged ; Male ; *Feces/microbiology ; *Iodine Radioisotopes ; *Hyperthyroidism/radiotherapy/microbiology ; Adult ; Prospective Studies ; Thyroid Neoplasms/radiotherapy/microbiology ; Aged ; Bacteria/classification/radiation effects/genetics/isolation &amp; purification ; Metagenomics/methods ; },
abstract = {Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.},
}
@article {pmid39940045,
year = {2025},
author = {Schropp, N and Bauer, A and Stanislas, V and Huang, KD and Lesker, TR and Bielecka, AA and Strowig, T and Michels, KB},
title = {The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {52},
pmid = {39940045},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cross-Over Studies ; Male ; Female ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fatty Acids, Volatile/metabolism ; *Fermented Foods/microbiology ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Young Adult ; Metabolome ; Healthy Volunteers ; },
abstract = {BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.<br><br>RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).<br><br>CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary&#xa0;interventions even though single species might be affected by sauerkraut consumption. Video Abstract.},
}
@article {pmid39939775,
year = {2025},
author = {Santos, CA and Morais, MAB and Mandelli, F and Lima, EA and Miyamoto, RY and Higasi, PMR and Araujo, EA and Paixão, DAA and Junior, JM and Motta, ML and Streit, RSA and Morão, LG and Silva, CBC and Wolf, LD and Terrasan, CRF and Bulka, NR and Diogo, JA and Fuzita, FJ and Colombari, FM and Santos, CR and Rodrigues, PT and Silva, DB and Grisel, S and Bernardes, JS and Terrapon, N and Lombard, V and Filho, AJC and Henrissat, B and Bissaro, B and Berrin, JG and Persinoti, GF and Murakami, MT},
title = {A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39939775},
issn = {1476-4687},
abstract = {The breakdown of cellulose is one of the most important reactions in nature[1,2] and is central to biomass conversion to fuels and chemicals[3]. However, the microfibrillar organization of cellulose and its complex interactions with other components of the plant cell wall poses a major challenge for enzymatic conversion[4]. Here, by mining the metagenomic 'dark matter' (unclassified DNA with unknown function) of a microbial community specialized in lignocellulose degradation, we discovered a metalloenzyme that oxidatively cleaves cellulose. This metalloenzyme acts on cellulose through an exo-type mechanism with C1 regioselectivity, resulting exclusively in cellobionic acid as a product. The crystal structure reveals a catalytic copper buried in a compact jelly-roll scaffold that features a flattened cellulose binding site. This metalloenzyme exhibits a homodimeric configuration that enables in situ hydrogen peroxide generation by one subunit while the other is productively interacting with cellulose. The secretome of an engineered strain of the fungus Trichoderma reesei expressing this metalloenzyme boosted the glucose release from pretreated lignocellulosic biomass under industrially relevant conditions, demonstrating its biotechnological potential. This discovery modifies the current understanding of bacterial redox enzymatic systems devoted to overcoming biomass recalcitrance[5-7]. Furthermore, it enables the conversion of agro-industrial residues into value-added bioproducts, thereby contributing to the transition to a sustainable and bio-based economy.},
}
@article {pmid39939365,
year = {2025},
author = {Soares, KO and Da Rocha, TF and Hale, VL and Vasconcelos, PC and do Nascimento, LJ and da Silva, NMV and Rodrigues, AE and de Oliveira, CJB},
title = {Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5293},
pmid = {39939365},
issn = {2045-2322},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Forests ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Ecosystem ; },
abstract = {The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.},
}
@article {pmid39939047,
year = {2025},
author = {Wu, BG and Zinter, MS},
title = {Metagenomic Sequencing for Personalized Treatment in Pneumonia: Does Better Detection Lead to Better Outcomes?.},
journal = {Chest},
volume = {167},
number = {2},
pages = {300-302},
doi = {10.1016/j.chest.2024.08.031},
pmid = {39939047},
issn = {1931-3543},
}
@article {pmid39938754,
year = {2025},
author = {Fernandes, M and Palmieri, O and Castellana, S and Spanetta, M and Latiano, T and Lupo, C and Masi, C and Cardile, C and Calvello, C and Izzi, F and Placidi, F and Mazza, T and Mercuri, NB and Latiano, A and Liguori, C},
title = {Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.},
journal = {Brain research bulletin},
volume = {},
number = {},
pages = {111251},
doi = {10.1016/j.brainresbull.2025.111251},
pmid = {39938754},
issn = {1873-2747},
abstract = {INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.<br><br>METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score&#x2265;10) to assess differences in clinical, polysomnographic and faecal data.<br><br>RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.<br><br>CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.},
}
@article {pmid39938727,
year = {2025},
author = {Braga, CM and da Silva, SP and Neto, JPN and Medeiros, DBA and Cruz, ACR and Sena do Nascimento, BL and Pinheiro, LRS and Martins, LC},
title = {Viral Metagenomics of Hematophagous Insects Collected in the Carajas Mining Complex, Pará State, Brazil.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107551},
doi = {10.1016/j.actatropica.2025.107551},
pmid = {39938727},
issn = {1873-6254},
abstract = {Hematophagous insects are vectors of viruses that cause diseases in humans and animals worldwide. Mosquitoes (Culicidae), biting midges (Ceratopogonidae), and sandflies (Psychodidae) were collected in three municipalities (Marabá, Canaã dos Carajás, and Curionópolis) in the state of Pará, Brazil, in 2019. Morphological keys were used for the taxonomic identification of insect species. High-throughput sequencing and metagenomic analysis were employed to characterize the viromes of the hematophagous insects. We characterized the virome of 839 insects grouped into 14 pools. A total of 729 million paired reads were generated, with 12 million viral sequences (3% of the reads). The families Reoviridae, Myoviridae, Retroviridae, and Poxviridae were found in all samples of this study. Phylogenies of RNA-dependent RNA polymerase (RdRp) from viruses of the families Chuviridae, Dicistroviridae, Flaviviridae, Iflaviridae, Mesoniviridae, Phenuiviridae, and Rhabdoviridae were performed. In this study, the first isolation of the Guaico Culex Virus (GCXV) in the northern region of Brazil was obtained from a pool of Culex (Melanoconion) spp. mosquitoes collected in Curionópolis. The data obtained in this study demonstrate that the Carajás region has an ecosystem rich in viruses. Additional studies are needed to understand the dynamics of viruses in vectors, vertebrates, and the human population in the region.},
}
@article {pmid39938449,
year = {2025},
author = {Ye, L and Yao, Z and Xuan, Q and Liu, Q and Bo, T},
title = {The impact of sleeve gastrectomy on MASH development by regulating the composition of gut microbiota and metabolic homeostasis.},
journal = {Biochemical and biophysical research communications},
volume = {752},
number = {},
pages = {151466},
doi = {10.1016/j.bbrc.2025.151466},
pmid = {39938449},
issn = {1090-2104},
abstract = {The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing annually, which is a global public health issue. Although clinical trials are lacking, observational studies indicate that bariatric surgery can alleviate the progression of MASH. Here, we performed sleeve gastrectomy (SG) and Sham surgery on 8-week-old mice, and then fed a AMLN diet for 24 weeks to construct a diet-inducted MASH mice model after 4-week post-surgery recovery. Applying a multi-omics approach combining metagenomics, metabolomics, and transcriptomics, we found that SG prevents the development of hepatic steatosis, inflammation, and fibrosis in MASH mice not only by significantly altering the structure of gut microbiota including s_Akkermansia muciniphila, s_Alistiples dispar, g_Helicobacter and s_uc_Oscillospiraceae, but also by modulating the levels of serum metabolites including l-arginine and taurocholic acid (TCA). These results suggest that SG and the alteration of gut microbiota and its related serum metabolites can be served as the effective therapeutic strategies for MASH.},
}
@article {pmid39938404,
year = {2025},
author = {d'Humières, C and Haviari, S and Petitjean, M and Deconinck, L and Gueye, S and Peiffer-Smadja, N and Chalal, L and Beldjoudi, N and Rossi, G and Nguyen, Y and Burdet, C and Perrineau, S and Le Pluart, D and Rahli, R and Thy, M and Szychowiak, P and Lescure, X and Leflon-Guibout, V and de Lastours, V and Ruppé, E},
title = {Comparison of clinical metagenomics with 16S rDNA Sanger sequencing for the bacteriological diagnosis of culture-negative samples.},
journal = {International journal of medical microbiology : IJMM},
volume = {318},
number = {},
pages = {151650},
doi = {10.1016/j.ijmm.2025.151650},
pmid = {39938404},
issn = {1618-0607},
abstract = {BACKGROUND: Currently, diagnosis of bacterial infections is based on culture, possibly followed by the amplification and sequencing (Sanger method) of the 16S rDNA - encoding gene when cultures are negative. Clinical metagenomics (CMg), i.e. the sequencing of a sample's entire nucleic acids, may allow for the identification of bacteria not detected by conventional methods. Here, we tested the performance of CMg compared to 16S rDNA sequencing (Sanger) in 50 patients with suspected bacterial infection but negative cultures.<br><br>METHODS: This is a prospective cohort study. Fifty patients (73 samples) with negative culture and a 16S rDNA sequencing demand (Sanger) were recruited from two sites. On the same samples, CMg (Illumina NextSeq) was also performed and compared to 16S rDNA Sanger sequencing. Bacteria were identified using MetaPhlAn4.<br><br>RESULTS: Among the 73 samples, 20 (27&#x202f;%, 17 patients) had a clinically relevant 16S rDNA Sanger sequencing result (used for patient management) while 11 (15&#x202f;%, 9 patients) were considered contaminants. At the patient level, the sensitivity of CMg was 70&#x202f;% (12/17) compared to 16S rDNA. In samples negative for 16S rDNA Sanger sequencing (n&#x202f;=&#x202f;53), CMg identified clinically-relevant bacteria in 10 samples (19&#x202f;%, 10 patients) with 14 additional bacteria.<br><br>CONCLUSIONS: CMg was not 100&#x202f;% sensitive when compared to 16S, supporting that it may not be a suitable replacement. However, CMg did find additional bacteria in samples negative for 16S rDNA Sanger. CMg could therefore be positioned as a complementary to 16S rDNA Sanger sequencing.},
}
@article {pmid39938372,
year = {2025},
author = {Guo, Y and Zhao, Y and Lin, K and Zheng, Q and Zhou, T},
title = {Metagenomic analysis of viral community during different municipal solid waste collection and treatment processes: Fate, hosts, and antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137520},
doi = {10.1016/j.jhazmat.2025.137520},
pmid = {39938372},
issn = {1873-3336},
abstract = {Municipal solid waste (MSW) serves as effective reservoirs of viruses and virus-associated antibiotic resistance genes (vir_ARGs), posing potential risks to human health. However, the composition of viral communities in different MSW collection and treatment processes remains unclear. Here, we profiled the viral communities and vir_ARGs in MSW leachate and aerosol samples from different MSW facilities based on metagenomic and virus enrichment-based viromic sequencings. Results showed that Microviridae and Caudoviricetes_Unclassified were the dominant viral families. Viral hosts were mainly distributed in the specific functional taxa of Bacillota. Additionally, the leachate properties and bacterial community structures significantly correlated with the viral community structures, implying that these environmental factors were the important drivers for viral distribution. The co-occurrence network analysis revealed the complex relationships between vir_ARGs and bacteria, suggesting that certain vir_ARGs have a broad host spectrum. Significant differences of viruses and vir_ARGs were observed between different sample types, but the viruses and vir_ARGs showed no significant differences across three sampling sites. Overall, this study highlights novel perspectives on the changes in viruses and vir_ARGs across the whole MSW collection and treatment processes, and provides valuable insights about the environmental factors affecting the profile of viral communities. These findings are crucial for elucidating the potential risks linked to the transmission of both viruses and ARGs.},
}
@article {pmid39938296,
year = {2025},
author = {Tan, L and Liang, J and Qin, Z and Ning, T and Wei, X and Yang, B and Wang, Q and Xu, Y and Shen, F},
title = {Unveiling the sustained effects of plant root exudates on soil microbiome and resistome and the related functional traits.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124485},
doi = {10.1016/j.jenvman.2025.124485},
pmid = {39938296},
issn = {1095-8630},
abstract = {Investigating the transmission mechanisms and influencing factors of antibiotic resistance genes (ARGs) in the soil-plant continuum is vital for mitigating ARG contamination and safeguarding plant and human health. Rhizosphere soil serves as a crucial interface for ARG propagation and transmission; however, it is unclear whether and how plant involved in regulating ARGs in their rhizosphere environment. Root exudates acting as vital links in the plant-soil-microbe interaction. Here, we examined the fluctuating patterns of the resistome and mobile genetic elements (MGEs) following exposure to four types of common root exudates: amino acids (AAs), sugars, long-chain organic acids (LCOAs), and short-chain organic acids (SCOAs). AAs exerted a rapid and pronounced effect, leading to a significant elevation in total ARG and MGE abundance by 3.18-fold and 21.06-fold, respectively, compared to the control group by day 7. Conversely, the impact of sugars manifested gradually over time. The influence of AAs and sugars persisted beyond 240 days post-treatment cessation. Importantly, the proliferation of ARGs was closely linked to the enrichment of plant growth-promoting bacteria (PGPBs) such as Pseudomonas, Cupriavidus, Azospirillum, Variovorax, and Ensifer. Functional analysis revealed that the potential features of ARGs and MGEs were associated with cell wall/membrane/envelope biogenesis, cell motility, and inorganic ion transport. This study offers novel insights into the factors influencing the dynamics of ARGs in the plant rhizosphere and may contribute to ecologically sustainable agricultural practices.},
}
@article {pmid39937671,
year = {2025},
author = {Su, Z and Liu, T and Guo, J and Zheng, M},
title = {Kinetic and Physiological Characterization of Acidophilic Nitrobacter spp. in a Nitrite-Oxidizing Culture.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10020},
pmid = {39937671},
issn = {1520-5851},
abstract = {Novel acidophilic nitrite-oxidizing Nitrobacter spp. were enriched, with kinetic and physiological features characterized comprehensively. The acidophilic Nitrobacter enrichment culture was cultivated in a membrane bioreactor at pH 4.6-5.5 for 500 days, with a relative abundance of 16S rRNA genes of 17.9 ± 0.5% during the characterization experiments. Metagenomic analysis recovered 2 Nitrobacter genomes, which corresponded to previously unknown species within the Nitrobacter genus with average nucleotide identity (ANI) < 91% compared to the publicly available genomes. In contrast to the known NOB, the acidophilic Nitrobacter enrichment culture exhibited strong tolerance to environmental stress, including low pH and free nitrous acid (FNA), and have low affinity for oxygen. Moreover, the acidophilic Nitrobacter enrichment culture also exhibited a higher nitrite affinity (Km = 0.19 ± 0.03 mg NO2[-]-N/L) than all currently characterized Nitrobacter cultures. These characteristics define acidophilic Nitrobacter as both a K-strategist and an adversity-strategist that tends to flourish in acidic activated sludge, where low pH (<5.5) and low nitrite levels suppress other nitrifiers. This study extends our understanding of nitrifiers growing in acidic environments and also provides a potential to remove nitrogen in acidic wastewater.},
}
@article {pmid39936903,
year = {2025},
author = {Elena, AX and Orel, N and Fang, P and Herndl, GJ and Berendonk, TU and Tinta, T and Klümper, U},
title = {Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0101224},
doi = {10.1128/msystems.01012-24},
pmid = {39936903},
issn = {2379-5077},
abstract = {Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from Aurelia aurita and Mnemiopsis leidyi recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. Vibrio was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a Vibrio isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential "One Health" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically Aurelia aurita and Mnemiopsis leidyi, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like Vibrio. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strategies to mitigate the spread of AMR in coastal ecosystems.},
}
@article {pmid39936895,
year = {2025},
author = {Paez-Diaz, JA and Nieves-Morales, R and Melendez-Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and Rios-Velazquez, C},
title = {Characterization of intestinal fungal communities through ITS amplicon from metagenomic libraries of sea cucumber (Holothuria glaberrima).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0132024},
doi = {10.1128/mra.01320-24},
pmid = {39936895},
issn = {2576-098X},
abstract = {The brown rock sea cucumber (Holothuria glaberrima) microbiome is vital for understanding its ecological dynamics. This study focuses on the microbial composition and abundance of fungi across different intestinal regions of H. glaberrima, giving insights into host-microbe interactions and supporting future ecological and comparative studies on their regeneration capabilities.},
}
@article {pmid39935633,
year = {2025},
author = {Wang, Y and Li, R and Wang, C and Sun, T and Zhang, H and Zhao, F and Liu, J and Hao, Y and Xie, X},
title = {The intestinal microbial community and function of Riptortus pedestris at different developmental stages and its effects on development.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1517280},
pmid = {39935633},
issn = {1664-302X},
abstract = {INTRODUCTION: Riptortus pedestris is a destructive pest that threatens multiple leguminous crops in China. The intestinal microbiota plays a crucial role in the growth and reproduction of host insects. However, the composition and function of the gut microbiota at different developmental stages remain unclear.<br><br>METHODS: Here, metagenomic sequencing was performed to clarify the gut microbial diversity and function in 2nd-, 3rd-, 4th-, and 5th- instar nymphs (2&#x202f;N-5&#x202f;N) and female adults (FAs) of R. pedestris and the effects of vital gut bacteria on development was detected. The gut bacteria have the stage specificity, indicating their function in the development of R. pedestris.<br><br>RESULTS: Enterococcus and Caballerronia were the predominant bacteria present during the development of the 2&#x202f;N-FAs. In addition, the microbial abundances in the 3&#x202f;N and 4&#x202f;N guts were significantly greater than those in the others guts. Furthermore, 5&#x202f;N harbored the abundant microbiota Burkholderia-Paraburkholderia-Caballeronia. The metabolic pathways were significantly enriched from 2&#x202f;N to FAs. Carbohydrate metabolism, including glycoside hydrolases (GHs) and glycosyl transferases (GTs), occurs throughout the entire developmental stage. Many antibiotic resistance genes (ARGs) were detected from 2&#x202f;N to FAs. The bacteria from Pseudomonadota and Bacillota presented a broad spectrum of antibiotic resistance. Excitingly, Burkholderia bacteria eliminated by antibiotic treatment were unable to molt normally, and their lifespan was shortened in nymphs, indicating that the gut microbiota had a significant effect on nymph development.<br><br>CONCLUSION: In summary, our results, for the first time, systematically illustrate the abundance and function across the gut microbiota from the different developmental stages of R. pedestris and demonstrate that the genera Burkholderia are crucial during the development of R. pedestris. This study provides the basis for stinkbug management strategies that focus on the pivotal gut microbiota.},
}
@article {pmid39935632,
year = {2025},
author = {Tang, Y and Wang, L and Fu, J and Zhou, F and Wei, H and Wu, X and Fan, S and Zhang, X},
title = {Unraveling the microecological mechanisms of phosphate-solubilizing Pseudomonas asiatica JP233 through metagenomics: insights into the roles of rhizosphere microbiota and predatory bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538117},
pmid = {39935632},
issn = {1664-302X},
abstract = {The effects of phosphate-solubilizing bacteria (PSB) on plant productivity are high variable under field conditions. Soil phosphorus (P) levels are proposed to impact PSB performance. Furthermore, the effect of exogenous PSB on rhizosphere microbial community and their functions are largely unexplored. Our study examined how different P background and fertilization affected the performance of PSB Pseudomonas asiatica JP233. We further conducted metagenomic sequencing to assess its impact on rhizosphere microbiota and functions, with a focus on genes related to soil P cycling. We found that JP233 could enhance P solubilization and tomato growth to different extent in both high and low P soils, irrespective of P fertilization. It was particularly effective in high P soil without extra fertilization. JP233 altered the rhizosphere microbial community, boosting taxa known for plant growth promotion. It also changed soil gene profiling, enriching pathways related to secondary metabolite biosynthesis, amino acids, carbon metabolism, and other key processes. Particularly, JP233 increased the abundance of most P cycle genes and strengthened their interconnections. Populations of certain predatory bacteria increased after JP233 inoculation. Our findings provide valuable insights into PSB's mechanisms for P solubilization and plant growth promotion, as well as potential adverse impacts of resident microbes on bioinoculants.},
}
@article {pmid39935631,
year = {2025},
author = {Redondo-Río, &#xc1; and Mundy, CJ and Tamames, J and Pedrós-Alió, C},
title = {Corrigendum: Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1534826},
doi = {10.3389/fmicb.2025.1534826},
pmid = {39935631},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1481702.].},
}
@article {pmid39935515,
year = {2024},
author = {Yao, L and Zhou, X and Jiang, X and Chen, H and Li, Y and Xiong, X and Tang, Y and Zhang, H and Qiao, P},
title = {High-fat diet promotes gestational diabetes mellitus through modulating gut microbiota and bile acid metabolism.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1480446},
pmid = {39935515},
issn = {1664-302X},
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a condition characterized by glucose intolerance during pregnancy, estimated to affect approximately 20% of the whole pregnancies and is increasing in prevalence globally. However, there is still a big gap in knowledge about the association between gut microbiota associated metabolism alterations and GDM development.<br><br>METHODS: All the participants accomplished the validated internet-based dietary questionnaire for Chinese and serum, fecal samples were collected. HFD, control diet or colesevelam intervention was fed to GDM mice models or Fxr-/- mice models, with or without antibiotics cocktail treatment. Fecal microbiota transplantation were used for further validation. Gut microbiota and metabolites were detected by metagenomic sequencing and high-performance liquid chromatography-mass spectrometry, respectively. Bile acids of serum, fecal samples from human and mice were analysised. Body weight, average feed intake, blood glucose, insulin levels and oral glucose tolerance test was performed among each groups. Expression levels of Fxr, Shp and Fgf15 mRNA and protein were detected by quantitative reverse transcription polymerase chain reaction and western blot, respectively.<br><br>RESULTS: Our data indicated that high fat diet (HFD) was linked with higher prevalence of GDM, and HFD was positively associated with poor prognosis in GDM patients. Moreover, compared with normal diet (ND) group, GDM patients from HFD group performed a loss of gut microbiota diversity and enrichment of Alistipes onderdonkii, Lachnospiraceae bacterium 1_7_58FAA, and Clostridium aspaaragiforme while ruduction of Akkermansiaceae, Paraprevotell xylaniphila, and Prevotella copri. Additionally, HFD aggravated GDM in mice and gut microbiota depletion by antibiotics crippled the effect of excess fat intake. BAs profile altered in HFD GDM patients and mice models. Fecal microbiota transplantation (FMT) further confirmed that gut microbiota contributed to bile acids (BAs) metabolic dysfunction during HFD-associated GDM development. Mechanically, HFD-FMT administration activated Fxr, Shp, and Fgf15 activity, disturbed the glucose metabolism and aggravated insulin resistance but not in HFD-FMT Fxr-/- mice and ND-FMT Fxr-/- mice. Furthermore, colesevelam intervention alleviated HFD-associated GDM development, improved BAs metabolism, suppressed Fxr, Shp, and Fgf15 activity only in WT mice but not in the Fxr-/- HFD&#x202f;+&#x202f;Colesevelam group and Fxr-/- HFD group. HFD induced GDM and contributed to poor prognosis in GDM parturients through inducing gut microbial dysbiosis and metabolic alteration, especially appeared in BAs profile. Moreover, Fxr pathway participated in regulating HFD-associated gut microbiota disordered BAs metabolites and aggravating GDM in mice.<br><br>DISCUSSION: Modulating gut microbiota and BAs metabolites could be a potential therapeutic strategy in the prevention and treatment of HFD-associated GDM.},
}
@article {pmid39935055,
year = {2025},
author = {Huang, Y and Zheng, X and Zhao, Z and Tao, J and Hu, T and Han, Z and Lin, T},
title = {Integration of manganese ores with activated carbon into constructed wetland for greenhouse gas emissions reduction.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124205},
doi = {10.1016/j.jenvman.2025.124205},
pmid = {39935055},
issn = {1095-8630},
mesh = {*Wetlands ; *Greenhouse Gases ; *Manganese/metabolism ; Charcoal/chemistry ; Nitrogen/metabolism ; Phosphorus/metabolism ; },
abstract = {Manganese oxide and activated carbon (AC) are widely employed in constructed wetlands (CWs) to remove nutrients and reduce greenhouse gas (GHG) emissions, however, the effect and mechanism of AC combined with manganese ores (MO) on GHG emissions remain unclear. In this study, the mechanisms of nutrient removal and GHG emissions reduction were investigated by three vertical subsurface-flow CWs: gravel (CW-B), manganese ores (MO) uniformly mixing with gravel (CW-M), or activated carbon (CW-MC). The average removal efficiencies of chemical oxygen demand, total nitrogen and total phosphorus in CW-MC were markedly improved compared to CW-B and CW-M, reaching 82.72%, 95.72% and 93.43%, respectively. Moreover, the global warming potential (CO2 equivalent) of CW-MC was reduced by 52.80% and 36.88% relative to CW-B and CW-M, respectively. Mixing of MO with AC reduced the loss of manganese and further enhanced the manganese cycling process by X-ray photoelectron spectroscope and concentration of Mn(Ⅱ) in CWs analysis. The introduction of MO and AC enhanced the PN/PS ratio of extracellular polymeric substances and facilitated extracellular electron transfer (EET). Furthermore, metagenomic analysis showed that the abundances of denitrifying, manganese oxidizing and electroactive bacteria genera were enhanced in the CW-MC, which promoted the transformation of nitrogen and manganese. Meanwhile, high abundances of denitrification and EET related genes were observed in CW-MC, improving denitrification efficiency and reducing N2O emission. This study elucidated the impacts and mechanisms of MO and AC on GHG emissions, providing a new insight to improve manganese-based CW performance.},
}
@article {pmid39933522,
year = {2025},
author = {Xu, CCY and Fugère, V and Barbosa da Costa, N and Beisner, BE and Bell, G and Cristescu, ME and Fussmann, GF and Gonzalez, A and Shapiro, BJ and Barrett, RDH},
title = {Pre-exposure to stress reduces loss of community and genetic diversity following severe environmental disturbance.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.01.037},
pmid = {39933522},
issn = {1879-0445},
abstract = {Environmental stress caused by anthropogenic impacts is increasing worldwide. Understanding the ecological and evolutionary consequences for biodiversity will be crucial for our ability to respond effectively. Historical exposure to environmental stress is expected to select for resistant species, shifting community composition toward more stress-tolerant taxa. Concurrent with this species sorting process, genotypes within resistant taxa that have the highest relative fitness under severe stress are expected to increase in frequency, leading to evolutionary adaptation. However, empirical demonstrations of these dual ecological and evolutionary processes in natural communities are rare. Here, we provide evidence for simultaneous species sorting and evolutionary adaptation across multiple species within a natural freshwater bacterial community. Using a two-phase stressor experimental design (acidification pre-exposure followed by severe acidification) in aquatic mesocosms, we show that pre-exposed communities were more resistant than naive communities to taxonomic loss when faced with severe acid stress. However, after sustained severe acidification, taxonomic richness of both pre-exposed and naive communities eventually converged. All communities experiencing severe acidification became dominated by an acidophilic bacterium, Acidiphilium rubrum, but this species retained greater genetic diversity and followed distinct evolutionary trajectories in pre-exposed relative to naive communities. These patterns were shared across other acidophilic species, providing repeated evidence for the impact of pre-exposure on evolutionary outcomes despite the convergence of community profiles. Our results underscore the need to consider both ecological and evolutionary processes to accurately predict the responses of natural communities to environmental change.},
}
@article {pmid39933221,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Li, Y and Tu, Y and Wei, Y and Bai, J and Liu, Y},
title = {Gut microbiota causes depressive phenotype by modulating glycerophospholipid and sphingolipid metabolism via the gut-brain axis.},
journal = {Psychiatry research},
volume = {346},
number = {},
pages = {116392},
doi = {10.1016/j.psychres.2025.116392},
pmid = {39933221},
issn = {1872-7123},
abstract = {Emerging evidence suggests that changes in the gut microbiota (GM) are related to prenatal depression onset, but the underlying molecular mechanisms remain obscure. This study was conducted to explore how disordered GM is involved in the onset of prenatal depression through the microbiome-gut-brain (MGB) axis. We transplanted fecal microbiota from women with and without prenatal depression into germ-free mice. Fecal metagenomic sequencing and LC-MS untargeted metabolomics analysis were performed to identify the GM composition, function, and metabolites in mice. Lipid metabolomics analysis was then used to characterize the lipid metabolism of brain tissue in mice. We found that mice transplanted with fecal microbiota from women with prenatal depression exhibited depressive-like behaviors as well as characteristic disorders of the phylum Firmicutes. Weighted Gene Correlation Network Analysis identified three microbial and one metabolic module in the gut, alongside two lipid metabolic modules in the brain, as significantly related to all depressive-like behaviors. These modules were enriched for glycerophospholipid and sphingolipid metabolism. In addition, the GM of mice with depressive-like behaviors were enriched and deficient in relevant functions and enzymes in the glycerophospholipid (mainly phosphatidylethanolamine) and sphingolipid (mainly hexosyl-ceramide) metabolic pathways, respectively. Consistently, glycerophospholipid and sphingolipid metabolites in the brains of depressive-like mice were up- and down-regulated. Increased phosphatidylethanolamine and decreased hexosyl-ceramide were significantly related to differential genera in the gut. Collectively, our findings provide a novel microbial and metabolic framework for understanding the role of the MGB axis in prenatal depression, indicating that the GM may be involved in the onset of depressive phenotypes by modulating central glycerophospholipid and sphingolipid metabolic homeostasis.},
}
@article {pmid39932999,
year = {2025},
author = {Tepekule, B and Barcik, W and Staiger, WI and Bergadà-Pijuan, J and Scheier, T and Brülisauer, L and Hall, AR and Günthard, HF and Hilty, M and Kouyos, RD and Brugger, SD},
title = {Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {7},
pages = {e2412742122},
doi = {10.1073/pnas.2412742122},
pmid = {39932999},
issn = {1091-6490},
support = {1449 M//Promedica Stiftung/ ; GRS-09420//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; GRS-09420//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; BSSGI0_155851//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; K-84804 - 01 - 01//UZH | Foundation for Research in Science and the Humanities (Stiftung f&#xfc;r wissenschaftliche Forschung)/ ; },
mesh = {*Probiotics/administration &amp; dosage/pharmacology ; *Staphylococcus aureus/drug effects ; Humans ; *Staphylococcal Infections/microbiology/drug therapy ; *RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Microbiota/drug effects ; Nose/microbiology ; Computer Simulation ; Adult ; },
abstract = {Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.},
}
@article {pmid39932948,
year = {2025},
author = {Gao, ZY and Zhao, XD and Chen, C and Zhao, FJ and Zhang, SY},
title = {Paddy Soil Flooding and Nonflooding Affect the Transcriptional Activity of Arsenic Methylation and Demethylation Communities.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08620},
pmid = {39932948},
issn = {1520-5851},
abstract = {The intermediate product methylarsenite [MMA(III)] of arsenic (As) methylation can be methylated to dimethylarsenate (DMA), which causes rice straighthead disease via the As methylation enzyme (ArsM), demethylated to arsenite via the As demethylation enzyme (ArsI), or excreted from cells via the MMA(III) efflux enzyme (ArsP). Whereas As methylation is commonly reported in flooded soils, As demethylation is mostly mediated by aerobes. We used custom-built ROCker models (accuracies of 99.7-99.9%) to quantify the short-read sequences carrying As genes and investigate the variations in the transcriptional activity of the arsM, arsI, and arsP genes in flooded and nonflooded paddy soils. We revealed significantly (p < 0.05) greater transcriptional activity of the arsM and arsP genes in flooded than nonflooded soils, whereas the transcriptional activity of the arsI genes was comparable. MMA(III) demethylation in flooded soils is possibly coupled with denitrification, as revealed by the significantly (p < 0.05) positively correlated genes in terms of transcriptional activity. Moreover, we showed that microbes coexpressing the arsM and arsI genes were dominated by Actinomycetota and Pseudomonadota. This study sheds light on the active microbial communities involved in As methylation and demethylation in paddy soils and provides insights into the prevention of rice straighthead disease.},
}
@article {pmid39932663,
year = {2025},
author = {da Silva Pereira, M and Alcantara, LM and de Freitas, LM and de Oliveira Ferreira, AL and Leal, PL},
title = {Microbial Rumen proteome analysis suggests Firmicutes and Bacteroidetes as key producers of lignocellulolytic enzymes and carbohydrate-binding modules.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39932663},
issn = {1678-4405},
support = {Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia/ ; Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Lignocellulosic biomass, rich in cellulose, hemicellulose, and lignin, offers a sustainable source for biofuels and and production of other materials such as polymers, paper, fabrics, bioplastics and biofertilizers. However, its complex structure hinders efficient conversion. Chemical, enzymatic, and microbial methods aim to unlock the trapped sugars and phenols. The rumen microbiome, a fascinating ecosystem within ruminant animals, holds particular promise. The Hungate 1000 project sequenced 410 microbial genomes from the rumen, enabling in silico screening for lignocellulolytic enzymes. This approach saves time and resources, supporting the development of sustainable bioconversion technologies aligned with the UN's 2030 agenda goals. Analysis of these 410 predicted proteomes revealed diverse carbohydrate-active enzymes (CAZymes) and carbohydrate-binding modules (CBMs) across various microorganisms. Notably, Firmicutes and Bacteroidetes dominated CAZyme and CBM production, suggesting collaborative efforts among different phyla during degradation. The presence of CBM50 and chitinases hints at the ability to utilize chitin from fungal cell walls. Interestingly, the absence of ligninolytic auxiliary activity enzymes reaffirms the rumen microbiome's incapability of directly degrading lignin. However, enzymes facilitating the loosening of the cell wall by cleaving lignin-hemicellulose linkages were identified. This suggests a strategy for making cellulose more accessible to hydrolytic enzymes. This study highlights the intricate relationship between rumen microbes, contributing necessary enzymes for plant cell wall deconstruction in this unique environment. Additionally, it underlines the power of in silico techniques for analyzing big data, paving the way for advancements in sustainable bioconversion.},
}
@article {pmid39932403,
year = {2025},
author = {Momo Cabrera, P and Bokulich, NA and Zimmermann, P},
title = {Evaluating stool microbiome integrity after domestic freezer storage using whole-metagenome sequencing, genome assembly, and antimicrobial resistance gene analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0227824},
doi = {10.1128/spectrum.02278-24},
pmid = {39932403},
issn = {2165-0497},
abstract = {UNLABELLED: The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with -80°C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples obtained from 20 children under 4 years of age with the use of shotgun metagenome sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4°C and analyzed within 24 hours, while others were frozen in domestic freezers (below -18°C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition.<br><br>IMPORTANCE: Most prior studies on sample storage have relied on amplicon sequencing, which is less applicable to metagenome sequencing-given considerations of contig quality and functional gene detection-and less reliable in representing microbial composition. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been previously investigated. Our findings suggest that stool samples stored in domestic freezers for up to 6 months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.},
}
@article {pmid39932299,
year = {2025},
author = {Cui, H and Wang, S and Fan, S and Long, H and Lin, J and Ding, W and Zhang, W},
title = {Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0241124},
doi = {10.1128/aem.02411-24},
pmid = {39932299},
issn = {1098-5336},
abstract = {UNLABELLED: Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (Leisingera aquaemixtae M597, Roseibium aggregatum S1616, Alloyangia pacifica T6124, and Sulfitobacter indolifex W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616-M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.<br><br>IMPORTANCE: Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.},
}
@article {pmid39931947,
year = {2025},
author = {Liu, Y and Zhao, T and Wang, Z and Zhang, Y and Shen, J and Lu, B},
title = {The microbiome- and metabolome-modulating activity of dietary cholesterol: insights from the small and large intestines.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo03049d},
pmid = {39931947},
issn = {2042-650X},
abstract = {Cholesterol is an important lipid molecule that affects the gut microbiome upon ingestion. We systematically investigated the effects of cholesterol on the microbiota of the large and small intestines using ex vivo and in vivo models, combining flow cytometry, metabolomics, and metagenomics. The results showed that cholesterol directly causes a loss of bacterial membrane polarity and integrity, as well as a reduction in microbial metabolic activity. Cholesterol directly affected the global metabolism of the large and small intestinal microbiota, including amino acid, carbohydrate, and nucleotide metabolism. Ex vivo and in vivo studies shared similar results, showing that cholesterol increased the abundance of the primary bile acid-metabolizing bacteria Clostridium and Dorea in the large intestinal microbiota, confirming the enrichment effect of cholesterol on these bacteria. In the in vivo model, increased conjugated bile acids in the small intestine and decreased abundance of BSH-containing Bifidobacterium were observed due to cholesterol. Only in vivo models have demonstrated that cholesterol increases phosphatidylcholine levels in both the small and large intestines, which may be related to the effects of cholesterol on host metabolism. The pro-inflammatory capacity of the intestinal microbiota was enhanced by cholesterol, as evidenced by the increased levels of IL-1β and TNF-α in THP-1 cells upon stimulation with cholesterol-treated microbiota. This study comprehensively elucidates the effects of cholesterol on the composition and metabolic functions of the microbiota in both the large and small intestines. It offers a novel perspective on the ways in which cholesterol affects host metabolism via the gut microbiome.},
}
@article {pmid39931676,
year = {2025},
author = {Dutkiewicz, Z and Singleton, CM and Sereika, M and Villada, JC and Mussig, AJ and Chuvochina, M and Albertsen, M and Schulz, F and Woyke, T and Nielsen, PH and Hugenholtz, P and Rinke, C},
title = {Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae147},
pmid = {39931676},
issn = {2730-6151},
abstract = {Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities, and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes and by proposing one of them (ABY1[TS]) to serve as the nomenclatural type for the species Patescibacterium danicum [TS] gen. nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicum [TS] in the Ca. Patescibacteria class ABY1. Based on these results, we propose Patescibacterium gen. nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (<1 Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, our proposal will provide nomenclatural stability to the fourth-largest phylum in the bacterial domain.},
}
@article {pmid39931490,
year = {2025},
author = {Gong, L and Li, X and Ji, L and Chen, G and Han, Z and Su, L and Wu, D},
title = {Characterization and comparison of gut microbiota in patients with acute pancreatitis by metagenomics and culturomics.},
journal = {Heliyon},
volume = {11},
number = {3},
pages = {e42243},
pmid = {39931490},
issn = {2405-8440},
abstract = {Acute pancreatitis (AP) is a common gastrointestinal disorder with a high mortality rate. This study sought to identify the microbial community structure in patients with AP using metagenomics and culturomics. Compared to healthy controls, patients with AP exhibited a significant decrease in alpha diversity; a higher abundance of unclassified Enterococcus species (sp), Enterococcus faecium, and Enterococcus faecalis; and a lower abundance of Eubacterium rectale. A total of 336 isolates from 25 genera and 44 species were obtained by sample cultivation. The dominant species identified in patients with AP were Enterococcus faecium and Klebsiella grimontii, whereas those in the healthy controls were Enterococcus faecium, Escherichia coli, and Bacteroides faecis. Our research has contributed to the expanded understanding of the genome, diversity, and function of the intestinal microbiota in patients with AP and provided some reference for selecting culture medium and sample processing methods.},
}
@article {pmid39931275,
year = {2024},
author = {Skoulakis, A and Skoufos, G and Ovsepian, A and Hatzigeorgiou, AG},
title = {Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1512304},
pmid = {39931275},
issn = {1664-302X},
abstract = {BACKGROUND: The presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.<br><br>METHODS: We analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.<br><br>RESULTS: Tissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to in silico contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus Sporisorium graminicola for the heart, the gram-positive bacterium Flavonifractor plautii for the colon tissue, and the gram-negative bacterium Bartonella machadoae for the liver.<br><br>CONCLUSION: The presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.},
}
@article {pmid39931171,
year = {2025},
author = {Yang, X and Pan, Y and Gao, CP and Li, H and Zhang, YH and Huang, CL and Cao, L and Xiao, SY and Zhou, Z},
title = {Prominence of Microbiota to Predict Fibrous Stenosis in Crohn's Disease.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {1413-1423},
pmid = {39931171},
issn = {1178-7031},
abstract = {PURPOSE: Intestinal fibrous stenosis due to Crohn's disease (CD) is highly prevalent. Although several clinical risk factors for fibrous stenosis have been identified, such as perianal fistulizing disease, small bowel disease location, and deep mucosal ulceration, predicting fibrous stenosis remains challenging. The intestinal microbiota plays a crucial role in the development and progression of CD. However, its role in intestinal fibrous stenosis is poorly understood. Leveraging a single-center cross-sectional study, we aimed to investigate the role of fecal microbiota in CD-associated fibrous stenosis.<br><br>METHODS: Using metagenomic analysis, we examined the differences in fecal microbiota between CD patients with intestinal fibrous stenosis and those without stenosis. We identified specific microbiota and assessed their predictive accuracy for intestinal fibrous stenosis. Additionally, we explored functional differences in intestinal microbiota between the two groups.<br><br>RESULTS: : Our investigation of fecal samples revealed no significant differences in the gut microbiota structure between patients with fibrous stenosis and those without stenosis in CD. However, taxonomically, we found 70 taxa with significantly different abundance (p < 0.05) between the two groups. Furthermore, LEfSe analysis indicated that g_Bacteroides and g_Enterocloster could predict intestinal fibrous stenosis while p_Actinobacteria, c_Actinomycetia, c_Bacilli, o_Lactobacillales, f_Streptococcaceae and g_Streptococcus could predict CD without stenosis. Functional analysis revealed differential enrichment in five metabolic pathways at the KEGG pathway level in CD patients with fibrous stenosis, including sphingolipid metabolism, lipoic acid metabolism, and biosynthesis of neomycin, kanamycin and gentamicin. In the eggNOG database, we observed differences in four functional categories between the two groups, encompassing cellular process, signaling, and metabolism.<br><br>CONCLUSION: Fecal microbiota significantly impacted intestinal fibrous stenosis in CD. Although there were no significant differences in alpha and beta diversities, fibrous stenosis was associated with changes in microbiota composition and function, suggesting the potential of fecal microbiota in predicting CD-associated fibrous stenosis.},
}
@article {pmid39931040,
year = {2025},
author = {Weng, D and Zhou, H and Huang, G and Cao, Q and Wang, H and Cao, Z and Xie, Q},
title = {Escherichia coli in the T11-12 Thoracic Vertebrae: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {693-702},
pmid = {39931040},
issn = {1178-6973},
abstract = {BACKGROUND: Pyogenic thoracic spondylitis is a rare but severe infection, particularly when complicated by sepsis and acute kidney injury (AKI). Early diagnosis and precise management are essential for improving outcomes, given the limitations of traditional microbiology detection methods in identifying the causative pathogens.<br><br>CASE PRESENTATION: A 68-year-old immunocompetent male presented with recurrent fever, fatigue, loss of appetite and initial evidence of sepsis and AKI upon admission. With the prompt computed tomography (CT)-guided percutaneous biopsy of the thoracic vertebrae, Escherichia coli was identified as the causative pathogen using metagenomic next-generation sequencing (mNGS). A diagnosis of pyogenic thoracic spondylitis was then made followed by the treatment of antibiotics optimized by therapeutic drug monitoring (TDM) techniques. With a total effective antibiotic treatment period of 7 weeks, the patient recovered without resorting to surgical interventions.<br><br>CONCLUSION: This is a rare case of acute thoracic spondylitis caused by E. coli, successfully treated without surgery. This case highlights the significant challenges in diagnosis and treatment. It underscores the value of mNGS in identifying rare infections and emphasizes the role of TDM in optimizing antibiotic therapy, providing a reference for future cases of rare and critical infections with fever of unknown origin.},
}
@article {pmid39930446,
year = {2025},
author = {Dong, L and Ji, Z and Hu, J and Jiang, Q and Wei, W},
title = {Oral microbiota shifts following tooth loss affect gut health.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {213},
pmid = {39930446},
issn = {1472-6831},
support = {YSP202314//Young Scientist Program of Beijing Stomatological Hospital, Capital Medical University/ ; },
mesh = {Animals ; *Tooth Loss/microbiology ; Mice ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; Saliva/microbiology ; Feces/microbiology ; Microbiota ; Mouth/microbiology ; Male ; },
abstract = {BACKGROUND: Tooth loss not only impairs oral function but also affects gut health by altering the host microbiota. Understanding the oral-gut axis can provide insights into systemic health implications following tooth loss.<br><br>METHODS: Using an animal model, we extracted the molars of C57 mice. Saliva and fecal samples were collected for 16S rRNA and metagenomic sequencing to analyze changes in the oral and gut microbiota. Pearson correlation analysis assessed the relationship between altered microbial communities.<br><br>RESULTS: The study found a significant reduction in oral microbiota diversity following tooth loss, with increased Proteobacteria and decreased Muribacter. Gut microbiota showed increased Firmicutes and decreased Bacteroidota. Correlations between oral and gut microbiota changes were observed, indicating a potential link between tooth loss and alterations in intestinal microbial balance.<br><br>CONCLUSION: In the mouse model, tooth loss disrupted the balance of the oral-gut microbiota, with potential implications for intestinal health. Although these findings are from a murine model, considering the existence of the oral-gut axis balance in the human body, it is reasonable to postulate that following tooth loss in humans, the health of the intestinal microecology may also warrant attention.},
}
@article {pmid39930163,
year = {2025},
author = {Kahraman Ilıkkan, &#xd6;},
title = {Lactobacillomics as a new notion in lactic acid bacteria research through omics integration.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {2},
pages = {68},
pmid = {39930163},
issn = {1573-0972},
mesh = {*Lactobacillales/genetics/metabolism ; *Probiotics ; *Metabolomics ; *Genomics/methods ; *Proteomics ; Fermentation ; Metagenomics ; Humans ; Genome, Bacterial ; },
abstract = {Omics technologies are a set of disciplines that analyze large-scale molecular data to understand biological systems in a holistic way. These technologies aim to reveal the structure, functions and interactions of organisms by studying processes at many levels of biomolecules, from the genome to metabolism. Lactobacillomics is introduced as an interdisciplinary field that integrates multiple "omics" technologies-including genomics, transcriptomics, proteomics, metabolomics, and metagenomics- to provide a comprehensive insight into "lactic acid bacteria" species. Lactobacillomics aims to elucidate the genetic, metabolic, and functional characteristics of lactic acid bacteria (LAB) species, providing insights into the mechanisms underlying their probiotic effects and contributions to the host microbiome. By analyzing genomes and metabolic pathways, researchers can identify specific genes responsible for health-promoting functions and desirable fermentation characteristics, which can guide the development of targeted probiotic strains with optimized health benefits. The integration of these omics data allows facilitating the discovery of biomarkers for health and disease states, the development of new probiotics tailored to specific populations or health conditions, and the optimization of fermentation processes to enhance the safety, flavor, and nutritional profile of fermented foods. A comprehensive review and bibliometric analysis were conducted to provide an overview of this promising field between 2005 and 2025 by examining Web of Science Core Collection data. Research results reveal trending topics, future perspectives, and key areas of growth within lactic acid bacteria (LAB) studies, particularly as they intersect with omics technologies.},
}
@article {pmid39930064,
year = {2025},
author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H},
title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {210},
pmid = {39930064},
issn = {2399-3642},
mesh = {*Museums ; *Metagenomics/methods ; *Genomics/methods ; Animals ; *Archaeology ; Greenland ; Bone and Bones ; DNA/genetics ; },
abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.},
}
@article {pmid39929976,
year = {2025},
author = {Sardar, P and Beresford-Jones, BS and Xia, W and Shabana, O and Suyama, S and Ramos, RJF and Soderholm, AT and Tourlomousis, P and Kuo, P and Evans, AC and Imianowski, CJ and Conti, AG and Wesolowski, AJ and Baker, NM and McCord, EAL and Okkenhaug, K and Whiteside, SK and Roychoudhuri, R and Bryant, CE and Cross, JR and Pedicord, VA},
title = {Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39929976},
issn = {2058-5276},
support = {206245/Z/17/Z//Wellcome Trust (Wellcome)/ ; 302351/Z/23/Z//Wellcome Trust (Wellcome)/ ; A2194//Rosetrees Trust/ ; EP/X024709/1//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors, such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. Here, by functionally analysing faecal metagenomes from 112 patients with melanoma, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumour mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumour immune responses, and LPS-binding antibiotics and a small-molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumour immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.},
}
@article {pmid39929376,
year = {2025},
author = {Wu, B and Tang, Y and Zhao, L and Gao, Y and Shen, X and Xiao, S and Yao, S and Qi, H and Shen, F},
title = {Integrated network pharmacological analysis and multi-omics techniques to reveal the mechanism of polydatin in the treatment of silicosis via gut-lung axis.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107030},
doi = {10.1016/j.ejps.2025.107030},
pmid = {39929376},
issn = {1879-0720},
abstract = {Silicosis is a pulmonary disease characterized by inflammation and progressive fibrosis. Previous studies have shown that polydatin (PD) has potential biological activity in key signaling pathways regulating inflammation and apoptosis. To investigate the effect of PD on rats with silicosis, this study used network pharmacology and molecular docking methods to determine the target of PD treatment for silicosis. The therapeutic effect of PD on silicosis was confirmed by measuring the lung injury score, hydroxyproline content, and mRNA expression levels of key targets. In addition, metagenomic sequencing and gas chromatography-mass spectrometry were used to determine the gut microbiota composition and targeted metabolomics analysis, respectively. The results showed that PD could inhibit the expression of inflammation-related indexes and apoptosis-related indexes at protein and mRNA levels. PD also regulates the diversity of the intestinal flora and the content of short-chain fatty acids. In conclusion, the current data suggest that PD has a protective effect against silica-induced lung injury and plays a protective role in regulating intestinal flora diversity and short-chain fatty acid levels through the gut-lung axis.},
}
@article {pmid39929003,
year = {2025},
author = {Bakir-Gungor, B and Temiz, M and Canakcimaksutoglu, B and Yousef, M},
title = {Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach.},
journal = {Computers in biology and medicine},
volume = {187},
number = {},
pages = {109813},
doi = {10.1016/j.compbiomed.2025.109813},
pmid = {39929003},
issn = {1879-0534},
abstract = {Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.},
}
@article {pmid39927868,
year = {2025},
author = {Zouiouich, S and Wan, Y and Vogtmann, E and Porras, C and Abnet, CC and Shi, J and Sinha, R},
title = {Sample size estimations based on human microbiome temporal stability over six months: a shallow shotgun metagenome sequencing analysis.},
journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-24-0839},
pmid = {39927868},
issn = {1538-7755},
abstract = {BACKGROUND: Biological factors impact the human microbiome, highlighting the need for reasonably estimating sample sizes in future population studies.<br><br>METHODS: We assessed the temporal stability of fecal microbiome diversity, species composition, and genes and functional pathways through shallow shotgun metagenome sequencing. Using intraclass correlation coefficients (ICC), we measured biological variability over six months. We estimated case numbers for 1:1 or 1:3 matched case-control studies, considering significance levels of 0.05 and 0.001 with 80% power, based on the collected fecal specimens per participant.<br><br>RESULTS: The fecal microbiome's temporal stability over six months varied (ICC <0.6) for most alpha and beta diversity metrics. Heterogeneity was seen in species, genes, and pathways stability (ICC 0.0-0.9). Detecting an odds ratio of 1.5 per standard deviation required 1,000-5,000 cases (0.05 significance for alpha and beta; 0.001 for species, genes, pathways) with equal cases and controls. Low-prevalent species needed 15,102 cases; high-prevalent species required 3,527. Similar needs applied to genes and pathways. In a 1:3 matched case-control study with one fecal specimen, 10,068 cases were needed for low-prevalent species; 2,351 for high-prevalent species. For odds ratios of 1.5 with multiple specimens, cases needed for low-prevalent species were 15,102 (one specimen), 8,267 (two specimens), and 5,989 (three specimens).<br><br>CONCLUSIONS: Detecting disease associations requires a large number of cases. Repeating prediagnostic samples and matching cases to more controls could decrease the needed number of cases for such detections.<br><br>IMPACT: Our results will help future epidemiologic studies design and implement well-powered microbiome studies.},
}
@article {pmid39927795,
year = {2025},
author = {Huang, D and Chen, Y and Li, C and Yang, S and Lin, L and Zhang, X and Su, X and Liu, L and Zhao, H and Luo, T and Cai, S and Ren, Q and Dong, H},
title = {Variations in salivary microbiome and metabolites are associated with immunotherapy efficacy in patients with advanced NSCLC.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0111524},
doi = {10.1128/msystems.01115-24},
pmid = {39927795},
issn = {2379-5077},
abstract = {Lung cancer is a leading cause of cancer mortality, with non-small cell lung cancer (NSCLC) comprising the majority of cases. Despite the advent of immune checkpoint inhibitors (ICIs), a significant number of patients fail to achieve a durable response, highlighting the need to understand the factors influencing treatment efficacy. Saliva samples and tumor samples were collected from 20 NSCLC patients. The salivary microbiota was profiled using metagenomic next-generation sequencing, and metabolites were analyzed via liquid chromatography-mass spectrometry to identify correlations among bacteria, metabolites, and immunotherapy responses. Immunohistochemistry (IHC) analysis of tissue samples verified the result. Besides, in vitro experiments and tumor tissue microarray, including 70 NSCLC patients, were utilized to further explore the potential mechanism linking the oral microbiome and immunotherapy efficacy. The study revealed several differential species and distinct metabolite compositions between responders and non-responders to ICI therapy in NSCLC and explored correlations and mechanisms between microbiota metabolites and immunotherapy resistance. Notably, it was found that several Neisseria and Actinomyces species were significantly enriched in responders and identified lipids and lipid-like molecules associated with PD-L1 expression levels and treatment outcomes. Importantly, several differential lipid molecules were associated with differential species. Further, in vitro experiments and IHC experiments indicated that abnormal fat metabolism linked to dysbiosis is correlated with immunotherapy resistance through regulation of CD8[+] T cell activity/infiltration and PD-L1 expression. Specific saliva microbiome and its associated lipids metabolites are significantly associated with the efficacy of ICI-based therapy in lung cancer. Our findings suggest that oral microbiome modulation and targeting lipid metabolism could improve immunotherapy responses, offering new avenues for personalized treatment strategies.IMPORTANCEIn non-small cell lung cancer, our study links specific salivary microbiome profiles and related lipid metabolites to the efficacy of immune checkpoint inhibitor (ICI) therapies. Responders showed enrichment of certain Neisseria and Actinomyces species and distinct lipid compositions. These lipids correlate with PD-L1 expression and CD8[+] T cell activity, affecting treatment outcomes. Our results imply that modulating the oral microbiome and targeting lipid metabolism may enhance ICI effectiveness, suggesting novel personalized therapeutic approaches.},
}
@article {pmid39927766,
year = {2025},
author = {Li, M and Chen, Z and Zhang, W and Wu, T and Qi, Q and Huo, YX},
title = {Customization of Ethylene Glycol (EG)-Induced BmoR-Based Biosensor for the Directed Evolution of PET Degrading Enzymes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2413205},
doi = {10.1002/advs.202413205},
pmid = {39927766},
issn = {2198-3844},
support = {31961133014//National Natural Science Foundation of China/ ; 22278033//National Natural Science Foundation of China/ ; 23130228E//Tangshan Science and Technology Bureau/ ; B2023105008//Natural Science Foundation of Hebei Province/ ; },
abstract = {The immense volume of plastic waste poses continuous threats to the ecosystem and human health. Despite substantial efforts to enhance the catalytic activity, robustness, expression, and tolerance of plastic-degrading enzymes, the lack of high-throughput screening (HTS) tools hinders efficient enzyme engineering for industrial applications. Herein, we develop a novel fluorescence-based HTS tool for evolving polyethylene terephthalate (PET) degrading enzymes by constructing an engineered BmoR-based biosensor targeting the PET breakdown product, ethylene glycol (EG). The EG-responsive biosensors, with notably enhanced dynamic range and operation range, are customized by fluorescence-activated cell sorting (FACS)-assisted transcription factor engineering. The ingeniously designed SUMO-MHETase-FastPETase (SMF) chimera successfully addresses the functional soluble expression of MHETase in Escherichia coli and mitigates the inhibitory effect of mono-(2-hydroxyethyl) terephthalic acid (MHET) intermediate commonly observed with PETase alone. The obtained SM[M3]F mutant demonstrates 1.59-fold higher terephthalic acid (TPA) production, with a 1.18-fold decrease in Km, a 1.29-fold increase in Vmax, and a 1.52-fold increase in kcat/Km, indicating stronger affinity and catalytic activity toward MHET. Furthermore, the SM[M3]F crude extract depolymerizes 5 g L[-1] bis-(2-hydroxyethyl) terephthalic acid (BHET) into TPA completely at 37 °C within 10 h, which is then directedly converted into value-added protocatechuic acid (PCA) (997.16 mg L[-1]) and gallic acid (GA) (411.69 mg L[-1]) at 30 °C, establishing an eco-friendly 'PET-BHET-MHET-TPA-PCA-GA' upcycling route. This study provides a valuable HTS tool for screening large-scale PET and MHET hydrolases candidates or metagenomic libraries, and propels the complete biodegradation and upcycling of PET waste.},
}
@article {pmid39927429,
year = {2025},
author = {Duan, X and Duan, H and Zhao, C and Feng, L and Zhao, G and Chen, Y},
title = {Genome-Centric Metagenomics and Metaproteomics Profiled the Shared and Unique Taxa in Isomeric Fatty Acid-Differentiated Anaerobic Co-Digestion of Food Waste and Sludge.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09839},
pmid = {39927429},
issn = {1520-5851},
abstract = {Fatty acids (FAs)-involving structures, widely occurring in production and life, have been increasingly considered as major feedstocks and potential platforms for renewable energy generation. However, the role of isomeric FAs (particularly trans-FAs) in high-concerned energy-reserving technology represented by anaerobic digestion (AD) remains unclear. This study displayed that trans-oleic acid (TOA, 10 mg/L) significantly increased methane production by 56% during the codigestion of food waste and sludge, whereas the same concentration of cis-oleic acid (COA) led to a slight 20% increase. Genome-centric meta-omics and biochemical tests indicated that acidogenic taxa that harbor and express distinct functions in the cell envelopes were primarily responsible for TOA/COA-differentiated AD. Four shared taxa, including three monodermal acidogens and one hydrogenotrophic methanogen, were common drivers of both TOA- and COA-enhanced AD, resulting in stronger acidification and hydrogenotrophic methanogenesis than in the control bioreactor without oleic acid. In addition to four shared species, two unique didermal acidogens were specific drivers of TOA-enhanced AD, demonstrating more robust acidification compared to that of COA-enhanced AD. This study profiled the geometry-dependent effects of isomeric FAs on AD, providing new insights into targeted regulation for energy conservation and decarbonization of FAs-involving feedstocks.},
}
@article {pmid39927333,
year = {2024},
author = {Safika, S and Indrawati, A and Hidayat, R and Puarada, ARR},
title = {Characterizing the gut microbiome of birds-of-paradise in the northwest lowland of Papua Island.},
journal = {Open veterinary journal},
volume = {14},
number = {12},
pages = {3345-3354},
pmid = {39927333},
issn = {2218-6050},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/isolation &amp; purification/classification/genetics ; Indonesia ; Feces/microbiology ; Passeriformes/microbiology ; },
abstract = {BACKGROUND: Birds-of-paradise, renowned for their stunning plumage and intricate mating rituals, have been extensively studied for their external characteristics. However, the microbial communities inhabiting their digestive tracts remain largely unexplored. The gut microbiome plays a vital role in host health and physiology, influencing digestion, nutrient absorption, and immune function. Understanding the microbiome of birds-of-paradise, particularly in their unique tropical rainforest habitats, may offer valuable insights into their adaptation and overall health.<br><br>AIM: This study aims to characterize the gut microbiome of birds-of-paradise and to explore the relationship between microbiome and host.<br><br>METHODS: Fecal samples were collected from Jayapura Regency, Indonesia, with non-invasive sampling methods. DNA was extracted using the DNeasy PowerSoil Pro Kit. Shotgun metagenomic sequencing was performed on the MGI DNBSEQ-G400 platform to obtain DNA sequences. DNA sequences were analyzed using DIAMOND followed by MEGAN6 to provide insights into the relative abundance of bacterial taxa within the microbiome.<br><br>RESULTS: Using Operational Taxonomy Unit analysis we identified 1,398,117 sequences from 5,048,280 initial sequences. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria were the dominant phyla, with other phyla present in smaller amounts. Burkholderiales, Hyphomicrobiales, Sphingobacteriales, and Enterobacterales were dominant orders, each with specific functional roles. Family and Genus-Level Abundance: Flavobacteriaceae, Comamonadaceae, and Sphingobacteriaceae were dominant families, while Flavobacterium, Delftia, and Pedobacter were dominant genera. Delftia sp., Pedobacter sp., Klebsiella pneumoniae, Achromobacter sp., Bacillus pumilus, Rhizobium sp., and Brevundimonas sp. were among the most abundant species.<br><br>CONCLUSION: The microbiome in the gut of birds-of-paradise is characterized by a diverse community of bacteria, fungi, and other microorganisms. The abundance of specific orders, families, and genera varies between samples, suggesting that differences in diet, habitat, or host genetics may influence microbiome composition. The findings reveal a diverse and complex microbial community that likely plays a crucial role in host health and physiology.},
}
@article {pmid39927261,
year = {2025},
author = {Hou, S and Jiang, Y and Zhang, F and Cheng, T and Zhao, D and Yao, J and Wen, P and Jin, L and Huang, S},
title = {Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1521108},
pmid = {39927261},
issn = {1664-302X},
abstract = {INTRODUCTION: The microbial composition of human breast milk and infant meconium offers critical insights into the early microbial colonization profile, and it greatly contributes to the infant's immune system and long-term health outcomes. However, analyzing these samples often faces technical challenges and limitations of low-resolution using conventional approaches due to their low microbial biomass.<br><br>METHODS: Here, we employed the type IIB restriction enzymes site-associated DNA sequencing for microbiome (2bRAD-M) as a reduced metagenomics method to address these issues and profile species-level microbial composition. We collected breast milk samples, maternal feces, and infant meconium, comparing the results from 2bRAD-M with those from both commonly used 16S rRNA amplicon sequencing and the gold-standard whole metagenomics sequencing (WMS).<br><br>RESULTS: The accuracy and robustness of 2bRAD-M were demonstrated through its consistently high correlation of microbial individual abundance and low whole-community-level distance with the paired WMS samples. Moreover, 2bRAD-M enabled us to identify clinical variables associated with infant microbiota variations and significant changes in microbial diversity across different lactation stages of breast milk.<br><br>DISCUSSION: This study underscores the importance of employing 2bRAD-M in future large-scale and longitudinal studies on maternal and infant microbiomes, thereby enhancing our understanding of microbial colonization in early life stages and demonstrating further translational potential.},
}
@article {pmid39927182,
year = {2025},
author = {Takeuchi, S and Kawada, JI and Suzuki, A and Sakamoto, K and Fukuda, Y and Horiba, K and Suzuki, T and Torii, Y and Shindo, Y and Ito, Y},
title = {Metagenomic Analysis of Lung Microbiome in Patients With Interstitial Lung Diseases and Sarcoidosis: An Experimental Study.},
journal = {Health science reports},
volume = {8},
number = {2},
pages = {e70328},
pmid = {39927182},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Interactions between the lung microbiome and pulmonary epithelium plays a pivotal role in shaping immunity in the lung. Idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease (ILD). Some patients with IPF develop episodic acute exacerbations often associated with microbial dysbiosis in the lungs. This study aimed to investigate etiologic agents as well as the lung microbiome in patients with ILDs and sarcoidosis.<br><br>METHODS: This study analyzed 31 patients divided into the IPF (IPF-stable, n&#x2009;=&#x2009;12), acute exacerbation of ILDs (AE-ILDs, n&#x2009;=&#x2009;6), and sarcoidosis (n&#x2009;=&#x2009;13) groups. Bronchoalveolar lavage fluid (BALF) samples were analyzed by RNA-based metagenomic next-generation sequencing (NGS) on an Illumina platform.<br><br>RESULTS: In total, 87 pathogens were detected using metagenomic NGS at the genus level. Prevotella, Streptococcus, and Veillonella dominated the BALF microbial communities, and sequence reads of these bacteria were abundant, especially in the sarcoidosis group. Conversely, only a small number of bacterial reads were detected in the AE-ILDs group, and the overall proportion of microbial composition differed from that of the other groups. No significant difference was found in community diversity (&#x3b1;-diversity) among the groups, whereas the structural similarity of the microflora (&#x3b2;-diversity) differed significantly between the AE-ILDs and sarcoidosis groups.<br><br>CONCLUSIONS: Bacterial sequence reads in BALF were smaller in both the IPF-stable and AE-ILD groups than in the sarcoidosis group. Dysbiosis in the lung microbiome has been observed in patients with AE-ILD and may be related to the progression of inflammation.},
}
@article {pmid39926599,
year = {2024},
author = {Guo, M and Gao, M and Gao, J and Zhang, T and Jin, X and Fan, J and Wang, Q and Li, X and Chen, J and Zhu, Z},
title = {Corrigendum: Identifying risk factors for secondary infection post-SARS-COV-2 infection in patients with severe and critical COVID-19.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1548101},
doi = {10.3389/fimmu.2024.1548101},
pmid = {39926599},
issn = {1664-3224},
abstract = {[This corrects the article DOI: 10.3389/fimmu.2021.715023.].},
}
@article {pmid39925879,
year = {2025},
author = {Gao, Y and Qin, G and Liang, S and Yin, J and Wang, B and Jiang, H and Liu, M and Luo, F and Li, X},
title = {Metagenomic Sequencing Combined with Metabolomics to Explore Gut Microbiota and Metabolic Changes in Mice with Acute Myocardial Infarction and the Potential Mechanism of Allicin.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {771-791},
pmid = {39925879},
issn = {1177-8881},
mesh = {Animals ; *Disulfides ; *Gastrointestinal Microbiome/drug effects ; *Sulfinic Acids/pharmacology/administration &amp; dosage ; Mice ; *Myocardial Infarction/drug therapy/metabolism ; Male ; *Metabolomics ; Metagenomics ; Mice, Inbred C57BL ; Administration, Oral ; Disease Models, Animal ; },
abstract = {BACKGROUND: Acute myocardial infarction (AMI) is a significant contributor to global morbidity and mortality. Allicin exhibits promising therapeutic potential in AMI as a primary bioactive component derived from garlic; however, its underlying mechanisms remain incompletely elucidated.<br><br>METHODS: Our study induced AMI in mice by ligating the left coronary artery, and administered allicin orally for 28 days. The cardioprotective effects of allicin treatment were comprehensively assessed using echocardiography, histopathological examinations, intestinal barrier function, and serum inflammatory factors. The potential mechanisms of allicin were elucidated through analysis of metagenomics and serum metabolomics. Network pharmacology (NP) was used to further investigate and validate the possible molecular mechanisms of allicin.<br><br>RESULTS: Our findings revealed allicin's capacity to ameliorate cardiac impairments, improve intestinal barrier integrity, and reduce serum IL-18 and IL-1&#x3b2; levels after AMI. Further analysis demonstrated that the administration of allicin has the potential to ameliorate intestinal flora disorder following AMI by modulating the abundance of beneficial bacteria, such as g_Lactobacillus, g_Prevotella, g_Alistipes, and g_Limosilactobacillus, while reducing the abundance of harmful bacteria g_Parasutterella. Additionally, it exhibits the ability to enhance myocardial energy metabolism flexibility through modulating metabolites and key enzymes associated with the fatty acid metabolic pathway. Mechanistically, NP and in vivo experiments indicated that allicin might suppress pyroptosis and reduce inflammatory response via blocked activation of the NF-&#x3ba;B-mediated NLRP3/Caspase-1/GSDMD pathway. Moreover, Spearman correlation analysis suggested a significant association between the allicin-induced alterations in microbiota and metabolites with cardiac function and inflammatory cytokines.<br><br>CONCLUSION: Our study demonstrated that allicin alleviated myocardial injury and reduced inflammatory response by inhibiting the NF-&#x3ba;B-mediated NLRP3/Caspase-1/GSDMD pathway while remodeling microbiota disturbance, improving serum metabolic disorder, and enhancing the intestinal barrier. These research findings offer a novel perspective on the potential therapeutic value of allicin as an adjunctive dietary supplement to conventional treatments for AMI.},
}
@article {pmid39925382,
year = {2025},
author = {Mcgonigal, M and Ito, K},
title = {From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment.},
journal = {Journal of genomics},
volume = {13},
number = {},
pages = {10-23},
pmid = {39925382},
issn = {1839-9940},
abstract = {High microbial diversity offers extensive benefits to both the environment and human health, contributing to ecosystem stability, nutrient cycling, and pathogen suppression. In built environments, factors such as building design, human activity, and cleaning protocols influence microbial communities. This study investigates the impact of landscape design on microbial diversity and function within the "Visionary Lab" exhibition in Tokyo, Japan, using 16S rRNA gene amplicon sequencing and shallow shotgun sequencing. Despite the limited sample size, the study suggests that the Visionary Lab samples may exhibit higher microbial diversity compared to other museum areas. Potential distinct microbial community structures may be correlated with sampling locations. However, despite this, no consistent patterns were observed in virulence factors or antimicrobial resistance genes across the samples. Metabolic function analysis showed varied profiles, suggesting diverse ecological interactions influenced that may be by the curated landscape. This suggest that the curated landscape design may have the potential to enhance microbial diversity, highlighting a possible avenue to create healthier and more sustainable built environments. However, the lack of consistent patterns in virulence factors and antimicrobial resistance genes underscores the complexity of microbial community dynamics.},
}
@article {pmid39925312,
year = {2025},
author = {Uçak, S and Yegin, Z and Yurt, MNZ and Altunbas, O and Sudagidan, M and Ozalp, VC},
title = {Bacterial Profiling of Brined Grapevine Leaves Collected from Different Local Markets in Türkiye.},
journal = {Chemistry &amp; biodiversity},
volume = {},
number = {},
pages = {e202403049},
doi = {10.1002/cbdv.202403049},
pmid = {39925312},
issn = {1612-1880},
abstract = {Microorganisms linked to the grapevine, Vitis vinifera, can impact crop quality, plant growth, and human and plant health. This study examined the bacterial community structures of brined grapevine leaves (n=56) taken from seven distinct regions in Türkiye using next-generation sequencing technology. Investigations were also conducted into the samples' chemical properties. Firmicutes was the dominant phylum, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Bacillaceae was the predominant family in the analyzed samples, followed by Clostridiaceae, Peptostreptococcaceae, and Enterobacteriaceae. Bacillus was the dominant genus, followed by Lysinibacillus and Clostridium sensu stricto. The samples exhibited differences in terms of pH, total acidity, and salt content. The pH values of the brined grapevine leaves ranged from 2.31 to 6.91, the acidity levels ranged from 0.09% to 1.80%, and the salt percentages ranged from 3.39% to 49.14%. This research provides pioneering information for bacterial community analysis of brined grapevine leaves.},
}
@article {pmid39924893,
year = {2025},
author = {Chen, Y and Fang, H and Chen, H and Liu, X and Zhao, J and Stanton, C and Ross, RP and Chen, W and Yang, B},
title = {Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2464945},
pmid = {39924893},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Colorectal Neoplasms/microbiology/metabolism/prevention &amp; control/pathology ; Humans ; *Bifidobacterium/metabolism/physiology ; *Linoleic Acids, Conjugated/metabolism ; Male ; Probiotics/administration &amp; dosage/pharmacology ; Female ; Carcinogenesis ; PPAR gamma/metabolism/genetics ; Fatty Acids/metabolism ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Middle Aged ; Apoptosis ; Disease Progression ; Butyric Acid/metabolism ; Disease Models, Animal ; },
abstract = {Colorectal cancer (CRC) represents the third most common cancer worldwide. Consequently, there is an urgent need to identify novel preventive and therapeutic strategies for CRC. This study aimed to screen for beneficial bacteria that have a preventive effect on CRC and to elucidate the potential mechanisms. Initially, we compared gut bacteria and bacterial metabolites of healthy volunteers and CRC patients, which demonstrated that intestinal conjugated linoleic acid (CLA), butyric acid, and Bifidobacterium in CRC patients were significantly lower than those in healthy volunteers, and these indicators were significantly negatively correlated with CRC. Next, spontaneous CRC mouse model were conducted to explore the effect of supplemental CLA-producing Bifidobacterium on CRC. Supplementation of mice with CLA-producing Bifidobacterium breve CCFM683 and B. pseudocatenulatum MY40C significantly prevented CRC. Moreover, molecular approaches demonstrated that CLA and the CLA-producing gene, bbi, were the key metabolites and genes for CCFM683 to prevent CRC. Inhibitor intervention results showed that PPAR-γ was the key receptor for preventing CRC. CCFM683 inhibited the NF-κB signaling pathway, up-regulated MUC2, Claudin-1, and ZO-1, and promoted tumor cell apoptosis via the CLA-PPAR-γ axis. Additionally, fecal microbiota transplantation (FMT) and metagenomic analysis showed that CCFM683 up-regulated Odoribacter splanchnicus through CLA production, which then prevented CRC by producing butyric acid, up-regulating TJ proteins, regulating cytokines, and regulating gut microbiota. These results will contribute to the clinical trials of Bifidobacterium and the theoretical research and development of CRC dietary products.},
}
@article {pmid39923562,
year = {2025},
author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E},
title = {The microbiome of Total Suspended Particles and its influence on the respiratory microbiome of healthy office workers.},
journal = {Ecotoxicology and environmental safety},
volume = {291},
number = {},
pages = {117874},
doi = {10.1016/j.ecoenv.2025.117874},
pmid = {39923562},
issn = {1090-2414},
abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM2.5 and PM10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae. Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.},
}
@article {pmid39923519,
year = {2025},
author = {Peng, Q and Cheng, S and Lin, J and Zheng, H and Xie, G},
title = {Metabolic and microbial functionality during the fermentation of traditional Amaranth stems: Insights from metagenomics, flavoromics, and metabolomics.},
journal = {Food chemistry},
volume = {474},
number = {},
pages = {143216},
doi = {10.1016/j.foodchem.2025.143216},
pmid = {39923519},
issn = {1873-7072},
abstract = {Fermented Amaranth stems is a traditional Chinese fermented vegetable known for its distinctive aroma, produced through natural microbial fermentation. However, the metabolic processes, flavor compounds, and microbial communities involved in its fermentation are not well understood. This study provides a comprehensive analysis using an integrated approach combining flavoromics, untargeted metabolomics, and metagenomics to examine the dynamic changes in metabolites and microbiota during fermentation. A total of 108 volatile organic compounds were identified, with sugar metabolism peaking on the third day of fermentation. The microbial community analysis revealed that key genera such as Pseudomonas, Acinetobacter, Pectobacterium, and Enterobacter play a significant role in flavor formation. The findings offer critical insights into the fermentation mechanisms and the production of flavor compounds, providing a foundation for optimizing fermentation processes and improving the flavor quality of fermented Amaranth stems. This research holds practical significance for enhancing food safety by controlling microbial communities during fermentation.},
}
@article {pmid39923424,
year = {2025},
author = {He, M and He, CQ and Ding, NZ},
title = {Human viruses: An ever-increasing list.},
journal = {Virology},
volume = {604},
number = {},
pages = {110445},
doi = {10.1016/j.virol.2025.110445},
pmid = {39923424},
issn = {1096-0341},
abstract = {It has been 124 years since yellow fever was demonstrated to be caused by a 'filterable agent'. While long-standing viral diseases, with the exception of smallpox, continue to be endemic, new ones have been emerging intermittently, primarily from a substantial zoonotic reservoir, leading to significant socioeconomic consequences. Currently, we are contending not only with the ongoing COVID-19 pandemic but with surges of various other viral infections. Recent metagenomic analyses have revealed a variety of novel human viruses whose health implications remain largely unclear. The following questions arise: How many human viruses have been identified? Which of these viruses are etiological agents of human diseases? This review aims to address the two inquiries and highlight the viruses that pose significant public health threats as outlined in the World Health Organization's Fact Sheets. Importantly, many human viruses are preventable; appropriate precautions can be implemented to mitigate the risk of infection.},
}
@article {pmid39923290,
year = {2025},
author = {Wang, S and Wu, M},
title = {Decoding the link between microbial secondary metabolites and colorectal cancer.},
journal = {Computational biology and chemistry},
volume = {115},
number = {},
pages = {108372},
doi = {10.1016/j.compbiolchem.2025.108372},
pmid = {39923290},
issn = {1476-928X},
abstract = {Colorectal cancer (CRC) is a prevalent form of cancer in humans, with the gut microbiota playing a significant role in its pathogenesis. Although previous research has primarily focused on the role of primary metabolites produced by gut microbes in CRC development, the role of secondary metabolites remains largely unexplored. Secondary metabolites are known to mediate crucial interactions between the microbiota and the host, potentially influencing CRC progression. However, their specific relationship to CRC pathogenesis is poorly understood. To address this gap, we performed a meta-analysis using fecal metagenomic data from a cohort of CRC patients and healthy controls, aiming to identify CRC-associated microbial secondary metabolite biosynthetic gene clusters (BGCs). Our findings not only provide valuable insights into the pathogenicity and carcinogenicity of CRC but also shed light on the potential mechanisms underlying its development.},
}
@article {pmid39923117,
year = {2025},
author = {Rouzé, T and Martayan, I and Marchet, C and Limasset, A},
title = {Fractional hitting sets for efficient multiset sketching.},
journal = {Algorithms for molecular biology : AMB},
volume = {20},
number = {1},
pages = {1},
pmid = {39923117},
issn = {1748-7188},
support = {IndexThePlanet, 101088572/ERC_/European Research Council/International ; AGATE ANR-21-CE45-0012//Agence Nationale de la Recherche/ ; },
abstract = {The exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashing techniques have successfully transformed large datasets into smaller, more manageable sketches while maintaining comparability using metrics such as Jaccard and containment indices. However, fixed-size sketches encounter difficulties when applied to divergent datasets. Scalable sketching methods, such as sourmash, provide valuable solutions but still lack resource-efficient, tailored indexing. Our objective is to create lighter sketches with comparable results while enhancing efficiency. We introduce the concept of Fractional Hitting Sets, a generalization of Universal Hitting Sets, which cover a specified fraction of the k-mer space. In theory and practice, we demonstrate the feasibility of achieving such coverage with simple but highly efficient schemes. By encoding the covered k-mers as super-k-mers, we provide a space-efficient exact representation that also enables optimized comparisons. Our novel tool, supersampler, implements this scheme, and experimental results with real bacterial collections closely match our theoretical findings. In comparison to sourmash, supersampler achieves similar outcomes while utilizing an order of magnitude less space and memory and operating several times faster. This highlights the potential of our approach in addressing the challenges presented by the ever-expanding landscape of genomic data. supersampler is an open-source software and can be accessed at https://github.com/TimRouze/supersampler . The data required to reproduce the results presented in this manuscript is available at https://github.com/TimRouze/supersampler/experiments .},
}
@article {pmid39922935,
year = {2025},
author = {Das, BK and Gadnayak, A and Chakraborty, HJ and Pradhan, SP and Raut, SS and Das, SK},
title = {Exploring microbial players for metagenomic profiling of carbon cycling bacteria in sundarban mangrove soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4784},
pmid = {39922935},
issn = {2045-2322},
mesh = {*Wetlands ; *Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/metabolism/classification ; *Carbon Cycle ; Carbon/metabolism ; Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; },
abstract = {The Sundarbans, the world's largest tidal mangrove forest, acts as a crucial ecosystem for production, conservation, and the cycling of carbon and nitrogen. The study explored the hypothesis that microbial communities in mangrove ecosystems exhibit unique taxonomic and functional traits that play a vital part in carbon cycling and ecosystem resilience. Using metagenomic analysis to evaluate microbial communities in mangrove and non-mangrove environment, evaluating their composition, functional functions, and ecological relevance. The analysis revealed distinct microbial profiles, in mangrove and non-mangrove environments, with bacteria, proteobacteria, and viruses being the most prevalent groups, with varying abundances in each environment. Functional and taxonomical analysis identified genes involved in carbon regulation, including Triacylglycerol lipase, NarG, DsrB, DNA-binding transcriptional dual regulator CRP, Vanillate O-demethylase oxygenase, succinate-CoA ligase, Tetrahydrofolate ligase, Carboxylase, Ribulose-1,5-bisphosphate carboxylase/oxygenase, Glycine hydroxymethyltransferase, MAG: urease, Endosymbiont of Oligobrachia haakonmosbiensis, Ribulose bisphosphate carboxylase, Aconitate hydratase AcnA, and nitrous oxide reductase, suggesting the metabolic versatility of these microbial communities for carbon cycling. The findings emphasize the key role of microbial activity in preserving mangrove ecosystem health and resilience, highlighting the intricate interplay between microbial diversity, functional capabilities, and environmental factors.},
}
@article {pmid39922085,
year = {2025},
author = {Florio, M and Crudele, L and Sallustio, F and Moschetta, A and Cariello, M and Gadaleta, RM},
title = {Disentangling the nutrition-microbiota liaison in inflammatory bowel disease.},
journal = {Molecular aspects of medicine},
volume = {102},
number = {},
pages = {101349},
doi = {10.1016/j.mam.2025.101349},
pmid = {39922085},
issn = {1872-9452},
abstract = {Inflammatory Bowel Disease (IBD) is a set of chronic intestinal inflammatory disorders affecting the gastrointestinal (GI) tract. Beside compromised intestinal barrier function and immune hyperactivation, a common IBD feature is dysbiosis, characterized by a reduction of some strains of Firmicutes, Bacteroidetes, Actinobacteria and an increase in Proteobacteria and pathobionts. Emerging evidence points to diet and nutrition-dependent gut microbiota (GM) modulation, as etiopathogenetic factors and adjuvant therapies in IBD. Currently, no nutritional regimen shows universal efficacy, and advice are controversial, especially those involving restrictive diets potentially resulting in malnutrition. This review provides an overview of the role of macronutrients, dietary protocols and GM modulation in IBD patients. A Western-like diet contributes to an aberrant mucosal immune response to commensal bacteria and impairment of the intestinal barrier integrity, thereby triggering intestinal inflammation. Conversely, a Mediterranean nutritional pattern appears to be one of the most beneficial dietetic regimens able to restore the host intestinal physiology, by promoting eubiosis and preserving the intestinal barrier and immune function, which in turn create a virtuous cycle improving patient adherence to the pattern. Further clinical studies are warranted, to corroborate current IBD nutritional guidelines, and develop more accurate models to move forward precision nutrition and ameliorate patients' quality of life.},
}
@article {pmid39921299,
year = {2025},
author = {Li, Z and Han, X and Cong, L and Singh, P and Paiva, P and Branson, Y and Li, W and Chen, Y and Jaradat, DMM and Lennartz, F and Bayer, T and Schmidt, L and Garscha, U and You, S and Fernandes, PA and Ramos, MJ and Bornscheuer, UT and Weber, G and Wei, R and Liu, W},
title = {Structure-Guided Engineering of a Versatile Urethanase Improves Its Polyurethane Depolymerization Activity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2416019},
doi = {10.1002/advs.202416019},
pmid = {39921299},
issn = {2198-3844},
support = {2023YFC3905000//National Key Research and Development Program of China/ ; 32371530//National Natural Science Foundation of China/ ; XDC0120400//Strategic Priority Research Program of the Chinese Academy of Science/ ; TSBICIP-PTJJ-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; TSBICIP-PTJJ-014//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; TSBICIP-IJCP-003//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; LA/P/0008/2020//FCT/MCTES/ ; UIDP/50006/2020//FCT/MCTES/ ; UIDB/50006/2020//FCT/MCTES/ ; NNF22OC0072891//Novo Nordisk Fonden/ ; EHPC-REG-2023R03-163//European High-Performance Computing Joint Undertaking/ ; KA2-HSC-10//Investment and Networking Fund of the Helmholtz Association/ ; KA-HSC-13//Investment and Networking Fund of the Helmholtz Association/ ; 870294//Horizon 2020 Framework Programme/ ; 953214//Horizon 2020 Framework Programme/ ; },
abstract = {Polyurethane (PUR), the fifth most prevalent synthetic polymer, substantially contributes to the global plastic waste problem. Biotechnology-based recycling methods have recently emerged as innovative solutions to plastic waste disposal and sparked interest among scientific communities and industrial stakeholders in discovering and designing highly active plastic-degrading enzymes. Here, the ligand-free crystal structure of UMG-SP2, a metagenome-derived urethanase with depolymerization activities, at 2.59 Å resolution, as well as its (co-)structures bound to a suicide hydrolase inhibitor and a short-chain carbamate substrate at 2.16 and 2.40 Å resolutions, respectively, is reported. Structural analysis and molecular dynamics simulations reveal that the flexible loop L3 consisting of residues 219-226 is crucial for regulating the hydrolytic activity of UMG-SP2. The semi-rational redesign of UMG-SP2 reveals superior variants, A141G and Q399A, exhibiting over 30.7- and 7.4-fold increased activities on polyester-PUR and a methylene diamine derivative of PUR, respectively, compared to the wild-type enzyme. These findings advance the understanding of the structure-function relationship of PUR-hydrolyzing enzymes, which hold great promise for developing effective industrial PUR recycling processes and mitigating the environmental footprint of plastic waste.},
}
@article {pmid39921224,
year = {2025},
author = {Vieira, S and Adão, H and Vicente, CSL},
title = {Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106963},
doi = {10.1016/j.marenvres.2025.106963},
pmid = {39921224},
issn = {1879-0291},
mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics ; Portugal ; *Estuaries ; *Ecosystem ; Environmental Monitoring ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; },
abstract = {Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.},
}
@article {pmid39921144,
year = {2025},
author = {Cook, D and Kocurek, B and Stonecipher, C and Welch, KD and Gardner, DR and Mammel, M and Reed, E and Ramachandran, P and Erickson, D and Commichaux, S and Ottesen, A},
title = {DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {256},
number = {},
pages = {108285},
doi = {10.1016/j.toxicon.2025.108285},
pmid = {39921144},
issn = {1879-3150},
abstract = {Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States including Salvia reflexa. Metagenomic data, genome skims and metabarcodes, have been used for identification and characterization of plants in complex botanical matrices including diet composition of animals, mixed forages, and herbal products. Here, chemistry, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case of Salvia reflexa (lanceleaf sage) poisoning that killed 165 cattle. Genome skims and metabarcoding provided similar estimates of the relative abundance of the Salvia in the hay samples when compared to chemical methods. Additionally, genome skims and metabarcoding provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA metabarcoding may provide useful tools for plant poisoning investigations.},
}
@article {pmid39921114,
year = {2025},
author = {Farooq, S and Talat, A and Dhariwal, A and Petersen, FC and Khan, AU},
title = {Transgenerational Gut Dysbiosis: Unveiling the Dynamics of Antibiotic Resistance through Mobile Genetic Elements from Mothers to Infants.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107458},
doi = {10.1016/j.ijantimicag.2025.107458},
pmid = {39921114},
issn = {1872-7913},
abstract = {The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens. This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs. The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1[st], 2[nd], 3[rd], 4[th], 8[th] and 12[th] months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, β-lactamases CblA-1, CfxA2, multi-drug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly Escherichia coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins. Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.},
}
@article {pmid39921005,
year = {2025},
author = {Wu, X and Wang, S and Zhao, W and Xi, Y and Li, S and Xin, F and Dong, W and Jia, H},
title = {Enhanced methane production through synergistic integration of quorum sensing Signals and microbial electrolysis in anaerobic digestion of low-quality biomass.},
journal = {Bioresource technology},
volume = {421},
number = {},
pages = {132153},
doi = {10.1016/j.biortech.2025.132153},
pmid = {39921005},
issn = {1873-2976},
abstract = {This study explored the synergistic effects of exogenous acyl homoserine lactones (AHLs) and microbial electrolysis (ME) on enhancing anaerobic digestion (AD) of low-quality biomass. The combined AHLs + ME strategy achieved a 79.50 % increase in cumulative methane production compared to the control, outperforming individual treatments. This enhancement was attributed to accelerated substrate degradation, selective enrichment of hydrogenotrophic methanogens (Methanobrevibacter, Methanobacterium, Methanofollis), and strengthened quorum sensing, electron transfer, and methane synthesis pathways. Metagenomic analysis revealed abundance upregulation of key genes involved in AHL synthesis (bjaI, rpaI, braI, rhiI) and sensing (solR, cepR, tofR), direct interspecies electron transfer (pilA, mtrC), and hydrogenotrophic methanogenesis (ftr, mvhD, vhuD, vhcD). This study offers a novel and sustainable strategy to optimize methane production from recalcitrant biomass, advancing AD-based waste-to-energy systems.},
}
@article {pmid39920962,
year = {2025},
author = {Wang, X and Gao, L and Wang, S and Zhang, X and Feng, R and Jia, S},
title = {Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes.},
journal = {Environmental research},
volume = {271},
number = {},
pages = {121037},
doi = {10.1016/j.envres.2025.121037},
pmid = {39920962},
issn = {1096-0953},
abstract = {Pesticide wastewater emerges as a typical refractory wastewater, characterized by complex composition and high toxicity, posing significant treatment challenges. Bacterial communities are responsible for biological treatment of refractory wastewater in full-scale pesticide wastewater treatment plants (PWWTPs), providing important implications for optimizing system performance and improving management strategies. However, the knowledge of their composition, diversity, function, assembly patterns, and biological interactions remains limited. Therefore, this study applied high-throughput sequencing, machine learning models, and statistical analysis to investigate key features of bacterial communities in eight PWWTPs. We found that Proteobacteria and Bacteroidota were the most abundant phyla, with Pseudomonas, Hyphomicrobium, Comamonas, and Thauera being dominant genera. Bacterial community distribution and diversity varied significantly among influents, sludges, and effluents, with sludges and effluents exhibiting higher diversity, richness, and evenness compared to influents. Deterministic processes primarily shaped the bacterial communities, accounting for 77.12%, 61.44%, and 64.05% of variation in influents, sludges, and effluents, respectively. Homogeneous selection explained 47.71%, 31.37%, and 31.37% of variation across these communities. Key modules (Module 1 in influents, Modules 3 and 4 in sludges, and Module 1 in effluents) were significantly associated with various metabolic and degradative functions (p < 0.05). Core taxa identified by Random Forest analysis were strongly linked to key metabolic and degradation functions, such as the metabolism of cofactors and vitamins, carbohydrates, and amino acids as well as the degradation of benzoate, aminobenzoate, nitrotoluene, chloroalkane, and chloroalkene. This study deepens our understanding of bacterial community dynamics and key features in pesticide wastewater treatment systems, offering scientific guidance for process optimization, efficiency improvement, and system stability assessment.},
}
@article {pmid39920864,
year = {2025},
author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT},
title = {Bacterial community assembly of specific pathogen-free neonatal mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {46},
pmid = {39920864},
issn = {2049-2618},
support = {R01AI139314/NH/NIH HHS/United States ; R01 AI139314/AI/NIAID NIH HHS/United States ; T32AI007163/NH/NIH HHS/United States ; F31AI167499/NH/NIH HHS/United States ; T32AI007172/NH/NIH HHS/United States ; 1065897//Crohn's and Colitis Foundation/ ; DGE-1745038//National Science Foundation/ ; },
mesh = {Animals ; Mice ; *Feces/microbiology ; *Animals, Newborn/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Specific Pathogen-Free Organisms ; *Mice, Inbred C57BL ; *Mice, Inbred BALB C ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbiota ; },
abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.<br><br>RESULTS: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14&#xa0;days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.<br><br>CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract.},
}
@article {pmid39920607,
year = {2025},
author = {Mai, G and Chen, J and Zhang, M and Zhang, W and Luo, Y and Dai, Y},
title = {Construction of a pathogenic microorganism detection method based on third-generation nanopore sequencing data.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {189},
pmid = {39920607},
issn = {1471-2334},
support = {24C0330//Project of Hunan Provincial Department of Education/ ; 22C0389//Project of Hunan Provincial Department of Education/ ; 24BSQD04//Hunan University of Arts and Science PhD Boosting Project/ ; E07023009//Hunan University of Arts and Science PhD Boosting Project/ ; 23YB07//Hunan University of Arts and Science Research Projects/ ; 24YB10//Hunan University of Arts and Science Research Projects/ ; },
mesh = {Humans ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *Bacteria/genetics/isolation &amp; purification/classification ; *Computational Biology/methods ; Respiratory Tract Infections/microbiology/diagnosis ; Female ; Male ; Adult ; Middle Aged ; Aged ; },
abstract = {BACKGROUND: Pathogenic microorganisms can cause infections, allergies, diarrhoea, tumours, other diseases, and even death. Therefore, the detection of pathogenic microorganisms is important.<br><br>METHODS: In this study, a bioinformatics pipeline was developed. First, a comprehensive and penetrating reference database of nucleic acids from pathogenic microorganisms was constructed, and sequence alignment analysis was performed via nanopore sequencing of metagenomic data collected from 40 patients with lower respiratory tract infection symptoms. The similarity, abundance, and matching length of the sequences were integrated to obtain a comprehensive parameter, all_ratio, which can be used to identify pathogenic microorganisms effectively.<br><br>RESULTS: Compared with two previous methods, i.e., pathogen identification via microbiological culture or a previously reported metagenomic pipeline, pathogens were detected in 23 out of the 40 samples using our method, with the same results as those of the previous two methods. In five samples, pathogens such as Streptococcus pneumoniae and Granulicatella adiacens that had not been detected via the previous two methods were detected using our method. Pathogens such as Streptococcus pneumoniae and Neisseria flavescens were detected in 12 samples via our method, in contrast to the results of the previous two methods. Therefore, it is presumed that the individuals from whom these samples were obtained may have been infected with two or more pathogenic microorganisms.<br><br>CONCLUSIONS: This study shows that our method can efficiently identify pathogenic microorganisms and even detect pathogenic microorganisms in samples that cannot be detected via other methods, thus supplementing existing methods.},
}
@article {pmid39920574,
year = {2025},
author = {Zhao, J and Su, HT and Zhang, D and Li, XT and Lu, MY and Du, J and Guo, JY and Gao, Y and Chen, XF and Wen, DH and Jia, SY and Wang, Y and Yang, QW},
title = {The role of mNGS in the diagnosis of talaromycosis and case series.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {191},
pmid = {39920574},
issn = {1471-2334},
support = {82272380//the National Natural Science Foundation of China/ ; 82272380//the National Natural Science Foundation of China/ ; 2022-PUMCH-B-028//National High Level Hospital Clinical Research Funding/ ; 2022-PUMCH-B-028//National High Level Hospital Clinical Research Funding/ ; 2021YFC2301002//the National Key Research and Development Program of China/ ; 2021YFC2301002//the National Key Research and Development Program of China/ ; 2023-PT330-01//Supported by the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2023-PT330-01//Supported by the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; *Talaromyces/isolation &amp; purification/genetics ; Male ; *Mycoses/diagnosis/drug therapy/microbiology ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; Adult ; Female ; Metagenomics ; Antifungal Agents/therapeutic use ; HIV Infections/complications ; Voriconazole/therapeutic use ; },
abstract = {BACKGROUND: Talaromycosis is a rare fungal infection characterized by non-specific clinical features, often resulting in misdiagnosis. This study aimed to analyze four classic cases of Talaromyces marneffei infection diagnosed using metagenomic next-generation sequencing (mNGS) to improve understanding of its diagnosis and treatment.<br><br>METHODS: This study retrospectively analyzed cases of T. marneffei identified through mNGS at Peking Union Medical College Hospital. Four confirmed cases of talaromycosis were selected based on clinical diagnoses, supplemented by a review of relevant literature. We reviewed and compared the clinical features, laboratory indicators, treatment regimens, and outcomes of these cases, which exhibited varied characteristics.<br><br>RESULTS: Among the four patients, two were human immunodeficiency virus (HIV)-positive, and two were HIV-negative. All the participants presented with fever and varying respiratory symptoms, with distinct clinical characteristics aiding diagnosis. Three cases exhibited significant pulmonary infection lesions. Both HIV-positive patients showed T. marneffei bloodstream dissemination and suffered mixed infection with virus. Within them, one case was positive in blood culture, blood mNGS and sputum culture. Another case was positive in blood and bone marrow cultures, brain tissue culture and mNGS. They were both treated with voriconazole and improved. Both HIV-negative patients were T. marneffei positive for BALF mNGS, and only one of them was positive for BALF culture. One of them was mix infected by fungi, bacteria, Mycobacterium tuberculosis and virus, improved by voriconzole and followed by introconaole. The other case was cured by introconazole.<br><br>CONCLUSIONS: Traditional diagnostic methods are limited by factors such as the long time and low sensitivity of fungal culture, the effect of prior antibiotic treatment, the invasiveness and complexities of tissue biopsies, and so on. Emerging technologies, particularly mNGS, offer advantages such as rapid processing, high accuracy, and comprehensive pathogen coverage, significantly reducing the risk of missed diagnoses and facilitating timely intervention.},
}
@article {pmid39919954,
year = {2025},
author = {Lin, T and Yu, Y and Luo, J and Yan, X and Qiu, Y and Tong, J and Wang, Y and Huang, X and Li, D and Zhang, Y and Yang, G},
title = {Clinical value of Metagenomic Next- and Third-Generation Sequencing applied in ultrasound-guided puncture biopsy for diagnosing lymph node tuberculosis.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2024.12.011},
pmid = {39919954},
issn = {1995-9133},
abstract = {OBJECTIVES: The aim of this study was to assess the clinical utility of metagenomic next-generation sequencing (mNGS) and metagenomic third-generation sequencing (mTGS) in diagnosing cervical lymph node tuberculosis through analysis of lymph node tissue.<br><br>METHODS: This study recruited 101 patients with suspected cervical lymph node tuberculosis and took samples under ultrasound guidance. Parallel culture, X-pert, mNGS and mTGS workflows to each sample were performed. Taking clinical diagnosis as the gold standard, We comparatively compared diagnosis performance of the four methods.<br><br>RESULTS: Clinically, 76 cases were diagnosed as lymph node tuberculosis and 20 cases were non-lymph node tuberculosis. Compared with clinical diagnosis, the sensitivities of mNGS and mTGS were 89.47&#xa0;% and 82.89&#xa0;%, respectively, significantly higher than those of culture and X-pert which were 43.28&#xa0;% and 68.42&#xa0;%, respectively (P&#xa0;<&#xa0;0.05). The specificity of mNGS and X-pert reached 100&#xa0;%, while those of culture and mTGS were 93.75&#xa0;% and 95&#xa0;%, respectively. And mNGS alone identified 7 species of bacteria, 3 species of viruses, and 5 species of fungi, and identified more mixed infections. Particularly, besides Mycobacterium tuberculosis detection, mNGS may be superior to mTGS for the detection of fungi. Pathogen identification of mNGS and mTGS is less affected by previous anti-tuberculosis drug usage.<br><br>CONCLUSION: mNGS and mTGS play a crucial role in the rapid diagnosis and accurate treatment on Cervical lymph node tuberculosis.},
}
@article {pmid39919574,
year = {2025},
author = {Zhang, L and Luo, Y and Lv, S and Liu, Y and Wang, R and Wang, Y and Lin, K and Liu, L},
title = {Performance of electro-assisted ecological floating bed in antibiotics and conventional pollutants degradation: Mechanisms and microbial response.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124393},
doi = {10.1016/j.jenvman.2025.124393},
pmid = {39919574},
issn = {1095-8630},
abstract = {Electro-assisted technology is promising for enhancing plant activity, optimizing functional microbial communities, and significantly strengthening pollutant removal efficiency. In this study, four reactors were designed as control group (CG), Hydrocotyle vulgaris L. ecological floating bed (PEFB), microbial fuel cell (MFC), and Hydrocotyle vulgaris L. ecological floating bed-microbial fuel cell (PEFB-MFC) to investigate the efficiency and mechanisms for the synchronous removal of conventional and antibiotic contaminants. Results showed that PEFB-MFC hold superior removal performance for sulfamethoxazole (61%), tetracycline (61%), CODCr (65%), NH4[+]-N (86%), TN (41%), and TP (51%). High-throughput sequencing indicated that Pseudomonadota and Actinomycetota were the predominant phyla in the different reactors. Metagenomic sequencing results showed that pollutant degradation-related metabolic functions, such as those involved in carbohydrate and amino acid metabolism in PEFB-MFC exhibited superior abundance compared to the other reactors. LC-MS analysis revealed sulfamethoxazole degradation occurred through active-site cleavage, and tetracycline underwent demethylation, aldehyde formation, dehydroxylation. This study offers a deeper insight into electro-enhanced PEFB on decontamination performance and functional microbial communities.},
}
@article {pmid39919405,
year = {2025},
author = {Xing, Y and Li, W and Liao, X and Wang, L and Wang, B and Peng, Y},
title = {Enhanced nitrogen removal from low C/N municipal wastewater in a step-feed integrated fixed-film activated sludge system: Synergizing anammox and partial denitrification with sludge fermentation liquid supplementation.},
journal = {Water research},
volume = {275},
number = {},
pages = {123211},
doi = {10.1016/j.watres.2025.123211},
pmid = {39919405},
issn = {1879-2448},
abstract = {The scarcity of rapidly biodegradable organics, which serve as essential electron donors for the partial denitrification (PD) process, significantly hinders the combined application of PD coupled with anammox (PDA) in municipal wastewater treatment plants. This study innovatively applied, for the first time, a step-feed strategy combined with the use of sludge fermentation liquid (SFL) as an external carbon source in an integrated fixed-film activated sludge (IFAS) system, successfully driving full nitrification and PDA to achieve advanced nitrogen removal from low C/N real municipal wastewater. Moreover, the associated nitrogen removal mechanism of this system was systematically analyzed. By employing second-step SFL feed as a supplementary carbon source, the nitrogen removal efficiency reached 92.26 ± 2.77 % and the effluent total inorganic nitrogen was 6.43 ± 2.23 mg/L, with anammox contributing approximately 70 % to total inorganic nitrogen removal. 16S rRNA gene sequencing and fluorescence in situ hybridization analysis unveiled the extensive cooperation and synergistic interactions among anammox bacteria, denitrifying bacteria, and nitrifying bacteria, with Candidatus Brocadia being highly enriched in biofilms with a relative abundance of 2.21 %. Metagenomic sequencing confirmed that the relative abundance of the narGHI gene was greater than that of the nirS gene, providing stable nitrite accumulation conditions for the anammox process. Overall, this study proposes an innovative synergistic treatment scheme that utilizes a step-feed full nitrification-PDA process driven by SFL to achieve advanced nitrogen removal in municipal wastewater treatment plants. This approach is characterized by low energy consumption, low operational costs and a high nitrogen removal efficiency.},
}
@article {pmid39919380,
year = {2025},
author = {Prosser, HM and Bortoluzzi, EM and Valeris-Chacin, RJ and Baker, EC and Scott, MA},
title = {Application of artificial intelligence and machine learning in bovine respiratory disease prevention, diagnosis, and classification.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-5},
doi = {10.2460/ajvr.24.10.0327},
pmid = {39919380},
issn = {1943-5681},
abstract = {Bovine respiratory disease (BRD) is the leading infectious disease in cattle, resulting in significant economic losses and welfare concerns in beef and dairy production systems. Traditional diagnostic methods for BRD typically rely on clinical observations and diagnostic laboratory tests, which can be time consuming with moderate diagnostic sensitivity. In recent years, machine learning (ML) and AI have emerged as powerful tools in animal health research, offering opportunities for improving BRD diagnostics and management. This review explores the current landscape of published literature on the use of ML and AI in BRD prevention, diagnostics, and classification. First, disease classification and pathogen identification models leveraging supervised models and metagenomic sequencing have identified specific community structure information in classifying specific BRD cases. From epidemiological datasets tracking disease outbreaks and risk factors, user-friendly platforms for producers and veterinarians are capable of being generated and deployed, providing customized scenarios, potential economic impacts, and pathogenic effects as a decision-support tool. Veterinarian-operated technologies, such as computer-aided lung auscultation stethoscopes, can automatically calculate lung scores and associated BRD severity likelihoods. Prediction and detection models used to leverage physical characteristics and feed consumption data provide novel methods of categorizing BRD risk. Finally, sensor technology monitoring behavioral or motion-based information provides continuous data on animal health and can enable early automated detection of BRD symptoms. Through synthesizing research in these key areas, this narrative review highlights the transformative potential of AI and ML in improving the accuracy, speed, and efficiency of BRD diagnostics, enhancing disease control and cattle welfare.},
}
@article {pmid39919372,
year = {2025},
author = {Swain, S and Sahoo, P and Biswal, S and Sethy, K and Panda, AN and Sahoo, N},
title = {Fecal bacterial microbiota diversity characterized for dogs with atopic dermatitis: its alteration and clinical recovery after meat-exclusion diet.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/ajvr.24.09.0274},
pmid = {39919372},
issn = {1943-5681},
abstract = {OBJECTIVE: To achieve clinical recovery in canine atopic dermatitis affected pet dogs via alteration of the gut microbiome, following a meat and egg exclusion diet for 60 days.<br><br>METHODS: 24 atopic dermatitis-affected pet dogs, all fed poultry meat and egg, and another 48 apparently healthy controls fed both poultry meat and egg (n = 24) or vegetable diet (24) were included in the study. The study was undertaken in the Bhubaneswar Smart City, Odisha, India, from July to December 2023. Fecal samples were collected at 2 points for DNA analysis, ie, on day 0 and day 60 of the change from a meat/egg-based diet to a vegetable-based diet. Extracted DNA samples were pooled category-wise and subjected to the gut microbiome analysis in the Nanopore sequencer targeting the 16S rRNA gene. Burrows-Wheeler Transform, Ferragina-Manzini index, and Krona charts were used for taxonomical classification and visualization of relative abundances of bacterial species within the metagenome. Alpha- and beta-diversity analyses were performed.<br><br>RESULTS: Atopic pets at day 0 showed elevation in the gut microbiome population with an adequate concentration of pathogens like Escherichia coli and Clostridiodes difficile with lower amounts of the beneficial bacteria like Lactobacillus sp, while the pets at 60 days after dietary intervention showed a significant decline in bacterial species like E coli and C difficile with higher amount of Lactobacillus sp. Both control groups showed variations of microbiome between them as well as from the atopic pets.<br><br>CONCLUSIONS: We found a close association of poultry meat/egg diet with gut microbiome population and atopic symptoms as well in dogs, and elimination of such diet could be helpful in clinical recovery.<br><br>CLINICAL RELEVANCE: Dietary intervention with the exclusion of potential allergens from poultry meat and egg sources can be an effective approach for the management of canine atopic dermatitis.},
}
@article {pmid39919360,
year = {2025},
author = {Lemons, JMS and Narrowe, AB and Firrman, J and Mahalak, KK and Liu, L and Higgins, S and Moustafa, AM and Baudot, A and Deyaert, S and Van den Abbeele, P},
title = {The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo.},
journal = {Food chemistry},
volume = {473},
number = {},
pages = {143037},
doi = {10.1016/j.foodchem.2025.143037},
pmid = {39919360},
issn = {1873-7072},
abstract = {Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.},
}
@article {pmid39919201,
year = {2025},
author = {Liu, C and Chen, Z and Wang, X and Deng, Y and Tao, L and Zhou, X and Deng, J},
title = {Response of Soil Phage Communities and Prokaryote-Phage Interactions to Long-Term Drought.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08448},
pmid = {39919201},
issn = {1520-5851},
abstract = {Soil moisture is a fundamental factor affecting terrestrial ecosystem functions. In this study, microscopic enumeration and joint metaviromic and metagenomic sequencing were employed together to investigate the impact of prolonged drought on soil phage communities and their interactions with prokaryotes in a subtropical evergreen forest. Our findings revealed a marked reduction in the abundances of prokaryotic and viral-like particles, by 73.1% and 75.2%, respectively, and significantly altered the structure of prokaryotic and phage communities under drought. Meanwhile, drought substantially increased the fraction of prokaryotic communities containing lysogenic phages by 163%, as well as the proportion of temperate phages. Nonetheless, drought likely amplified negative prokaryote-phage interactions given the nearly doubled proportion of negative links in the prokaryote-phage co-occurrence network, as well as the higher frequency and diversity of antiphage defense systems found in prokaryotic genomes. Under drought, soil phages exerted greater top-down control on typical soil k-strategists including Acidobacteria and Chloroflexi. Moreover, phage-encoded auxiliary metabolic genes may impact host metabolism in biosynthesis-related functions. Collectively, the findings of this study underscore the profound impact of drought on soil phages and prokaryote-phage interactions. These results also emphasize the importance of managing soil moisture levels during soil amendment and microbiome manipulation to account for the influence of soil phages.},
}
@article {pmid39918326,
year = {2025},
author = {Kos, D and Jelinski, M and Ruzzini, A},
title = {Retrospective analysis of antimicrobial resistance associated with bovine respiratory disease.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0190924},
doi = {10.1128/aem.01909-24},
pmid = {39918326},
issn = {1098-5336},
abstract = {The administration and utility of antibiotics to control and treat bovine respiratory disease (BRD) in beef cattle feedlots is a growing concern. Antimicrobial resistance (AMR) among BRD-associated bacterial pathogens has been the subject of cultivation-dependent and cultivation-independent surveillance. Bacterial genome sequencing and metagenomic approaches facilitate the characterization of AMR in the beef industry; however, the current collection of cattle-associated AMR research programs lack connections to each other. A more integrated view of how antimicrobial use (AMU) is related to resistance at a gene level is needed. We sought to establish a catalog of commonly observed AMR genes (ARGs) in opportunistic bacterial pathogens that contribute to BRD using publicly available data sets that were generated by the scientific community with and without AMU in mind. The presence of these clinically relevant ARGs appeared to differ by geography. Greater sampling in North America facilitated the generation of a list of ARGs often encoded by Mannheimia haemolytica and Pasteurella multocida. Detection of clinically relevant ARGs in shotgun metagenomes of cattle-associated and accessible feedlot samples such as water, soil, and feces was possible but limited by relative sequence read abundance. An exception was the tylosin esterase-encoding gene estT, which is among the most frequently observed ARGs in M. haemolytica and feedlot-related metagenomic data sets. Finally, by re-evaluating studies on the impact of AMU on AMR in beef production systems, we show that conventional practices, including in-feed antibiotic use, increase the relative abundance of ARGs in animal-derived samples.IMPORTANCEThis retrospective analysis delivers a list of ARGs found in opportunistic pathogens that contribute to BRD. The high incidence of BRD in North America is linked to the origin and implementation of metaphylaxis to mitigate detrimental animal losses at feedlots. Notably, ARGs commonly observed in these pathogens isolated in North America were not conserved across the globe, underscoring the relationship between regional AMU and AMR. A positive relationship was also observed between the relative abundance of ARGs in cattle-associated metagenomes with greater exposure to antibiotics. Overall, this analysis should help to guide future surveillance efforts and experimental designs to more directly evaluate the impacts of feedlot practices on AMR.},
}
@article {pmid39917835,
year = {2025},
author = {Hoffbeck, C and Middleton, DMRL and Wallbank, JA and Boey, JS and Taylor, MW},
title = {Culture-Independent Species-Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17685},
doi = {10.1111/mec.17685},
pmid = {39917835},
issn = {1365-294X},
support = {//University of Auckland Doctoral Scholarship/ ; },
abstract = {The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within Bacteroides fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles, Bacteroides is a dominant, 'core' gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two-pronged approach to better characterise Bacteroides populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species-level distributions of Bacteroides members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for Bacteroides from reptiles, birds, amphibians and mammals, to compare the functional potential of Bacteroides in different host taxa. The 16S rRNA gene analyses revealed that B. acidifaciens is the most common Bacteroides species in reptile guts, and that different orders of reptiles differ in which Bacteroides species they harbour. The taxonomy of Bacteroides species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome-assembled genomes for Bacteroides species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique Bacteroides MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of Bacteroides species across broad comparisons, but with some differences between reptile groups, and that Bacteroides appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.},
}
@article {pmid39917570,
year = {2025},
author = {Xu, L and Xiong, Y and Fang, C},
title = {Omadacycline for the Treatment of Severe Legionella Pneumonia Complicated with Multiple Organ Failure: A Case Report.},
journal = {International medical case reports journal},
volume = {18},
number = {},
pages = {217-222},
pmid = {39917570},
issn = {1179-142X},
abstract = {BACKGROUND: Fluoroquinolones and macrolides are the preferred antibiotics for treating Legionnaires' disease. However, the limited utility of these antibiotics in cases of organ dysfunction is a major problem. Omadacycline is a novel tetracycline antibiotic with a good safety profile and in vitro antibacterial activity against Legionella, but it lacks validation by clinical data.<br><br>CASE DESCRIPTION: Here, we report a case of severe pneumonia caused by Legionella infection. The patient was empirically treated with antibiotics, after admission but had a poor clinical outcome with severe hepatic and renal insufficiency. After Legionella infection was confirmed by metagenomic next-generation sequencing, the patient was switched to omadacycline antibiotic therapy and eventually discharged after recovery.<br><br>CONCLUSION: The results of this study suggest that metagenomic next-generation sequencing can facilitate early diagnosis of Legionnaires' disease, and omadacycline can be an alternative antibiotic treatment for severe Legionnaires' disease, especially in patients experiencing multiple organ failure.},
}
@article {pmid39917349,
year = {2025},
author = {Tigga, A and Mallappa, RH and Muniyappa, SK and Kadyan, S and Pradhan, D and Niharika, ES and Grover, S},
title = {16S metagenomics and metabolomics unveil the microbial compositions and metabolite profiles in Dahi, a traditional Indian fermented milk product prepared by the backslopping method.},
journal = {Journal of food science and technology},
volume = {62},
number = {3},
pages = {584-597},
pmid = {39917349},
issn = {0022-1155},
abstract = {UNLABELLED: Fermentation of milk contributes to an array of organoleptic and nutritional changes, which is largely governed by the metabolic activity of starter cultures. Dahi, a popular traditional fermented milk product of India, varies considerably from its commercial counterparts due to diversity in household production practices and the use of undefined microbial consortia as inoculants. Herein, we investigated the unexplored bacterial signatures and metabolic profiles of traditional Dahi from northern region of India using 16S metagenomics and untargeted gas chromatography-mass spectrophotometry. We found Firmicutes followed by Proteobacteria as the dominant phyla, while Lactobacillus and Streptococcus were the most prevalent lactic acid bacterial genera many species of which also serves as thermophilic starters. Notably, differential abundance of environmental bacteria like Bacilli, Prevotella, Oscillospira, Ruminococcus, and Acinetobacter were also observed in different samples. The study also revealed a total of 62 metabolites belonging to amino acids, fatty acids, sugars, and others metabolic intermediates, which also varied among regions. This highlights different production practices as influenced by milk type, heating methods, container choices and inoculum types leading to distinct microbiota succession and associated metabolites. This study provides valuable insights into the complexities as well as health benefits of indigenous fermented milks particularly Dahi and paves the way for future exploration of novel probiotic strains.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-024-06050-9.},
}
@article {pmid39917348,
year = {2025},
author = {Shuba, AA and Bogdanova, EV and Anokhina, EP and Umarkhanov, RU},
title = {Current trends in the determination of microbiological indicators of dairy products.},
journal = {Journal of food science and technology},
volume = {62},
number = {3},
pages = {453-470},
pmid = {39917348},
issn = {0022-1155},
abstract = {UNLABELLED: Milk and dairy products are the most common and widely consumed foods. At the same time, milk is often contaminated with pathogenic microorganisms by endo- and exogenous ways, which can cause various defects in raw materials and finished products. Recently, new techniques have been developed for monitoring microbiological indicators of milk, which are characterized by simplicity, ease of use and high reliability. In addition, the analysis time using the new techniques is significantly reduced compared to traditional ones. The review considers the microflora of milk and ways of its contamination with pathogenic microorganisms, as well as new methods for monitoring microbiological indicators that will be useful for specialists in the dairy industry.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-025-06207-0.},
}
@article {pmid39917331,
year = {2025},
author = {Ranganath, N and Bisono Garcia, B and Vaillant, J and Katragadda, S and Kerkelis, M and Abu Saleh, O and Fida, M},
title = {From Chart Biopsy to Liquid Biopsy: Evaluating the Diagnostic Yield and Clinical Impact of Plasma Microbial Cell-Free DNA Next-Generation Sequencing in the Management of Fever of Unknown Origin.},
journal = {Open forum infectious diseases},
volume = {12},
number = {2},
pages = {ofaf038},
pmid = {39917331},
issn = {2328-8957},
abstract = {BACKGROUND: The underlying cause of fever of unknown origin (FUO) remains unidentified in up to 51% of cases despite systematic evaluation. Microbial cell-free DNA next-generation sequencing (mcfDNA-NGS) offers an agnostic, noninvasive approach to pathogen identification, but the utility and clinical impact of this assay in FUO remain unknown.<br><br>METHODS: This retrospective cohort study evaluated adult patients referred for FUO evaluation at a tertiary medical center between November 2019 and November 2023. Patients underwent both standard microbiologic testing (ST) and mcfDNA-NGS. Diagnostic impact was assessed in 4 domains: new diagnoses, earlier time to diagnosis, avoidance of invasive procedures, and non-hypothesis-driven diagnoses. Logistic regression was used to identify predictors of positive mcfDNA-NGS testing.<br><br>RESULTS: Among 176 patients, mcfDNA-NGS was positive in 44.3%, with 49% of these cases considered clinically significant. Infectious cause of FUO was identified in 39% of patients, noninfectious in 35%, and unknown in 26%. mcfDNA-NGS contributed to a positive diagnostic impact in 30% of cases, mainly by earlier diagnosis (16%) and potential for avoidance of invasive procedures (10%). Positive mcfDNA-NGS was significantly associated with higher Charlson comorbidity index score (odds ratio [OR], 1.22; P < .001) and white blood cell (WBC) count &#x2264;4.5 &#xd7; 10[9] cells/L (OR, 8.61; P < .001). Conversely, FUO without localization was associated with a decreased likelihood of positive mcfNDA testing (OR, 0.18; P < .001).<br><br>CONCLUSIONS: mcfDNA-NGS effectively complements ST in diagnosing FUO, providing earlier detection and minimizing invasive testing. Clinical predictors such as high comorbidity and low WBC count may guide the optimal use of mcfDNA-NGS in FUO. Prospective evaluation of optimal timing and use of mcfDNA-NGS and cost-benefit analysis in FUO is needed.},
}
@article {pmid39917268,
year = {2024},
author = {Zhang, W and Jian, X and Ding, S and Chang, J and Ji, S and Chi, Y},
title = {Insights into the gut microbiota characteristics between the organic and traditional feeding chickens based on amplicon and metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1509461},
pmid = {39917268},
issn = {1664-302X},
abstract = {Intestinal microorganisms play a crucial role in chicken health and production performance, especially in the research of traditional and organic feeding methods. The intestinal contents of organic and feed chickens were analyzed by 16S rRNA gene and metagenome technology. The results showed that the microbial diversity of organic chickens was significantly higher than that of the feed chickens, especially the key microorganisms, such as Enterococcus, were more abundant in organic chickens. The functional analysis of metagenome revealed the significant difference in the metabolic function of intestinal microorganisms between them. The present study provides new insights into the gut microbiota characteristics of the organic and feed chicken based on amplicon and metagenomic sequencing. Our results are helpful to fully illustrate the effects of different feeding methods on intestinal microorganisms in chickens and can offer a more scientific basis for chicken production management.},
}
@article {pmid39916977,
year = {2025},
author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Hamdan Alkhraisat, M},
title = {Effect of implant abutment surface treatments on bacterial biofilm composition and structure.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2459922},
pmid = {39916977},
issn = {2000-2297},
abstract = {BACKGROUND: For the long-term success of dental implants, implant abutment surface should promote the attachment of oral epithelial cells and reduce bacterial adhesion. Titanium nitride (TiN) coatings show antimicrobial properties. Nevertheless, there is a lack of clinical trials that assess the biofilm formation on TiN abutments in the context of clinical practice. Thus, the objective of this study was to evaluate the effect of different abutment surfaces (machined, TiN and TiN oxidized) on bacterial biofilm composition and structure.<br><br>MATERIALS AND METHODS: Implant abutments were connected to the dental implants. Bacterial communities were sampled at 1 and 60&#x2009;days later. The relationship between surface, periodontal indices and bacterial community dynamics was assessed using 16S rRNA metagenomics. A total of 17 patients were involved in this study (14 included in final analyses: 15 machined, 16 TiN and 14 TiN oxidized abutments).<br><br>RESULTS: No significant differences between surfaces were found considering taxa abundance, most alpha diversity metrics or community structure. Time showed a significant effect on diversity and also on the abundance of several bacterial taxa.<br><br>CONCLUSIONS: These results indicate that the effect of the three tested abutment surfaces on biofilm structure and composition was negligible, whereas patient and time exert strong influences on bacterial biofilm formation at different scales.},
}
@article {pmid39916938,
year = {2024},
author = {Liu, Y and Yang, B and Qi, Q and Liu, S and Du, Y and Ye, L and Zhou, Q},
title = {Metagenomic next-generation sequencing for lung cancer low respiratory tract infections diagnosis and characterizing microbiome features.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1518199},
pmid = {39916938},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/diagnosis ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota/genetics ; Male ; *Bacteria/genetics/classification/isolation &amp; purification ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; Fungi/isolation &amp; purification/classification/genetics ; Coinfection/microbiology/diagnosis/virology ; Adult ; Metagenome ; Aged, 80 and over ; },
abstract = {BACKGROUND: The capability of mNGS in diagnosing suspected LRTIs and characterizing the respiratory microbiome in lung cancer patients requires further evaluation.<br><br>METHODS: This study evaluated mNGS diagnostic performance and utilized background microbial sequences to characterize LRT microbiome in these patients. GSVA was used to analyze the potential functions of identified genera.<br><br>RESULTS: Bacteria were the most common pathogens (n=74) in LRTIs of lung cancer patients, and polymicrobial infections predominated compared to monomicrobial infections (p<0.001). In diagnosing LRTIs in lung cancer patients, the pathogen detection rate of mNGS (83.3%, 70/84) was significantly higher than that of sputum culture (34.5%, 29/84) (p<0.001). This result was consistent with that of non-lung cancer patients (p<0.001). Furthermore, in the specific detection of bacteria (95.7% vs. 22.6%) and fungi (96.0% vs. 22.2%), the detection rate of mNGS was also significantly higher than that of CMTs mainly based on culture (p<0.001, p<0.001). However, in the detection of CMV/EBV viruses, there was no significant difference between the detection rate of mNGS and that of viral DNA quantification (p = 1.000 and 0.152). mNGS analysis revealed Prevotella, Streptococcus, Veillonella, Rothia, and Capnocytophaga as the most prevalent genera in the LRT of lung cancer patients. GSVA revealed significant correlations between these genera and tumor metabolic pathways as well as various signaling pathways including PI3K, Hippo, and p53.<br><br>CONCLUSION: mNGS showed a higher pathogen detection rate than culture-based CMTs in lung cancer patients with LRTIs, and also characterizing LRT microbiome composition and revealing potential microbial functions linked to lung carcinogenesis.},
}
@article {pmid39915809,
year = {2025},
author = {Zhang, Y and Li, HZ and Breed, M and Tang, Z and Cui, L and Zhu, YG and Sun, X},
title = {Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {42},
pmid = {39915809},
issn = {2049-2618},
support = {2022T150635//fellowship of China Postdoctoral Science Foundation/ ; 42407166//National Natural Science Foundation of China/ ; 42307165//National Natural Science Foundation of China/ ; 32361143523//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2023YFF1304601//National Key Research and Development Program of China/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; *Snails/microbiology/genetics ; *Global Warming ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/classification/drug effects ; Soil/chemistry ; Soil Microbiology ; beta-Lactamases/genetics ; Metagenomics ; Metagenome ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.<br><br>METHODS: We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.<br><br>RESULTS: We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.<br><br>CONCLUSIONS: The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.},
}
@article {pmid39915364,
year = {2025},
author = {de Castro Oliveira, W and Marques, PH and Erhardt, MM and Felice, AG and Tristão, CLAM and Aburjaile, FF and Oliveira, MBPP and Dos Santos Richards, NSP},
title = {Metagenomic analysis and proteins prediction of emerging pathogens in artisanal cheese.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {39915364},
issn = {1573-501X},
abstract = {Currently, reports of the presence of emerging pathogens in cheeses are low and new outbreaks have occurred at an alarming rate, with the Vibrio and Aeromonas genera being the main causes of gastroenteritis in the world. Therefore, Multi-Omics integration has been a strategy to identify and develop detection methods for these pathogens in food. We investigated the presence of emerging pathogens in artisanal cheeses and predicted proteins with immunogenic potential, in silico, for food diagnostics. For this, multiomics integration was used: (a) metagenomics; (b) subtractive genomics; and (c) pan-genomics. Eight species of the genera Vibrio and Aeromonas were identified, the latter being the most abundant (89.7%) and identified in eight regions, with emphasis on the species A. caviae and A. veronii. Pan-genomic analyses revealed intra- and inter-species differences in both genera. Essential, non-cytoplasmic proteins were identified, without homology and with immunological potential for the species researched. Functional annotation of genes present in pan-genomic subsets reveals functionality between the core genome (transcription; amino acid transport and metabolism; and inorganic ion transport and metabolism) and the shared genome (signal transduction and carbohydrate transport and metabolism). A reinterpretation of the genomic plasticity of V. furnissii reveals the presence of mobile genetic elements critical for virulence in human isolates and the RTX toxin, also identified in this species, is present in the pathogenicity islands of V. alginolyticus and V. fluvialis. Collectively, the results provide important information for the development of a diagnostic strategy for emerging pathogens in food using immunoassays.},
}
@article {pmid39915243,
year = {2025},
author = {Zhao, S and Lin, H and Li, W and Xu, X and Wu, Q and Wang, Z and Shi, J and Chen, Y and Ye, L and Xi, L and Chen, L and Yuan, M and Su, J and Gao, A and Jin, J and Ying, X and Wang, X and Ye, Y and Sun, Y and Zhang, Y and Deng, X and Shen, B and Gu, W and Ning, G and Wang, W and Hong, J and Wang, J and Liu, R},
title = {Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2462261},
pmid = {39915243},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Bile Acids and Salts/metabolism ; *Weight Loss ; Mice ; *Gastrectomy ; Humans ; Male ; *Clostridium/metabolism/genetics ; *Mice, Inbred C57BL ; *Obesity/microbiology/metabolism/surgery ; Receptors, G-Protein-Coupled/metabolism/genetics ; Fecal Microbiota Transplantation ; Female ; Adult ; Feces/microbiology ; Symbiosis ; Bariatric Surgery ; Adipose Tissue/metabolism ; },
abstract = {The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.},
}
@article {pmid39914338,
year = {2025},
author = {Yang, Y and Li, Q and Xiao, Y and Shen, Y and Wei, R and Zhang, Y and Zhang, W and Lei, N and Pei, X},
title = {Unravelling of the interaction mechanism of PFOA with submerged macrophytes and epiphytic biofilms at gene and molecular level.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137418},
doi = {10.1016/j.jhazmat.2025.137418},
pmid = {39914338},
issn = {1873-3336},
abstract = {Perfluorooctanoic acid (PFOA) is a global concern for the remediation of aquatic environments due to its toxicity, persistence and bioaccumulation. To gain a comprehensive understanding of the effects of PFOA on submerged macrophytes and epiphytic biofilms in eutrophic waters, as well as the mechanisms of PFOA and nutrient removal by submerged macrophyte-biofilm system, plant-attached biofilms were cultured under PFOA stress. Results indicated that PFOA exposure leads to an increase in ROS in plants, seriously damaging cellular systems, activating enzyme antioxidants to protect plant cells from oxidative damage. Additionally, PFOA affects microbial diversity, structure and function in biofilms, with Cyanobacteria and Proteobacteria being the dominant groups. While impacting both plants and biofilms, PFOA will be absorbed by them. PFOA binds to channel proteins (ULX0, VIH9) on plant cells and enters the plant, thus removing it from the environment. Plant co-cultivation has the highest pollutant removal rate of PFOA, reaching to 33.00 %. Furthermore, metagenomics analyses revealed that alterations in genes associated with N (nxrB, nxrA) and P (phoR, pstA) cycling of in the biofilm microorganisms facilitated the removal of N and P, with removal rates of 98.00 % and 99.42 %, respectively. These findings contribute to the ecological assessment of PFOA and provide valuable sights into the mechanisms of PFOA, N and P removal in eutrophic lakes by plants and epiphytic biofilms.},
}
@article {pmid39914332,
year = {2025},
author = {Rossi, M and Vergara, A and Troisi, R and Alberico, M and Carraturo, F and Salamone, M and Giordano, S and Capozzi, F and Spagnuolo, V and de Magistris, FA and Donadio, C and Scognamiglio, V and Vedi, V and Guida, M},
title = {Microplastics, microfibers and associated microbiota biofilm analysis in seawater, a case study from the Vesuvian Coast, southern Italy.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137468},
doi = {10.1016/j.jhazmat.2025.137468},
pmid = {39914332},
issn = {1873-3336},
abstract = {The growing concerns regarding pollution from microplastics (MPs) and microfibers (MFs) have driven the scientific community to develop new solutions for monitoring ecosystems. However, many of the proposed technologies still include protocols for treating environmental samples that may alter plastic materials, leading to inaccurate results both in observation and in counting. For this reason, we are refining a protocol, based on optical microscopy without the use of pretreatments, applicable to different environmental matrices, which allows not only counting but also a complete morphological characterization of MPs and MFs. Previously, the protocol has successfully been tested on marine sediments from the Vesuvian area of the Gulf of Naples (Italy) with good results. In the present study, we tested the protocol on MPs and MFs in seawater samples collected from the same geographical area to provide a comprehensive overview of their distribution in the marine environments. The protocol enabled not only the morphological characterization of MPs and MFs but also the collection of information on the colonies of microorganisms present on the microparticles. Next Generation Sequencing (NGS) metagenomic technologies enabled us to characterize the microbiota composition of the sampled MPs, the so-called Plastisphere. The analytical approach allowed the characterization of several potentially pathogenic bacteria, which represent a potential threat to the environment and human health. In fact, they may exploit their ability to form biofilms on plastics to proliferate in marine ecosystems.},
}
@article {pmid39914322,
year = {2025},
author = {SiMa, X and Li, Y and Yu, Z and Gu, H and Liu, J and Liu, J and Fang, R and Hu, X and Liu, X and Wang, G and Tang, C and Franks, A and Wu, J and Miao, S and Qiao, Y and Jin, J},
title = {Long-term warming offsets the beneficial effect of elevated CO2 on mineral associated organic carbon in Mollisols.},
journal = {The Science of the total environment},
volume = {966},
number = {},
pages = {178698},
doi = {10.1016/j.scitotenv.2025.178698},
pmid = {39914322},
issn = {1879-1026},
abstract = {The stability of soil organic carbon (SOC) is fundamentally important to the carbon-climate feedback because soils act as a major carbon source or sink under climate change. The uncertainty of SOC stability in farming soils in response to climate change necessitates mechanistic studies on microbial attributes to the change of SOC. Here, we used open-top chambers to simulate elevated CO2 (eCO2) and warming for 12 years in a soybean-grown Mollisol. We did not find the change of SOC stock under eCO2 or warming. Although eCO2 resulted in the accumulation of mineral-associated organic carbon, this effect diminished under warming. The amplicon sequencing of 16S gene indicated a significant change in microbial community composition under warming or eCO2. The metagenomic sequencing demonstrated that warming increased the abundances of microbial genes related to decomposition of labile carbon such as hemicellulose and pectin. The warming-induced stimulation of microbial catabolic metabolisms on organic carbon decomposition might have accelerated SOC turnover, which may offset the increased mineral-associated organic carbon of the Mollisol under eCO2. Long-term eCO2 and warming might not significantly alter the SOC stock or stability but accelerate carbon cycling in farming Mollisols.},
}
@article {pmid39914059,
year = {2025},
author = {Lyu, B and Manna, B and Zhou, X and Leung, IKH and Singhal, N},
title = {Microbial metabolic enzymes, pathways and microbial hosts for co-metabolic degradation of organic micropollutants in wastewater.},
journal = {Water research},
volume = {276},
number = {},
pages = {123229},
doi = {10.1016/j.watres.2025.123229},
pmid = {39914059},
issn = {1879-2448},
abstract = {Organic micropollutants (OMPs) in wastewater present significant environmental challenges, but effective removal strategies are hindered by our limited understanding of their co-metabolic biodegradation. We aim to elucidate the microbial enzymes, metabolic pathways, and community members involved in OMP co-metabolic degradation, thereby paving the way for more effective wastewater treatment strategies. We integrated multi-omics (metagenomics, metaproteomics, and metabolomics) and functional group analysis to investigate 24 OMPs under three aeration conditions. Our findings reveal that oxidoreductases, particularly cytochrome P450s and peroxidases, are crucial for recalcitrant OMPs containing halogen groups (-Cl, -F) like fluoxetine and diuron. Hydrolases, including amidases, are instrumental in targeting amide-containing (-CONH2) OMPs such as bezafibrate and carbamazepine. Regarding microbial metabolism involved in OMP co-metabolic degradation, we found that amino acid metabolism is crucial for degrading amine-containing (-NH2) OMPs like metoprolol and citalopram. Lipid metabolism, particularly for fatty acids, contributes to the degradation of carboxylic acid (-COOH) containing OMPs such as bezafibrate and naproxen. Finally, with Actinobacteria, Bacteroidetes, and Proteobacteria emerging as primary contributors to these functionalities, we established connections between OMP functional groups, degradation enzymes, metabolic pathways, and microbial phyla. Our findings provide generalized insights into structure-function relationships in OMP co-metabolic degradation, offering the potential for improved wastewater treatment strategies.},
}
@article {pmid39913347,
year = {2025},
author = {Phan, HV and Yasuda, S and Oba, K and Tsukamoto, H and Hori, T and Kuroiwa, M and Terada, A},
title = {Active bacteria driving N2O mitigation and dissimilatory nitrate reduction to ammonium in ammonia recovery bioreactors.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf021},
pmid = {39913347},
issn = {1751-7370},
abstract = {Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge system for retaining ammonia whereas removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the system is essential to optimize system performance. Here, we employed metagenomics and metatranscriptomics analyses to characterize the microbial community structure and activity during the transition from a microoxic to an oxic condition. A hybrid approach combining high-quality short reads and Nanopore long reads reconstructed 98 medium- to high-quality non-redundant metagenome-assembled genomes from the communities. The suppressed bacterial ammonia monooxygenase (amoA) expression was upregulated after shifting from a microoxic to an oxic condition. Seventy-three reconstructed metagenome-assembled genomes (>74% of the total) from 11 bacterial phyla harbored genes encoding proteins involved in nitrate respiration; 39 (~53%) carried N2O reductase (nosZ) genes with the predominance of clade II nosZ (31 metagenome-assembled genomes), and 24 (~33%) possessed nitrite reductase (ammonia-forming) genes (nrfA). Clade II nosZ and nrfA genes exhibited the highest and second-highest expressions among nitrogen metabolism genes, indicating robust N2O consumption and ammonification. Non-denitrifying clade II nosZ bacteria, Cloacibacterium spp., in the most abundant and active phylum Bacteroioda, were likely major N2O sinks. Elevated dissolved oxygen concentration inhibited clade II nosZ expression but not nrfA expression, potentially switching phenotypes from N2O reduction to ammonification. Collectively, the multi-omics analysis illuminated bacteria responsible for N2O reduction and ammonification in microoxic and oxic conditions, facilitating high-performance ammonia recovery.},
}
@article {pmid39913343,
year = {2025},
author = {Davidovich, C and Erokhina, K and Gupta, CL and Zhu, YG and Su, JQ and Djordjevic, SP and Wyrsch, ER and Blum, SE and Cytryn, E},
title = {Occurrence of "under-the-radar" antibiotic resistance in anthropogenically affected produce.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae261},
pmid = {39913343},
issn = {1751-7370},
abstract = {With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and antimicrobial resistance indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality treated wastewater-irrigated soil, and potentially proliferate under favorable conditions. This "under-the-radar" phenomenon was further investigated here, in treated wastewater-irrigated and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically relevant multidrug-resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and treated wastewater-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and antimicrobial resistance determinants in anthropogenically affected agroenvironments, providing a platform to improve quantitative microbial risk assessment models in the future.},
}
@article {pmid39913342,
year = {2025},
author = {Martin, H and Rogers, LA and Moushtaq, L and Brindley, AA and Forbes, P and Quintion, AR and Murphy, ARJ and Hipperson, H and Daniell, TJ and Ndeh, D and Amsbury, S and Hitchcock, A and Lidbury, IDEA},
title = {Metabolism of hemicelluloses by root-associated Bacteroidota species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf022},
pmid = {39913342},
issn = {1751-7370},
abstract = {Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant bacteria for capturing simple carbon exudates. Instead, bacteroidota possess TonB-dependent transporters predicted to import glycans produced by plant polysaccharide breakdown. Metatranscriptomics (oat rhizosphere) identified several TonB-dependent transporters genes that were highly expressed in Flavobacterium (phylum Bacteroidota). Using Flavobacterium johnsoniae as the model, we experimentally validated the function of one highly expressed TonB-dependent transporters, identifying a conserved Xyloglucan Utilisation Loci conferring an ability to import xyloglucan, the major hemicellulose secreted from plant roots. Xyloglucan utilisation loci harbour an endoxyloglucanase related to family 5 subfamily 4 subclade 2D glycoside hydrolases carrying a mutation that we demonstrate is required for full activity towards xyloglucan. Based on analysing 700 soil metagenomes, subclade 2D glycoside hydrolases have radiated in soil and are prevalent among plant-associated bacteroidota and certain taxa affiliated with Gammaproteobacteria. In bacteroidota, particularly Flavobacterium species, xyloglucan utilisation loci organisation was highly conserved, which may increase their competitive ability to utilise xyloglucan. Given bacteroidota lack high-affinity nutrient transporters for simple carbon, instead possessing xyloglucan utilisation loci and similar gene clusters, our data suggests hemicellulose exudates provide them with an important carbon source in the rhizosphere.},
}
@article {pmid39912643,
year = {2025},
author = {Hotchkiss, MZ and Poulain, AJ and Forrest, JRK},
title = {Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0203624},
doi = {10.1128/aem.02036-24},
pmid = {39912643},
issn = {1098-5336},
abstract = {Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.},
}
@article {pmid39911714,
year = {2024},
author = {Wang, Y and Jiang, X and Xi, Y and Wei, S and Ning, S and Zhang, W},
title = {Novel cycloviruses identified by mining human blood metagenomic data show close relationship to those from animals.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1522416},
pmid = {39911714},
issn = {1664-302X},
abstract = {The family Circoviridae includes the genera Circovirus and Cyclovirus. Cycloviruses have been found in serum samples from chronic HBV, HCV, or HIV-infected individuals as well as asymptomatic blood donors. However, research on cycloviruses is relatively limited. We used viral metagenomics to mine, analyze, and visualize the human blood virome, successfully identifying three new genomes, each encoding Rep and Capsid proteins. These proteins are crucial for viral replication and host-cell interaction: the Rep protein is involved in initiating viral genome replication, while the Capsid protein plays a key role in the assembly of new virions and the virus's ability to interact with host immune systems. Distance matrix and phylogenetic analyses show that these cycloviruses share high sequence similarity with viruses found in both humans and animals across different regions of Africa. This finding not only confirms the presence of previously uncharacterized cycloviruses in human blood, but also provides insight into their potential role in host transmission and their ecological significance. Further research is needed to explore the functional roles of these cycloviruses in viral pathogenesis, particularly how they may influence host immunity and contribute to chronic infections. Additionally, studies investigating the host range and mechanisms of cross-species transmission will be essential to understanding the broader implications of cycloviruses in human and animal health.},
}
@article {pmid39911711,
year = {2024},
author = {Kimeklis, AK and Gladkov, GV and Orlova, OV and Lisina, TO and Afonin, AM and Aksenova, TS and Kichko, AA and Lapidus, AL and Abakumov, EV and Andronov, EE},
title = {Metagenomic insights into the development of microbial communities of straw and leaf composts.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1485353},
pmid = {39911711},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.<br><br>METHODS: Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.<br><br>RESULTS: In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.<br><br>DISCUSSION: Our study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.},
}
@article {pmid39911706,
year = {2024},
author = {Leon-Gomez, P and Romero, VI},
title = {Human papillomavirus, vaginal microbiota and metagenomics: the interplay between development and progression of cervical cancer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1515258},
pmid = {39911706},
issn = {1664-302X},
abstract = {Persistent infection with oncogenic human papillomavirus (HPV) types, such as HPV 16 or 18, is a major factor in cervical cancer development. However, only a small percentage of infected women develop cancer, indicating that other factors are involved. Emerging evidence links vaginal microbiota with HPV persistence and cancer progression. Alterations in microbial composition, function, and metabolic pathways may contribute to this process. Despite the potential of metagenomics to explore these interactions, studies on the vaginal microbiota's role in cervical cancer are limited. This review systematically examines the relationship between cervical microbiota, HPV, and cervical cancer by analyzing studies from PubMed, EBSCO, and Scopus. We highlight how microbial diversity influences HPV persistence and cancer progression, noting that healthy women typically have lower microbiota diversity and higher Lactobacillus abundance compared to HPV-infected women, who exhibit increased Gardenella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., associated with dysbiosis. We discuss how microbial diversity is associated with HPV persistence and cancer progression, noting that studies suggest healthy women typically have lower microbiota diversity and higher Lactobacillus abundance, while HPV-infected women exhibit increased Gardnerella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., indicative of dysbiosis. Potential markers such as Gardnerella and Prevotella have been identified as potential microbiome biomarkers associated with HPV infection and cervical cancer progression. The review also discusses microbiome-related gene expression changes in cervical cancer patients. However, further research is needed to validate these findings and explore additional microbiome alterations in cancer progression.},
}
@article {pmid39911666,
year = {2024},
author = {Liu, H and Zhou, K and Zhong, C and Guan, M},
title = {Combination of metagenomic next-generation sequencing and morphology for identifying Coccidioides immitis: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1500014},
pmid = {39911666},
issn = {2296-858X},
abstract = {Coccidioidomycosis is a systemic infection caused by the dimorphic fungus Coccidioides spp., endemic to the Southwestern United States and Central and South America. In this article, we report a case of Coccidioides immitis-induced meningitis in a 27-year-old man who was experiencing recurrent fever and headache. His cerebrospinal fluid (CSF) biochemical markers indicated an infection in the central nervous system. However, repeated routine cultures of the CSF for bacterial detection were all negative. Only metagenomic next-generation sequencing (mNGS) detected low reads of C. immitis. To verify the mNGS results, the Clinical Microbiology Laboratory in Huashan Hospital optimized its culture conditions. Ultimately, 12 days after sampling, the fungal bottle containing the cerebrospinal fluid tested positive. Furthermore, the diagnosis of C. immitis was then confirmed by smear staining combined with morphological characteristics of the colony, which provided an important etiological basis for clinical diagnosis and treatment. As coccidioidomycosis is a rare disease in China, its pathogen-specific diagnostic methods are limited. In this case, we combined two universal methods, mNGS and traditional morphological observation, to confirm the diagnosis. This combined strategy is critical for quick and accurate diagnosis.},
}
@article {pmid39911250,
year = {2025},
author = {Li, H and Chen, Y and Xia, Z and Zhuang, D and Cong, F and Lian, YX},
title = {Metagenomic investigation of viruses in green sea turtles (Chelonia mydas).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492038},
pmid = {39911250},
issn = {1664-302X},
abstract = {Green sea turtles are listed on the International Union for Conservation of Nature's Red List of Threatened Species. Thus, conservation efforts, including investigation of factors affecting the health of green sea turtles, are critical. Viral communities play vital roles in maintaining animal health. In the present study, shotgun metagenomics was used for the first time to survey viruses in the feces of green sea turtles. Most viral contigs were DNA viruses that mainly belonged to Caudoviricetes, followed by Crassvirales. Additionally, most of the viral contigs were not assigned to any known family or genus, implying a large knowledge gap in the taxonomy of green sea turtle gut viruses. Host prediction showed that most viruses were connected to two phyla: Bacteroidetes and Firmicutes. Furthermore, KEGG enrichment analysis showed that the viral genes were mainly involved in phage-associated and metabolic pathways. Phylogenetic tree reconstruction of Caudovirales terminase large-subunit (TerL) protein showed that most of the sequences were phylogenetically distant. This study expands our understanding of the viral diversity in green sea turtles. In particular, analysis of the virome RNA fraction is exceedingly important for investigating intestinal viromes; therefore, future studies could use metatranscriptomics to study RNA viruses.},
}
@article {pmid39910644,
year = {2025},
author = {Alamoudi, R and Barozzi, A and Michoud, G and Van Goethem, MW and Odobel, C and Chen, Y and Marasco, R and Daffonchio, D},
title = {Metabolic redundancy and specialisation of novel sulfide-oxidizing Sulfurimonas and Sulfurovum along the brine-seawater interface of the Kebrit Deep.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {19},
pmid = {39910644},
issn = {2524-6372},
support = {5569-OFP2023//King Abdullah University of Science and Technology/ ; },
abstract = {BACKGROUND: Members of the Campylobacterota phylum are dominant key players in sulfidic environments, where they make up a stable portion of sulfide-oxidizing bacterial communities. Despite the significance of these bacteria in primary production being well recognised in several ecosystems, their genomic and metabolic traits in sulfidic deep hypersaline anoxic basins (DHABs) remain largely unexplored. This knowledge gap not only hampers our understanding of their adaptation and functional role in DHABs but also their ecological interactions with other microorganisms in these unique ecosystems.<br><br>RESULTS: Metabolic reconstructions from metagenome-assembled genomes (MAGs) of sulfide-oxidizing Campylobacterota were conducted at 10 cm spatial resolution within the halocline of the brine-seawater interface (BSI, salinity 91-155 PSU) of the 1466 m deep sulfidic Kebrit Deep in the Red Sea. Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which&#xa0;differ from those found in mildly saline deep-sea sulfidic pools. They are stratified along the BSI and utilise the reductive tricarboxylic acid cycle to fix carbon dioxide, acting as primary producers. Their energy generation processes include aerobic or anaerobic-nitrate-dependent sulfide oxidation, as well as hydrogen oxidation. In addition to the&#xa0;osmoprotectant pathways commonly observed&#xa0;in Campylobacterota, such as&#xa0;the synthesis and uptake of proline and glutamate, the two Kebrit Deep Sulfurovum species exhibit genomic signatures for ectoine synthesis, further aiding their&#xa0;adaptation to high salinity. This combination of metabolic redundancy and specialisation within the confined spatial boundaries (~1&#xa0;m) of the BSI is pivotal in governing microbial interactions, including those with sulfate-reducers, heterotrophs, and other primary producers.<br><br>CONCLUSIONS: These results show how the selective pressures mediated by the sulfidic and hypersaline conditions of Kebrit Deep have resulted in novel, adapted and metabolically redundant Sulfurimonas and Sulfurovum species that contribute to the energy coupling, nutrient turnover and metabolic continuity along the physico-chemical gradient of the BSI.},
}
@article {pmid39910065,
year = {2025},
author = {Fumagalli, A and Castells-Nobau, A and Trivedi, D and Garre-Olmo, J and Puig, J and Ramos, R and Ramió-Torrentà, L and Pérez-Brocal, V and Moya, A and Swann, J and Martin-Garcia, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2455506},
pmid = {39910065},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; Humans ; *Cognition ; *Histidine/metabolism ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Methanobrevibacter/metabolism/genetics ; Metagenomics ; Archaea/metabolism/classification/genetics ; Cohort Studies ; Animals ; Adult ; },
abstract = {The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.},
}
@article {pmid39910055,
year = {2025},
author = {Song, B and Tria, FDK and Skejo, J},
title = {Prokaryotic cellulase gene clusters derived from 2,305 metagenomes.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {218},
pmid = {39910055},
issn = {2052-4463},
mesh = {*Cellulase/genetics/chemistry ; *Metagenome ; *Multigene Family ; Cellulases/genetics/chemistry ; Cellulose ; },
abstract = {Cellulose is a carbon source widespread in nature. However, it is a difficult task for any organism to get carbon atoms from the cellulose as it has a highly complex structure. Only a few taxonomic groups are known to decompose cellulose. They do it by producing cellulases, the various enzymes which break beta-glycosidic bonds in the cellulose. Cellulases were identified in 1,735 metagenomes from 225 bioprojects. The set of 12,837 metagenome-derived cellulases encompass three catalytic functions: exoglucanases (CBH, 1,042), endoglucanases (EG, 5,685), and beta-glucosidases (βG, 6,110). All three enzymatic functions are thought to be necessary for driving cellulase to a cascade of reactions that can make cellulose available as glucose. These metagenome-derived cellulases were clustered into protein families for each EC category individually, resulting in a total of 136 clusters, with the majority observed for EG (97 clusters), followed by βG (19 clusters) and CBH (19 clusters). These clusters provided a useful cellulase dataset for future research on cellulase utilization.},
}
@article {pmid39909853,
year = {2025},
author = {Hirota, K and Salim, F and Yamada, T},
title = {DeepES: Deep learning-based enzyme screening to identify orphan enzyme genes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf053},
pmid = {39909853},
issn = {1367-4811},
abstract = {MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions.<br><br>RESULTS: Therefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria.<br><br>AVAILABILITY: DeepES is available at https://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid39909332,
year = {2025},
author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J},
title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {368},
number = {},
pages = {125787},
doi = {10.1016/j.envpol.2025.125787},
pmid = {39909332},
issn = {1873-6424},
abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.},
}
@article {pmid39909254,
year = {2025},
author = {Yan, Q and Wang, W and Fan, Z and Wei, Y and Yu, R and Pan, T and Wang, N and Lu, W and Li, B and Fang, Z},
title = {Chickpea-resistant starch exhibits bioactive function for alleviating atopic dermatitis via regulating butyrate production.},
journal = {International journal of biological macromolecules},
volume = {303},
number = {},
pages = {140661},
doi = {10.1016/j.ijbiomac.2025.140661},
pmid = {39909254},
issn = {1879-0003},
abstract = {Resistant starch (RS) is one of the bioactive polysaccharides to produce Short-chain fatty acids (SCFAs) in the colon and contributes to allergic diseases including atopic dermatitis (AD). However, the bioactive mechanism of RS relieving AD needs to be elucidated. In this study, RS was prepared using chickpeas. Its microstructure and crystal structure were thoroughly characterized. Chickpea RS significantly improved the clinical symptoms and restored Th1/Th2 immune balance in mice with AD induced by calcipotriol. These benefits were eliminated by antibiotic cocktail treatment, suggesting that gut microbiota mediated the alleviation effects of chickpea RS on AD. Based on metagenomic sequencing and untargeted metabolomic analysis, chickpea RS treatment significantly increased the proportions of Butyricimonas virosa, Bifidobacterium pseudolongum, and Faecalibaculum rodentium, and a total of 206 differential metabolites were altered, especially the increase in propionate and butyrate production. Furthermore, we found that acylated butyrate, but not propionate, improved the pathological characteristics by activating GPR109A, which inhibit the phosphorylation levels of IκB-α, p50, p65, JNK, and p-JNK. Collectively, chickpea RS exhibited the bioactive function for regulating the communication of the gut-skin axis via regulating butyrate production to activate GPR109A.},
}
@article {pmid39909096,
year = {2025},
author = {Zhang, Z and Liu, R and Zheng, W and Lan, Y and Li, Y},
title = {Specialized genera and niche partitioning promote the biosynthesis of short-chain fatty acids in anaerobic cofermentation of sewage sludge and protein-rich waste.},
journal = {Environmental research},
volume = {271},
number = {},
pages = {121034},
doi = {10.1016/j.envres.2025.121034},
pmid = {39909096},
issn = {1096-0953},
abstract = {Elucidating the relationships among various microorganisms and their reactions to environmental fluctuations, such as dissolved organic matter (DOM), remains a key objective in the anaerobic cofermentation (ACF) of sewage sludge (SS) and protein-rich waste (PRW); however, this topic is inadequately understood. In this study, the microbial traits associated with the biosynthesis of short-chain fatty acids (SCFAs) were investigated in the ACF of SS in conjunction with four distinct PRWs (pupa, fishmeal, maize gluten, and soybean meal). Compared with those in the SS-only reactor, the first-order rate constants for biosolid dissolution in the SS/PRW reactors were increased by 1.9-4.0-fold. Pupa performed best among the four PRWs in the ACF process, with the solubilization rate increasing from 9.4% (SS-only reactor) to 33.5%. The copious and readily biodegradable DOM created a unique niche for functional microbes, leading to reframing of the microfloral structure. Specialized genera, such as Holophaga, Alistipes, and Geothrix, were responsible for SCFA biosynthesis in the SS/pupa reactor. The highly differentiated, low-redundancy microecosystem constructed in the SS/pupa reactor contributed to the independent functioning of the hydrolyzers and acidogens, resulting in an SCFA yield that was 6.9-fold greater than that in the SS-only reactor. In addition, the ACF of SS/pupa resulted in the genes encoding the NiFe hydrogenase and Wood-Ljungdahl pathway being intact, which promoted the synthesis of SCFAs, especially acetate. These findings offer new insights into the microbiological mechanisms that augment SCFA generation by the ACF of SS/PRW in terms of microorganism fate, metabolic network relationships, and microecosystem niche.},
}
@article {pmid39909037,
year = {2025},
author = {Lim, B and Xu, J and Wierzbicki, IH and Gonzalez, CG and Chen, Z and Gonzalez, DJ and Gao, X and Goodman, AL},
title = {A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.01.008},
pmid = {39909037},
issn = {1934-6069},
abstract = {Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.},
}
@article {pmid39909032,
year = {2025},
author = {Zhu, X and Hu, M and Huang, X and Li, L and Lin, X and Shao, X and Li, J and Du, X and Zhang, X and Sun, R and Tong, T and Ma, Y and Ning, L and Jiang, Y and Zhang, Y and Shao, Y and Wang, Z and Zhou, Y and Ding, J and Zhao, Y and Xuan, B and Zhang, H and Zhang, Y and Hong, J and Fang, JY and Xiao, X and Shen, B and He, S and Chen, H},
title = {Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2024.12.013},
pmid = {39909032},
issn = {1932-7420},
abstract = {Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.},
}
@article {pmid39908950,
year = {2025},
author = {Alonso-Vásquez, T and Fagorzi, C and Mengoni, A and Oliva, M and Cavalieri, D and Pretti, C and Cangioli, L and Bacci, G and Ugolini, A},
title = {Metagenomic surveys show a widespread diffusion of antibiotic resistance genes in a transect from urbanized to marine protected area.},
journal = {Marine pollution bulletin},
volume = {213},
number = {},
pages = {117640},
doi = {10.1016/j.marpolbul.2025.117640},
pmid = {39908950},
issn = {1879-3363},
abstract = {Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria.},
}
@article {pmid39908754,
year = {2025},
author = {Li, Y and Xiao, L and Zeng, XC},
title = {Hydrogen gas oxidation-driven reductive mobilization of arsenic in solid phase contributing to arsenite contamination in groundwater: Insights from metagenomic and microcosm analyses.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137444},
doi = {10.1016/j.jhazmat.2025.137444},
pmid = {39908754},
issn = {1873-3336},
abstract = {Hydrogen gas (H2) is naturally produced by biological and non-biological reactions in various environmental niches. However, the influence of H2 on microbial processes that cause the mobilization and release of arsenic from solid phase into groundwater remains to be resolved. Given that dissimilatory arsenate [As(V)]-respiring prokaryotes (DARPs) have been demonstrated to significantly contribute to the formation of As-contaminated groundwater, our study specifically examined the interactions between H2 and DARPs. We prepared an enriched DARP population from As-contaminated soils. Metagenomic analyses of the DARP population revealed that approximately 46.7 % of the qualified DARPs' MAGs contain at least one type I Ni-Fe hydrogenase. The Ni-Fe hydrogenase proteins in DARPs show unique diversity. Functional assays indicate that the DARP population exhibited notable activity in oxidizing H2 while concurrently reducing As(V) under strictly anaerobic conditions. Arsenic release assays indicate that the DARP population is highly proficient at catalyzing the reductive mobilization of arsenic in scorodite, using hydrogen as the electron donor. These findings offer the initial evidence that H2 can directly promote the formation of arsenic-contaminated groundwater mediated by DARPs, a biogeochemical process that has long been overlooked. Therefore, this study increases our insight into the microbial mechanisms involved in the formation of arsenic-contaminated groundwater.},
}
@article {pmid39908679,
year = {2025},
author = {Cao, S and Fang, J and Koch, K and Fan, X and Al-Hazmi, HE and Du, R and Wells, GF},
title = {Fluoride-induced stress shapes partial denitrification granules to sustain microbial metabolism.},
journal = {Water research},
volume = {275},
number = {},
pages = {123239},
doi = {10.1016/j.watres.2025.123239},
pmid = {39908679},
issn = {1879-2448},
abstract = {The presence of fluoride ions (F[-]) in nitrogen-rich wastewater from photovoltaic and semiconductor industries introduces a significant challenge to biological treatment processes, particularly for the innovative partial denitrification (PD) process, which supplies nitrite for anaerobic ammonium oxidation (Anammox). This study provides the first comprehensive and systematic investigation of the effects of F[-] stress on the granule-based PD process through batch tests and long-term operation. Results indicate that PD activity remains resilient to F[-] shock up to 1.5 g/L but is markedly impaired at concentrations of 2.0-3.0 g/L, despite maintaining a nitrate-to-nitrite transformation ratio (NTR) of approximately 80 %. Under long-term F[-] stress at 0.5 g/L, NTR gradually reduces to 50 %, but subsequently recovers to and maintains at 70 %. The increased secretion of loosely bound extracellular polymeric substances and proteins likely enhances the resistance of PD granules to F[-] stress, though excessive amounts degrade their settling properties. F[-]-induced microbial community succession shapes a predominance of medium granules (1.0 < d < 2.0 mm of 60.2 %) by enhancing aggregation of smaller granules and disintegration of larger ones. This enhances the mechanical strength and microbial activity of PD granules, aiding in resistance to F[-] stress to sustain microbial metabolism. Thauera is selectively enriched under long-term F[-] stress, with upregulated nirBDS genes contributing to the reduced NTR. Additionally, increased electron metabolism activity and a robust antioxidative response help to maintain higher microbial metabolic activity, mitigating F[-]-induced oxidative stress. These findings advance our understanding of the resilience and adaptability of the PD process under F[-] stress, providing critical insights for optimizing biological wastewater treatment systems in challenging environments.},
}
@article {pmid39908385,
year = {2025},
author = {Griffiths, ME and Broos, A and Morales, J and Tu, IT and Bergner, L and Behdenna, A and Valderrama Bazan, W and Tello, C and Carrera, JE and Recuenco, S and Streicker, DG and Viana, M},
title = {Dynamics of influenza transmission in vampire bats revealed by longitudinal monitoring and a large-scale anthropogenic perturbation.},
journal = {Science advances},
volume = {11},
number = {6},
pages = {eads1267},
pmid = {39908385},
issn = {2375-2548},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Chiroptera/virology ; Animals ; Orthomyxoviridae Infections/transmission/virology/veterinary ; Humans ; Bayes Theorem ; Peru/epidemiology ; Zoonoses/transmission/virology ; Longitudinal Studies ; },
abstract = {Interrupting pathogen transmission between species is a priority strategy to mitigate zoonotic threats. However, avoiding counterproductive interventions requires knowing animal reservoirs of infection and the dynamics of transmission within them, neither of which are easily ascertained from the cross-sectional surveys that now dominate investigations into newly discovered viruses. We used biobanked sera and metagenomic data to reconstruct the transmission of recently discovered bat-associated influenza virus (BIV; H18N11) over 12 years in three zones of Peru. Mechanistic models fit under a Bayesian framework, which enabled joint inference from serological and molecular data, showed that common vampire bats maintain BIV independently of the now assumed fruit bat reservoir through immune waning and seasonal transmission pulses. A large-scale vampire bat cull targeting rabies incidentally halved BIV transmission, confirming vampire bats as maintenance hosts. Our results show how combining field studies, perturbation responses, and multi-data-type models can elucidate pathogen dynamics in nature and reveal pathogen-dependent effects of interventions.},
}
@article {pmid39908317,
year = {2025},
author = {Weinheimer, AR and Ha, AD and Aylward, FO},
title = {Towards a unifying phylogenomic framework for tailed phages.},
journal = {PLoS genetics},
volume = {21},
number = {2},
pages = {e1011595},
doi = {10.1371/journal.pgen.1011595},
pmid = {39908317},
issn = {1553-7404},
abstract = {Classifying viruses systematically has remained a key challenge of virology due to the absence of universal genes and vast genetic diversity of viruses. In particular, the most dominant and diverse group of viruses, the tailed double-stranded DNA viruses of prokaryotes belonging to the class Caudoviricetes, lack sufficient homology in the genetic machinery that unifies them to reconstruct inclusive, stable phylogenies of these genes. While previous approaches to organize tailed phage diversity have managed to distinguish various taxonomic levels, these methods are limited in scalability and reproducibility, and they do not include modes of evolution, like gene gains and losses. Here, we present a novel, comprehensive, and reproducible framework for examining evolutionary relationships of tailed phages. In this framework, we compare phage genomes based on presences and absences of a fixed set of gene families which is used as binary trait data that is input into maximum likelihood models and include heterogeneous rates of trait losses and gains. Our resulting phylogeny stably recovers known taxonomic families of tailed phages, with and without the inclusion of metagenomic phages. We also quantify the mosaicism of replication and structural genes among known families. Our results suggest that these exchanges likely underpin the emergence of new families. Additionally, we apply this framework to large phages (>100 kilobases) to map emergences of traits associated with genome expansion. Taken together, this evolutionary framework for charting and organizing tailed phage diversity improves the systemization of phage taxonomy, which can unify phage studies and advance our understanding of their evolution.},
}
@article {pmid39908139,
year = {2025},
author = {Zhang, Z and Guo, Q and Yang, Z and Sun, Y and Jiang, S and He, Y and Li, J and Zhang, J},
title = {Bifidobacterium adolescentis-derived nicotinic acid improves host skeletal muscle mitochondrial function to ameliorate sarcopenia.},
journal = {Cell reports},
volume = {44},
number = {2},
pages = {115265},
doi = {10.1016/j.celrep.2025.115265},
pmid = {39908139},
issn = {2211-1247},
abstract = {Sarcopenia significantly diminishes quality of life and increases mortality risk in older adults. While the connection between the gut microbiome and muscle health is recognized, the underlying mechanisms are poorly understood. In this study, shotgun metagenomics revealed that Bifidobacterium adolescentis is notably depleted in individuals with sarcopenia, correlating with reduced muscle mass and function. This finding was validated in aged mice. Metabolomics analysis identified nicotinic acid as a key metabolite produced by B. adolescentis, linked to improvements in muscle mass and functionality in individuals with sarcopenia. Mechanistically, nicotinic acid restores nicotinamide adenine dinucleotide (NAD+) levels in muscle, inhibits the FoxO3/Atrogin-1/Murf-1 axis, and promotes satellite cell proliferation, reducing muscle atrophy. Additionally, NAD+ activation enhances the silent-information-regulator 1 (SIRT1)/peroxisome-proliferator-activated-receptor-γ-coactivator 1-alpha (PGC-1α) axis, stimulating mitochondrial biogenesis and promoting oxidative metabolism in slow-twitch fibers, ultimately improving muscle function. Our findings suggest that B. adolescentis-derived nicotinic acid could be a promising therapeutic strategy for individuals with sarcopenia.},
}
@article {pmid39907890,
year = {2025},
author = {Ramos-Lopez, O},
title = {Personalizing Dietary Polyphenols for Health Maintenance and Disease Management: A Nutrigenetic Approach.},
journal = {Current nutrition reports},
volume = {14},
number = {1},
pages = {29},
pmid = {39907890},
issn = {2161-3311},
mesh = {Humans ; *Polyphenols/pharmacology ; *Nutrigenomics ; *Dietary Supplements ; Polymorphism, Single Nucleotide ; Diet ; Precision Medicine ; Flavonoids/pharmacology ; },
abstract = {PURPOSE OF THE REVIEW: This literature review provides examples of the influence of certain genetic variants on health outcomes after dietary polyphenol consumption or supplementation. Available evidence is organized according to the major classes of polyphenols (flavonoids, phenolic acids, stilbenes, lignans, and tannins) and their derived subgroups.<br><br>RECENT FINDINGS: Nutrigenetic studies have identified mainly single nucleotide polymorphisms located within genes involved in the biotransformation of phenolic acids, stilbenes, lignans and several flavonoid molecules. These genetic variants may affect polyphenol metabolism rates and related predisposition to chronic non-communicable diseases. Moreover, differential cardiometabolic outcomes upon polyphenol supplementation as dietary sources or nutraceuticals have been modulated by specific genotypes. Although current evidence is still limited, growing gene-polyphenol interactions are contributing to systematically elucidate the biological functions of polyphenols; determine individual risk phenotypes to specific diseases or particular responses upon polyphenol exposure; and facilitate the prescription of personalized genotype-based doses of dietary polyphenols to optimize related health benefits. Additionally, the integration of genetics with other omics insights (epigenomics, transcriptomics, metagenomics, and metabolomics) trough biological systems and high-dimensional data analyses and interpretation may provide a more comprehensive understanding of polyphenol metabolism for precision nutrition applications in health and disease.},
}
@article {pmid39907344,
year = {2025},
author = {Cuong, NC and Hung, NV and Linh, TK and Loi, NTT and Tung, QN and Tuyen, DT and Anh, DTN},
title = {Structure of fungal community and culturable fungi on the discolored surfaces of pine storage boxes in the tropical region in Dong Nai, Vietnam.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e289015},
doi = {10.1590/1519-6984.289015},
pmid = {39907344},
issn = {1678-4375},
mesh = {Vietnam ; *Fungi/classification/isolation &amp; purification/genetics ; *Wood/microbiology ; *Pinus/microbiology ; Tropical Climate ; Mycobiome ; },
abstract = {Wood and wood-based materials are commonly used for storage, but their surfaces are prone to biodegradation by microorganisms, especially fungi. This study focuses on the microbial communities on pine wood storage boxes treated with an anti-termite and mold solution in a tropical region in Dong Nai, Vietnam. We isolated 13 fungal strains from these surfaces and classified them into six genera: Rhizopus, Aspergillus, Fusarium, Curvularia, Penicillium, and Trichoderma. Enzyme activity tests revealed that strains Curvularia eragrostidis TD4.2 and Aspergillus sydowii TD5 were the most effective producers of cellulase, amylase, and laccase. Shotgun metagenomics analysis of the biological sample of the discolored surface of pine storage boxes indicated that Ascomycota was the dominant phylum, with Dothideomycetes and Sordariomycetes as the prevalent class. Aureobasidium (0.33%) and Chaetomium (1.1%) were the most abundant genera in the Dothideomycetes and Sordariomycetes, respectively. This research illustrates the complexity of microbial communities on wood surfaces, providing insights into the fungal dynamics affecting wooden storage materials in tropical climates.},
}
@article {pmid39907343,
year = {2025},
author = {Alifia, L and Zulaika, E and Soeprijanto, S and Hamzah, A and Luqman, A},
title = {Microbial diversity and biotechnological potential of mangrove leaf litter in Kebun Raya Mangrove, Surabaya, Indonesia.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e288968},
doi = {10.1590/1519-6984.288968},
pmid = {39907343},
issn = {1678-4375},
mesh = {Indonesia ; *Plant Leaves/microbiology ; *Rhizophoraceae/microbiology ; *Avicennia/microbiology ; Biodiversity ; Bacteria/classification/genetics/isolation &amp; purification ; Wetlands ; },
abstract = {Mangrove ecosystems play a crucial role in maintaining ecological balance with leaf litter serving as an important substrate for diverse microbial communities. This study investigates the microbial communities inhabiting leaf litter from four different mangrove species: Rhizophora apiculata, Rhizophora stylosa, Sonneratia caseolaris, and Avicennia marina collected from Kebun Raya Mangrove, Surabaya, Indonesia. Using metagenomic sequencing, we revealed that Proteobacteria were predominant, followed by Chlorobi and Actinobacteria in the samples. Interestingly, we detected notable populations of anaerobic bacteria, including genus of Chlorobaculum and Allochromatium. Metagenomic analyses exhibited high levels of adaptation to stressors, evidenced by the prevalence of genes conferring resistance to antibiotics (e.g., beta-lactams, tetracyclines), heavy metals (e.g., chromium, arsenic), and hydrocarbons. Furthermore, the metagenomic analysis revealed the presence of genes involved in the biosynthesis of polyunsaturated fatty acids (PUFAs), antimicrobial compounds, and plant growth-promoting activities. These findings highlight the potential of mangrove leaf litter as a reservoir of beneficial microbes with diverse biotechnological applications, including bioremediation, nutraceuticals, pharmaceuticals, and agriculture.},
}
@article {pmid39907107,
year = {2025},
author = {Salamzade, R and Tran, PQ and Martin, C and Manson, AL and Gilmore, MS and Earl, AM and Anantharaman, K and Kalan, LR},
title = {zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.},
journal = {Nucleic acids research},
volume = {53},
number = {3},
pages = {},
pmid = {39907107},
issn = {1362-4962},
support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818//Broad Institute/ ; NIAID U19AI142720/NH/NIH HHS/United States ; },
mesh = {*Multigene Family ; *Evolution, Molecular ; Software ; Genomics/methods ; Viruses/genetics/classification ; Metagenome/genetics ; },
abstract = {Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to handle thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) performing population genetic investigations of BGCs for a fungal species, and (iii) uncovering evolutionary trends for a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.},
}
@article {pmid39906849,
year = {2025},
author = {Vinogradova, E and Jarmukhanov, Z and Nurgaziyev, M and Kossumov, A and Nurgozhina, A and Mukhanbetzhanov, N and Sergazy, S and Chulenabyeva, L and Issilbayeva, A and Askarova, S and Kaiyrlykyzy, A and Rakhimova, S and Kozhamkulov, U and Kairov, U and Khassenbekova, Z and Tarzhanova, D and Akilzhanova, A and Lee, JH and Terwilliger, J and Sailybayeva, A and Bekbossynova, M and Zhumadilov, Z and Kozhakhmetov, S and Kushugulova, A},
title = {Enterococcus dysbiosis as a mediator of vitamin D deficiency-associated memory impairments.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41969},
pmid = {39906849},
issn = {2405-8440},
abstract = {Low vitamin D status is linked to disturbance in cognitive performance. This study explored possible ways how composition and functional capacity of the gut microbiome affects vitamin D metabolism, directing serum vitamin D (VitD) levels and memory impairmets. It was found that gut microbiome composition, characterized by an increase in the relative abundance of Enterococcus and correlated with vitamin D deficiency and, as consequence, with memory impairments. A key mechanism identified in the study was the differential utilization of short-chain fatty acids (SCFAs) produced by gut bacteria as substrates for synthesizing vitamin D3 precursor in the skin. This finding confirms a complex interplay between the gut microbiome, host metabolism, and cognitive health, highlighting the potential significance of targeting Enterococcus dysbiosis in future preventive and therapeutic strategies to address VitD deficiency-related memory impairments. These results underscore the importance of understanding and modulating gut microbiome composition to optimize VitD status and cognitive function.},
}
@article {pmid39906540,
year = {2024},
author = {Jiang, N and Chen, Z and Ren, Y and Xie, S and Yao, Z and Jiang, D and Zhang, Y and Chen, L},
title = {How do various strategies for returning residues change microbiota modulation: potential implications for soil health.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1495682},
pmid = {39906540},
issn = {1664-302X},
abstract = {INTRODUCTION: Residue incorporation is a crucial aspect of anthropogenic land management practices in agricultural fields. However, the effects of various returning strategies on the soil microbiota, which play an essential vital role in maintaining soil health, remains largely unexplored.<br><br>METHODS: In a study conducted, different residue management strategies were implemented, involving the application of chemical fertilizers and residues that had undergone chopping (SD), composting (SC), and pyrolysis (BC) processes, with conventional fertilization serving as the control (CK).<br><br>RESULTS AND DISCUSSION: Using metagenomic sequencing, the analysis revealed that while all residue returning strategies had minimal effects on the diversity (both &#x3b1; and &#x3b2;) of microbiota, they did significantly alter microbial functional genes related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling, as well as the presence of antibiotic resistance genes (ARGs) and pathogens. Specifically, chopped residues were found to enhance microbial genes associated with C, N, P, and S cycling, while composted residues primarily stimulated C and S cycling. Furthermore, all residue treatments resulted in a disruption of relationships among nutrient cycles, with varying degrees of impact observed across the different management strategies, with the sequence of impact being SD&#x202f;<&#x202f;SC&#x202f;<&#x202f;BC. Moreover, the residue additions resulted in the accumulation of ARGs, while only SC caused an increase in certain pathogens. Finally, through analyzing the correlation network among indices that exhibited active responses to residue additions, potential indicators for functional changes in response to residue additions were identified. This study further offered recommendations for future cropland management practices aimed at enhancing soil health through microbiomes.},
}
@article {pmid39906303,
year = {2025},
author = {Takada, K and Holmes, EC},
title = {Genome sizes of animal RNA viruses reflect phylogenetic constraints.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf005},
pmid = {39906303},
issn = {2057-1577},
abstract = {Animal genomes are characterized by extensive variation in size. RNA viruses similarly exhibit substantial genomic diversity, with genome lengths ranging from 1.7 to ∼64 kb. Despite the myriad of novel viruses discovered by metagenomics, we know little of the factors that shape the evolution of the genome size in RNA viruses. We analyzed the variation in genome sizes across orders and families of animal RNA viruses. We found that RNA viruses can have highly variable genome sizes within and among orders, with the Nidovirales (including the Coronaviridae) exhibiting both significantly larger genomes and a greater range of genome sizes than other orders. In the Bunyavirales, Amarillovirales, Nidovirales, and Picornavirales, the genome sizes of invertebrate-associated RNA viruses were significantly larger than those that infect vertebrates, in contrast to their animal hosts in which vertebrates commonly have larger genomes than invertebrates. However, in the Mononegavirales, vertebrate viruses were significantly larger than those viruses associated with invertebrates. There were similarly complex associations between genome size and patterns of genome segmentation. In the Bunyavirales, Reovirales, and Nidovirales, viruses with segmented genomes, or that possessed a large number of segments, had significantly larger genome sizes than viruses with nonsegmented genomes or a small number of segments, while in Articulavirales, there were no significant differences in genome size among viruses possessing any number of genome segments. More broadly, our analysis revealed that taxonomic position (i.e. RNA virus order) had a greater impact on genome size than whether viruses infected vertebrates or invertebrates or their pattern of genome segmentation. Hence, the phylogenetic constraints on genome size are of sufficient magnitude to shape some other aspects of virus evolution.},
}
@article {pmid39906212,
year = {2024},
author = {Xi, Z and Chen, J and Wang, L and Lu, A},
title = {Characteristics of lower respiratory microbiota in children's refractory Mycoplasma pneumoniae pneumonia pre- and post-COVID-19 era.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1438777},
pmid = {39906212},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *COVID-19/immunology/microbiology ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia, Mycoplasma/microbiology ; Mycoplasma pneumoniae/genetics/isolation &amp; purification ; SARS-CoV-2 ; Infant ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial ; RNA, Ribosomal, 23S/genetics ; Respiratory System/microbiology/virology ; },
abstract = {INTRODUCTION: Little was known about the characteristics of low respiratory tract (LRT) microbiota of refractory M. pneumoniae pneumonia (RMPP) in children before and after the COVID-19 pandemic.<br><br>METHODS: Forty-two children diagnosed with RMPP in 2019 (Y2019 group) and 33 children diagnosed with RMPP in 2023 (Y2023 group), entered into the study. The characteristics of the clinical findings were examined, and the LRT microbiota was analyzed by metagenomic next generation sequencing.<br><br>RESULTS: The ratio of consolidate, atelectasis, lung necrosis, and erythema multiforme in Y2023 group was significantly higher than that in Y2019 (P<0.05). Mycoplasmoides pneumoniae was the top species of the LRT microbiota in both groups. The rate of macrolide resistance MP in Y2023 was significantly higher than that in Y2019 (P<0.05), and the mutant site was all 23S rRNA A2063G. There were no significant differences in &#x3b1;-diversity and &#x3b2;-diversity of LRT microbiota between Y2019 and Y2023 group. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers of LRT microbiota in children with RMPP of Y2023. The abundance of Mycoplasmoides pneumoniae positively correlated with the levels of D-dimer and LDH, negatively correlated with the counts of CD3[+] T cells, CD8[+] T cells, CD19[+] B cells and CD16[+]CD56[+] NK cells.<br><br>DISCUSSION: Our study showed that high abundance of MP was correlated with the severity of RMPP and decrease of immune cells. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers in microbiota of LRT in children with RMPP post COVID-19 era.},
}
@article {pmid39906158,
year = {2025},
author = {Hunter, B and Cromwell, T and Shim, H},
title = {Nanopore sequencing of protozoa: Decoding biological information on a string of biochemical molecules into human-readable signals.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {440-450},
pmid = {39906158},
issn = {2001-0370},
abstract = {Biological information is encoded in a sequence of biochemical molecules such as nucleic acids and amino acids, and nanopore sequencing is a long-read sequencing technology capable of directly decoding these molecules into human-readable signals. The long reads from nanopore sequencing offer the advantage of obtaining contiguous information, which is particularly beneficial for decoding complex or repetitive regions in a genome. In this study, we investigated the efficacy of nanopore sequencing in decoding biological information from distinctive genomes in metagenomic samples, which pose significant challenges for traditional short-read sequencing technologies. Specifically, we sequenced blood and fecal samples from mice infected with Trypanosoma brucei, a unicellular protozoan known for its hypervariable and dynamic regions that help it evade host immunity. Such characteristics are also prevalent in other host-dependent parasites, such as bacteriophages. The taxonomic classification results showed a high proportion of nanopore reads identified as T. brucei in the infected blood samples, with no significant identification in the control blood samples and fecal samples. Furthermore, metagenomic de novo assembly of these nanopore reads yielded contigs that mapped to the reference genome of T. brucei in the infected blood samples with over 96 % accuracy. This exploratory work demonstrates the potential of nanopore sequencing for the challenging task of classifying and assembling hypervariable and dynamic genomes from metagenomic samples.},
}
@article {pmid39906131,
year = {2025},
author = {Babalola, OO and Enagbonma, BJ},
title = {Dataset of shotgun metagenomic evaluation of Sorghum bicolor rhizosphere microbiome in soils preceded by Glycine max.},
journal = {Data in brief},
volume = {58},
number = {},
pages = {111270},
pmid = {39906131},
issn = {2352-3409},
abstract = {The dataset presents the microbial diversity, community structure, and functional potential of the rhizosphere microbiome associated with Sorghum bicolor in response to crop rotation involving a Glycine max precursor. Soil samples were collected from the rhizospheres of two Sorghum bicolor cultivars, Avenger and NS55, cultivated in soils previously used for Glycine max and cultivated in soils that have not previously been used for Glycine max cultivation, as follows: i) Sorghum bicolor Avenger (SA1, SA2, and SA3) cultivated in soils previously used for Glycine max, ii) Sorghum bicolor NS55 (SN1, SN2, and SN3) grown in soils that had been cultivated with Glycine max, iii) Sorghum bicolor Avenger (RA1, RA2, and RA3) cultivated in soils not previously used for Glycine max, iv) Sorghum bicolor NS55 (RN1, RN2, and RN3) grown in soils not previously cultivated with Glycine max. Thereafter, the shotgun sequencing was done to assess the microbial composition and functional genes from the extracted DNA. The effective metagenome after QC of the twelve samples include SA1 (99.72%), SA2 (99.50%), SA3 (99.68%), SN1 (99.75%), SN2 (99.76%), SN3 (99.70%), RA1 (99.72%), RA2 (99.77%), RN3 (99.72%), RN1 (99.67%), RN2 (99.68%), and RN3 (99.54%). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA1166458 (SA1, SA2, and SA3), PRJNA1166463 (SN1, SN2, and SN3), PRJNA1166623 (RA1, RA2, and RA3), PRJNA1166627 (RN1, RN2 and RN3). Actinomycetota and Function unknown dominated the microbiomes across all cropping systems. The insights gained from this dataset hold promise for advancing sustainable agricultural practices, particularly through optimizing crop rotations, developing microbial bioinoculants, and enhancing soil health. Furthermore, the functional data and the function unknown from this dataset could enrich our understanding of microbial roles in nutrient cycling, plant growth promotion, and stress mitigation, which are critical for addressing challenges in food security and environmental sustainability.},
}
@article {pmid39906066,
year = {2025},
author = {Zhang, J and Jiao, Y and Liu, K and Situ, W and Menghe, B and Chen, Y and Zha, M},
title = {Characterizing microbial diversity and metabolic pathways in yak milk and fermented yak milk based on metagenomics: A study from Ganzi Tibetan autonomous prefecture.},
journal = {Food chemistry: X},
volume = {25},
number = {},
pages = {102198},
pmid = {39906066},
issn = {2590-1575},
abstract = {Kangding and Litang are the capital and pivotal county respectively within Ganzi. The region's distinctive geographical and climatic environment has endowed yak milk (YM) and its products with unique microbial resources, which play a crucial role in product quality and flavor. Therefore, it is important to understand their microbiota. We analyzed microbiota and metabolic pathways in YM. Results revealed 207 species, with Pseudomonas unclassified, Acinetobacter johnsonii dominant in YM, and Lactobacillus delbrueckii, Streptococcus thermophilus in fermented yak milk (FYM). YM exhibited lower microbial and bacteriophage diversity. Bacteriophage diversity was primarily targeting harmful microbes. Yak and camel milk showed similarities, while koumiss and fermented camel milk shared dominant bacteria. Metabolic pathways in YM were enriched with carbohydrates, amino acids, fats, and purine metabolism. In conclusion, this study provides information on the microbial resources and related metabolic pathways in yak milk and naturally fermented yak milk in the Ganzi region of China.},
}
@article {pmid39905573,
year = {2025},
author = {Armstrong, E and Liu, R and Pollock, J and Huibner, S and Udayakumar, S and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Yegorov, S and Kimani, J and Beattie, T and Coburn, B and Kaul, R},
title = {Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {39},
pmid = {39905573},
issn = {2049-2618},
support = {Canada Graduate Scholarship/CAPMC/CIHR/Canada ; Vanier Canada Graduate Scholarship/CAPMC/CIHR/Canada ; PJT-180629/CAPMC/CIHR/Canada ; MR/R023182/1//Medical Research Council and the UK Foreign, Commonwealth and Development Office/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *Vaginosis, Bacterial/microbiology/immunology ; Kenya ; *Microbiota ; Adult ; *Sex Workers ; *Bacterial Load ; Bacteria/classification/genetics/isolation &amp; purification ; Young Adult ; Interleukin-1alpha/metabolism ; Cytokines/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Lactobacillus/isolation &amp; purification ; },
abstract = {BACKGROUND: The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.<br><br>RESULTS: We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1&#x3b1;, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.<br><br>CONCLUSIONS: Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.},
}
@article {pmid39905490,
year = {2025},
author = {Molina-Pardines, C and Haro-Moreno, JM and Rodriguez-Valera, F and López-Pérez, M},
title = {Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {41},
pmid = {39905490},
issn = {2049-2618},
support = {PRE2021-098122//Ministerio de Econom&#xed;a y Competitividad/ ; PID2020-118052GB-I00//Ministerio de Econom&#xed;a y Competitividad/ ; 2021/PER/00020//Ministerio de Universidades/ ; },
mesh = {*Metagenomics/methods ; Mediterranean Sea ; *Genetic Variation ; Microbiota/genetics ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/microbiology ; },
abstract = {BACKGROUND: The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.<br><br>RESULTS: The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~&#x2009;81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was&#xa0;located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).<br><br>CONCLUSIONS: This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn,&#xa0;mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.},
}
@article {pmid39905469,
year = {2025},
author = {Li, S and Zhan, Y and Wang, Y and Li, W and Wang, X and Wang, H and Sun, W and Cao, X and Li, Z and Ye, F},
title = {One-step diagnosis of infection and lung cancer using metagenomic sequencing.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {48},
pmid = {39905469},
issn = {1465-993X},
support = {No. 2021YFC2301101//National Key Research and Development Program/ ; No. 82100118//Youth fund of National Natural Science Foundation of China/ ; 92048203//National Natural Science Foundation of China/ ; No. 2022SKLID308//the Science Foundation for the State Key Laboratory for Infectious Disease Prevention and Control of China/ ; },
mesh = {Humans ; *Lung Neoplasms/genetics/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Respiratory Tract Infections/diagnosis/microbiology/genetics ; Adult ; },
abstract = {BACKGROUND: Traditional detection methods face challenges in meeting the diverse clinical needs for diagnosing both lung cancer and infections within a single test. Onco-mNGS has emerged as a promising solution capable of accurately identifying infectious pathogens and tumors simultaneously. However, critical evidence is still lacking regarding its diagnostic performance in distinguishing between pulmonary infections, tumors, and non-infectious, non-tumor conditions in real clinical settings.<br><br>METHODS: In this study, data were gathered from 223 participants presenting symptoms of lung infection or tumor who underwent Onco-mNGS testing. Patients were categorized into four groups based on clinical diagnoses: infection, tumor, tumor with infection, and non-infection-non-tumor. Comparisons were made across different groups, subtypes, and stages of lung cancer regarding copy number variation (CNV) patterns, microbiome compositions, and clinical detection indices.<br><br>RESULTS: Compared to conventional infection testing methods, Onco-mNGS demonstrates superior infection detection performance, boasting a sensitivity of 81.82%, specificity of 72.55%, and an overall accuracy of 77.58%. In lung cancer diagnosis, Onco-mNGS showcases excellent diagnostic capabilities with sensitivity, specificity, accuracy, positive predictive value, and negative predictive value reaching 88.46%, 100%, 91.41%, 100%, and 90.98%, respectively. In bronchoalveolar lavage fluid (BALF) samples, these values stand at 87.5%, 100%, 94.74%, 100%, and 91.67%, respectively. Notably, more abundant CNV mutation types and higher mutation rates were observed in adenocarcinoma (ADC) compared to squamous cell carcinoma (SCC). Concurrently, onco-mNGS data revealed specific enrichment of Capnocytophaga sputigeria in the ADC group and Candida parapsilosis in the SCC group. These species exhibited significant correlations with C reaction protein (CRP) and CA153 values. Furthermore, Haemophilus influenzae was enriched in the early-stage SCC group and significantly associated with CRP values.<br><br>CONCLUSIONS: Onco-mNGS has exhibited exceptional efficiencies in the detection and differentiation of infection and lung cancer. This study provides a novel technological option for achieving single-step precise and swift detection of lung cancer.},
}
@article {pmid39905327,
year = {2025},
author = {Wei, M and Gu, K and Qin, J and Lu, X and Feng, J and Mao, S and Li, M and Li, Z and Wang, C},
title = {Complex and severe infection in a 67-year-old liver transplant recipient due to Cunninghamella elegans, Bordetella bronchiseptica, and Pneumocystis jirovecii.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {164},
pmid = {39905327},
issn = {1471-2334},
support = {23YF1431300//the Yangfan Project of Science and Technology Commission of Shanghai Municipality/ ; GWVI-11.1-11//3-Year Action Plan for Strengthening Public Health System in Shanghai/ ; PW2021D-09//Pudong New Area Joint Project/ ; },
mesh = {Aged ; *Bordetella bronchiseptica/isolation &amp; purification/genetics ; Male ; Humans ; *Cunninghamella/isolation &amp; purification ; *Bordetella Infections/microbiology/diagnosis/drug therapy ; *Coinfection/microbiology ; *Pneumocystis carinii/isolation &amp; purification/genetics ; Mucormycosis/microbiology/drug therapy/diagnosis ; Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology ; Pneumonia, Pneumocystis/microbiology/drug therapy/diagnosis ; },
abstract = {INTRODUCTION: Cunninghamella elegans infections cause rare and severe mucormycosis. Bordetella bronchiseptica and Pneumocystis jirovecii relate to pneumonia. They are all clinically uncommon pathogens and no reports of co-infections have been reported.<br><br>CASE PRESENTATION: Here we present a case of a 67-year-old male patient who initially presented with fever, chills, and mild cough. B. bronchiseptica, P. jirovecii, Aspergillus fumigatus, and human alphaherpesvirus 1 (HSV1) were detected by clinical metagenomic next-generation sequencing (mNGS) of his bronchoalveolar lavage fluid (BLAF). Despite receiving anti-infective treatment, the patient rapidly developed respiratory failure and was transferred to the intensive care unit. Subsequent mNGS testing further revealed the presence of C. elegans, indicating that different pathogens played dominant roles at various stages of the disease progression. The routine culture also identified several of the above pathogens, but the results were reported much later than those of mNGS. Eventually, imaging findings and symptoms of the patient improved with comprehensive antibiotic coverage, and he was transferred to a lower-level hospital for rehabilitation treatment.<br><br>CONCLUSIONS: This is the first detailed report of the combined infection of B. bronchiseptica, P. jirovecii, and C. elegans. During the treatment process, we also observed rare and unusual neurological side effects: visual and auditory hallucinations, restlessness, and aphasia. Also, the case indicates that traditional methods are insufficient for the etiological diagnosis needs of critical and severe patient populations, and timely use of mNGS should be recommended.},
}
@article {pmid39905038,
year = {2025},
author = {Qu, Q and Dou, Q and Xiang, Z and Yu, B and Chen, L and Fan, Z and Zhao, X and Yang, S and Zeng, P},
title = {Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {24},
pmid = {39905038},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; Humans ; China ; *Metabolic Diseases/microbiology/etiology ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Diet ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Life Style ; Socioeconomic Factors ; },
abstract = {Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.},
}
@article {pmid39904998,
year = {2025},
author = {Boulton, W and Salamov, A and Grigoriev, IV and Calhoun, S and LaButti, K and Riley, R and Barry, K and Fong, AA and Hoppe, CJM and Metfies, K and Oetjen, K and Eggers, SL and Müller, O and Gardner, J and Granskog, MA and Torstensson, A and Oggier, M and Larsen, A and Bratbak, G and Toseland, A and Leggett, RM and Moulton, V and Mock, T},
title = {Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {204},
pmid = {39904998},
issn = {2052-4463},
mesh = {Arctic Regions ; *Metagenome ; Oceans and Seas ; Expeditions ; Ecosystem ; Ice Cover/microbiology ; },
abstract = {The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.},
}
@article {pmid39904149,
year = {2025},
author = {Lang, G and Ye, W and Chen, G and Zhu, T and Li, X and Chen, J and Miao, X and Su, F and Xu, L},
title = {Emerging and stirring Amoebic liver abscess in HIV seropositive men who have sex with men in South-Eastern China.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {3},
pages = {116696},
doi = {10.1016/j.diagmicrobio.2025.116696},
pmid = {39904149},
issn = {1879-0070},
abstract = {Amebic liver abscess (ALA) is rare in Chinese population due to dietary habit. Nine Chinese HIV-seropositive men who have sex with men (MSM) with occurrence of amebic liver abscess (ALA) was retrospectively studied. Six participants had concurrent HIV/Syphilis and two had HIV/HCV. Symptoms primarily included fever, abdominal discomfort, and diarrhea. All participants showed intrahepatic abscesses, mainly in liver segments 6, 7, and 8, while two had additional extrahepatic amebic abscesses. Those with CD4 count < 100 cells/μL exhibited multiple and larger liver abscesses. Metagenomic Next-Generation Sequencing (mNGS) conclusively revealed Entamoeba histolytica despite bacterial culture and smear tests' negative results. All affected individuals were treated with percutaneous catheter drainage and metronidazole for at least 10 days. In summary, HIV-positive MSM are prone to develop ALA, and CD4 count < 100 cells/μL is a risk for occurrence of multiple and larger ALA. The optimal ALA treatment course for ALA remains dabatable.},
}
@article {pmid39904008,
year = {2025},
author = {Bohra, V and Lai, KK and Lam, KL and Tam, NF and Jing-Liang, S and Lee, FW},
title = {Metagenomic surveillance reveals different structure and function of microbial community associated with mangrove pneumatophores and their surrounding matrices.},
journal = {Marine pollution bulletin},
volume = {213},
number = {},
pages = {117614},
doi = {10.1016/j.marpolbul.2025.117614},
pmid = {39904008},
issn = {1879-3363},
abstract = {Present research employed metagenomics to explore the structural and functional diversity of microorganisms in two matrices of pneumatophore: adhered sediments (PS) and epiphytes (PE) of Avicennia marina. These were compared with microorganisms in surrounding environments: tidal water (TW), mudflat sediment (MF) and mangrove sediment (MS). Results revealed that bacteria made up over 95 % of the microbial community across all five matrices, with the dominance of phylum Proteobacteria, because of their metabolic flexibility and ability to survive in harsh mangrove environment. The bacterial community in PS and PE were similar to TW but differed from those in MF and MS, implying their provenance from TW. The high relative abundance of genes involved in nitrate and sulfur reduction pathways in PS and PE indicates pneumatophore bacteria helps in enhancing nitrogen and sulfur availability. This study is the first to explore the functional significance of pneumatophore-adhered prokaryotic communities using metagenomics.},
}
@article {pmid39903999,
year = {2025},
author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A},
title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128084},
doi = {10.1016/j.micres.2025.128084},
pmid = {39903999},
issn = {1618-0623},
abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.},
}
@article {pmid39903699,
year = {2025},
author = {Roothans, N and van Loosdrecht, MCM and Laureni, M},
title = {Metabolic labour division trade-offs in denitrifying microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf020},
pmid = {39903699},
issn = {1751-7370},
abstract = {Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification - the stepwise reduction of nitrate and nitrite to nitrogenous gases - is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.},
}
@article {pmid39903340,
year = {2025},
author = {Yan, Z and Zheng, Z and Cao, L and Zhu, Z and Zhou, C and Sun, Q and Tang, B and Zhao, G},
title = {Altered gut microbiome and serum metabolome profiles associated with essential tremor.},
journal = {Metabolic brain disease},
volume = {40},
number = {2},
pages = {118},
pmid = {39903340},
issn = {1573-7365},
support = {U20A20355//National Natural Science Foundation of China/ ; WKJ-ZJ-ZZ08//Major Health Science and Technology Program of Zhejiang Province/ ; LZ23H090004//Key Projects of Zhejiang Provincial Natural Science Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *Essential Tremor/blood/microbiology ; Male ; Female ; Middle Aged ; Aged ; Dysbiosis/blood ; Lipid Metabolism/physiology ; },
abstract = {The genetic predisposition and environmental factors both trigger the complex neurological dyskinesia of essential tremor (ET). Gut dysbiosis may facilitate the occurrence and development of neurological diseases. Therefore, it is worth exploring the inner connections between gut microbiota and ET. First, the gut microbiota of 19 ET patients and 21 healthy controls (HCs) were analysed with metagenomics approach. Second, the potential linkages between gut microbiome and serum metabolome profiles were explored by integrative analysis. The gut microbiota disorders were present in ET patients. The LEfSe method showed a significant decrease in Bacteroides. The functional analysis revealed that there were differences in gut microbial apoptosis, retinol metabolism, and steroid hormone biosynthesis pathways. The levels of various lipids and lipid-like molecules alter in serum of ET patients, which correlated with altered gut microbial abundance, indicating the alterations in lipid metabolism involved in apoptosis pathway in ET. All of these data point to the gut dysbiosis in ET, and some changed gut microbial species were linked to abnormalities in blood lipid metabolism, which open up new avenues for investigation into the pathophysiology of ET.},
}
@article {pmid39902982,
year = {2025},
author = {Zhao, M and Shi, Y and Zhang, C and Lu, M and Shen, M and Xie, L and Wang, L and Lu, A},
title = {Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0108724},
doi = {10.1128/spectrum.01087-24},
pmid = {39902982},
issn = {2165-0497},
abstract = {UNLABELLED: Pneumonia is the leading cause of morbidity and mortality in children and needs rapid and accurate pathogenic diagnosis. The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMTs) for pathogen detection in children with severe or refractory pneumonia. In this retrospective study, the clinical data of 127 children with severe or refractory pneumonia admitted to the respiratory department from June 2021 to March 2022 were analyzed. BALF mNGS and CMTs were utilized for pathogen diagnosis and comparison of their detection performance for different pathogens. The pathogenic diagnosis rate was 95.28% (121/127) by combining mNGS and CMTs. mNGS had significantly higher overall (96.06% vs 72.44%, P < 0.001), bacterial (69.29% vs 12.60%, P < 0.001), and fungal (11.81% vs 3.15%, P = 0.009) detection rates than CMTs. However, there was no significant difference of detection rates between them for respiratory viruses (33.86% vs 33.75%, P = 0.99) and Mycoplasma pneumoniae (48.03% vs 45.67%, P = 0.71). The sensitivities of mNGS for total pathogens, bacteria, and fungi were 99.17%, 100%, and 87.50%, respectively, which were higher than those of CMTs. CMTs for M. pneumoniae had the highest sensitivity (91.23%) compared with mNGS (89.47%) and multiplex PCR (88.57%). For respiratory viruses, mNGS and mPCR had similar sensitivities (97.67% vs 96.43%). mNGS was superior to CMTs in bacterial and fungal detection, while it was comparable to multiplex PCR for the detection of M. pneumoniae and respiratory viruses. Different detection methods should be rationalized for different pathogens.<br><br>IMPORTANCE: This study on 127 patients with severe and refractory pneumonia showed that mNGS was significantly superior to CMTs in terms of bacterial and fungal detection. We also found that multiplex PCR assay was comparable to mNGS for the detection of Mycoplasma pneumoniae and respiratory viruses and may have greater application advantages in combination with CMTs, such as M. pneumoniae IgM. For severe and refractory pneumonia, or when empiric treatment is not effective, collecting BALF for mNGS can help to quickly identify the causative organisms at an early stage. It is also important to choose more appropriate methods or combinations for different pathogens.},
}
@article {pmid39902954,
year = {2025},
author = {Tran, L and Lansing, L and Cunningham, M and Ho, J and Deckers, T and Newman, T and Wu, L and Gregoris, AS and Zorz, J and Muntz, L and Lee, K and Trépanier-Leroux, D and Conflitti, IM and Pepinelli, M and Walsh, EM and Morfin, N and Powell, JE and Moran, N and Hoover, SE and Pernal, SF and Currie, RW and Giovenazzo, P and Guzman-Novoa, E and Jabbari, H and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Gut microbiome metagenomic sequences of honey bees (Apis mellifera) exposed to crops.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0073124},
doi = {10.1128/mra.00731-24},
pmid = {39902954},
issn = {2576-098X},
abstract = {The gut microbiome of the European honey bee (Apis mellifera) is vital to its health, yet large-scale studies are scarce. We present metagenomic sequencing data from 180 samples collected near and far from eight crops across Canada over 2 years. These data sets will help address various biological and environmental questions.},
}
@article {pmid39902937,
year = {2025},
author = {Tian, C and Zhang, T and Zhuang, D and Luo, Y and Li, T and Zhao, F and Sang, J and Tang, Z and Jiang, P and Zhang, T and Liu, P and Zhu, L and Zhang, Z},
title = {Industrialization drives the gut microbiome and resistome of the Chinese populations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0137224},
doi = {10.1128/msystems.01372-24},
pmid = {39902937},
issn = {2379-5077},
abstract = {UNLABELLED: Industrialization has driven lifestyle changes in eastern and western Chinese populations, yet we have a poor understanding of the dynamic changes in their gut microbiome and resistome under industrialization, which is essential for the scientific management of public health. Here, this study employed metagenomics to analyze the gut microbiota of 1,382 healthy individuals from China, including 415 individuals from the eastern region of advanced industrialization and 967 individuals from the western region of developing industrialization. Compared with western populations, eastern populations show a significant increase in interindividual dissimilarity of microbial species composition and metabolic pathways but a significant decrease in intraindividual species and functional diversity. Furthermore, our results found significantly less abundance and richness of antibiotic resistance genes (ARGs) in the gut microbiota of eastern populations, alongside a lower prevalence of unique core ARG subtypes. For the 12 core ARG types shared between eastern and western populations, the mean relative abundance of two types was notably higher in the eastern populations, while eight core ARG types had significantly higher mean relative abundance in the western populations. Based on the reconstruction of metagenomic assembled genomes, we found that Escherichia coli genomes from western populations carried more virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to those from eastern populations. This large-scale study for the first time revealed industrialization potentially led to unexpected alterations of the gut microbiome and resistome between eastern and western populations that provide a vital implication for Chinese public health and may aid in the development of region-specific strategies for managing pathogenic infections.<br><br>IMPORTANCE: As China experiences rapid but uneven industrialization, understanding its effect on people's gut bacteria is critical for public health. This study reveals how industrialization may reshape the health risks related to gut bacteria and antibiotic resistance. This work provides crucial information to help create customized public health policies for different regions.},
}
@article {pmid39901928,
year = {2025},
author = {Demirci, M and Çubuk, C and Dasdemir, F and Saribas, AS and Balcıoglu, EB and Ozbey, D and Yorulmaz, D and Olmez Hanci, T and Basa, S and Kocazeybek, BS},
title = {Comparative microbial metagenomic analysis of drinking water plants and wastewater treatment plants in Istanbul.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1488268},
pmid = {39901928},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) and drinking-water treatment plants (DWTPs) are critical for public health due to the potential risks posed by microorganisms that may persist after treatment. The aim of this study was to detect the microbiome profiles of waters from both DWTPs and WWTPs under the Istanbul Water and Sewerage Administration (ISKI), identify the antimicrobial resistance profiles in all these facilities, and observe the differences in the microbiome between the inlet and outlet of different WWTPs.<br><br>METHODS: A total of 52 samples were examined, comprising 18 samples from DWTPs and 34 samples from WWTPs. All water samples underwent pre-isolation filtration. DNA isolation was conducted using filter material, followed by sequencing on a NovaSeq 6000 instrument. Kraken2 tools and R scripts were used for statistical analysis and data visualization.<br><br>RESULTS: The microbial metagenomic analysis identified 71 phyla, 113 classes, 217 orders, 480 families, and 1,282 genera across all samples. There were unclassified microbes (53.14% vs. 58.75%), Eukaryota (3.64% vs. 3.5%), Archaea (0.08% vs. 0.03%), bacteria (42% vs. 36.25%), and viruses (0.02% vs. 0.04%) in the raw water and ozonation unit outlet of DWTPs. The inlet and outlet of WWTPs showed unclassified microbes (52.68% vs. 59.62%), Eukaryota (0.6% vs. 1.72%), Archaea (0.26% vs. 0.15%), bacteria (46.43% vs. 38.43%), and viruses (0.05% vs. 0.04%). No statistically significant results were found in the analysis of raw waters collected from DWTPs and samples taken from the ozonation unit outlet-from the phylum level to the genus level (p&#x202f;>&#x202f;0.05). The inlet and outlet points of WWTPs showed no statistically significant results from the phylum to species levels (p&#x202f;>&#x202f;0.05). The most detected genera were Desulfobacter (4.82%) in preliminary WWTPs, Thauera (1.93%) in biological WWTPs, Pseudomonas (1.44%) in advanced biological WWTPs, Acidovorax (1.85%) in biological package WWTPs, and Pseudomonas (11.55%) in plant-based WWTPs. No antimicrobial resistance gene markers were detected in water samples from raw water inlets and ozonation unit outlets from DWTPs, membrane wastewater recovery plants, or ultraviolet (UV) recycling facilities. The ANT(3&#x2033;), Erm, and Sul resistance gene markers were detected in all raw WWTPs samples.<br><br>DISCUSSION: There were no significant microbial risk differentiation between biological WWTPs and advanced biological WWTPs. The data could serve as preliminary information for future research. More extensive studies are needed, with multiple sample tracking in these facilities and their feeding basins.},
}
@article {pmid39901264,
year = {2025},
author = {Liu, C and Song, X and Liu, J and Zong, L and Xu, T and Han, X and Li, F and Li, B and Zhu, H and Shi, D},
title = {Consistency between metagenomic next-generation sequencing versus traditional microbiological tests for infective disease: systemic review and meta-analysis.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {55},
pmid = {39901264},
issn = {1466-609X},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sepsis/diagnosis/microbiology ; },
abstract = {BACKGROUND: Pathogen identification is essential in sepsis and septic shock. Metagenomic next-generation sequencing (mNGS) is a novel pathogen detection method with several advantages over traditional tests. However, the consistency between mNGS and traditional pathogen tests requires further investigation.<br><br>OBJECTIVES: We aimed to assess the consistency between mNGS and traditional pathogen tests and to identify the factors influencing this consistency.<br><br>METHODS: This systematic review and meta-analysis involved a comprehensive search of mNGS and traditional pathogen tests in PubMed, Embase, Scopus, Web of Science, and the Cochrane Library. Data from included studies were extracted, and kappa consistency between mNGS and traditional tests was calculated. Study quality was evaluated using the QUADAS-2 tool.<br><br>RESULTS: The search identified 415 studies, of which 27 were included in the analysis, involving 4112 individuals. Meta-analysis showed a pooled consistency of 0.319&#x2009;&#xb1;&#x2009;0.013 (p&#x2009;<&#x2009;0.001), indicating a moderate relationship. In terms of sample type, cerebrospinal fluid showed the highest pooled kappa consistency at 0.500&#x2009;&#xb1;&#x2009;0.029 (p&#x2009;<&#x2009;0.001). Immunocompromised patients had a lower pooled kappa consistency of 0.294&#x2009;&#xb1;&#x2009;0.014 (p&#x2009;<&#x2009;0.001) compared to 0.321&#x2009;&#xb1;&#x2009;0.028 (p&#x2009;<&#x2009;0.001) in immunocompetent patients. Positive percent agreement of mNGS was 83.63% over traditional microbiological test, and negative percent agreement was 54.59%.<br><br>CONCLUSION: This review demonstrates a moderate relationship between mNGS and traditional pathogen tests, indicating a complex relationship between these two methods. Sterile samples show higher consistency than non-sterile samples. Immune function deficiency may reduce the consistency between mNGS and traditional tests. Further research is needed on the use of mNGS in sepsis and septic shock.},
}
@article {pmid39901058,
year = {2025},
author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {527-540},
pmid = {39901058},
issn = {2058-5276},
support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.},
}
@article {pmid39900940,
year = {2025},
author = {Prabhaharan, D and Go, YW and Kim, H and Kang, S and Sang, BI},
title = {Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {198},
pmid = {39900940},
issn = {2052-4463},
support = {MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; },
mesh = {Republic of Korea ; *Biofuels ; *Metagenome ; *Bioreactors ; Microbiota ; Anaerobiosis ; },
abstract = {Biogas production through the anaerobic digestion (AD) of organic waste plays a crucial role in promoting sustainability and closing the carbon cycle. Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. However, substantial knowledge gaps persist, particularly in understanding the specific microbial communities involved in biogas production in countries such as South Korea. The present dataset addresses one of these gaps by providing comprehensive information on the metagenomes of five full-scale mesophilic biogas reactors in South Korea. From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. Of these, 187 MAGs (46.7%) were classified as high-quality based on Minimum Information about Metagenome-Assembled Genome (MIMAG) standards. The data presented here contribute to a broader understanding of biogas-specific microbial communities and offers a significant resource for future studies and advancements in sustainable biogas production.},
}
@article {pmid39900713,
year = {2025},
author = {Zhang, L and Zheng, C and Sun, Y and Chen, X and Wang, Y and Xiang, H and Liang, Y and Wei, F and Zhang, Y},
title = {Diagnostic tests performance in detecting Pneumocystis jirovecii: A systematic review and meta-analysis.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39900713},
issn = {1435-4373},
support = {BRWEP2024W042180101//Beijing Research Ward Excellence Program, BRWEP/ ; },
abstract = {BACKGROUND AND OBJECTIVE: Pneumocystis jirovecii (Pj) pneumonia (PJP) is a life-threatening opportunistic infection primarily affecting immunocompromised individuals. Detecting Pj is challenging, particularly in distinguishing between Pj colonization (PJC) and infection. We aimed to systematically evaluate the diagnostic accuracy of various tests in differentiating Pj colonization from infection.<br><br>METHODS: Systematic reviews and meta-analyses were performed. Searches were conducted in PubMed, Embase, and Web of Science. Original clinical studies reporting sensitivity and specificity data for diagnostic tests such as quantitative polymerase chain reaction (qPCR), nested PCR, (1,3)-Beta-D glucan (BDG), metagenomic next-generation sequencing (mNGS), and digital PCR (ddPCR) to differentiate PJC from PJP were included. Quality assessment was performed using QUADAS-2 tool, and data processing followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Diagnostic performance was evaluated using either a random-effects or fixed-effects model.<br><br>RESULTS: Twenty-eight studies (2,550 patients, 1,445 with PJP) were included, with moderate methodological quality. The pooled sensitivity of these diagnostic tests was 0.80 (95% CI 0.77-0.82) and specificity was 0.83 (95% CI 0.81-0.85), with a diagnostic odds ratio (DOR) of 23.12. Among the individual tests, BDG (5 studies) showed high pooled sensitivity (0.83, 95% CI 0.77-0.88) but lower specificity (0.78, 95% CI 0.69-0.85). mNGS (3 studies) had the highest performance, with pooled sensitivity and specificity both at 0.87 (95% CI 0.80-0.92 and 95% CI 0.77-0.94, respectively), and the highest DOR of 41.57. qPCR (19 studies) demonstrated adequate pooled sensitivity (0.78, 95% CI 0.76-0.81) and high specificity (0.83, 95% CI 0.81-0.86), with a DOR of 20.44.<br><br>CONCLUSION: While BDG has low specificity and mNGS is costly with no standardized interpretation, along with the limited number of relevant studies in BDG and mNGS, this meta-analysis concluded that qPCR remains valuable for distinguishing P. jirovecii infection from colonization. A well-designed randomized clinical trial that standardizes the technical aspects of the qPCR protocol is needed to assess its effectiveness and provide a solid basis for clinical diagnosis.},
}
@article {pmid39900569,
year = {2025},
author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M},
title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1326},
pmid = {39900569},
issn = {2041-1723},
mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; },
abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.},
}
@article {pmid39900484,
year = {2025},
author = {Van Etten, J and Stephens, TG and Bhattacharya, D},
title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70048},
pmid = {39900484},
issn = {1462-2920},
support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.},
}
@article {pmid39900123,
year = {2025},
author = {Soto-Rodriguez, SA and Quiroz-Guzman, E and Gomez-Gil, B and Lozano-Olvera, R and Aguilar-Rendon, KG and Serrano-Hernández, JM and González-Gómez, JP and Chaidez, C},
title = {Phage cocktail against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei: Genomic, biological, and pathological characterization.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107354},
doi = {10.1016/j.micpath.2025.107354},
pmid = {39900123},
issn = {1096-1208},
abstract = {Phages vB_Pd_PDCC-1, vB_Vc_SrVc9, and vB_Vp_PvVp11 were found to be lytic against Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (AHPND) and other pathogenic vibrios. The complete genomic and biological characterization of phage vB_Vp_PvVp1 was conducted, and a cocktail of these three phages was applied to juvenile Penaeus vannamei infected with V. parahaemolyticus AHPND. Water samples collected during the challenges were analyzed using metagenomics. At the end of the experimental infection, the phage cocktail did not improve shrimp survival compared to the positive control group (infected only with bacteria). This suggests the emergence of phage-resistant V. parahaemolyticus strains. However, a significantly lower mortality rate was observed 12 h post-infection, along with a shortening of the disease course in the phage therapy treatment. A phage-resistant strain of V. parahaemolyticus AHPND was in vitro isolated. For the first time, we report the identification of nucleotide variants in the glycosyltransferase gene of this mutant strain through genome sequencing. Although the phage cocktail was ineffective in controlling AHPND, some protective benefits of phage therapy were noted in P. vannamei during the acute phase-the most critical stage-compared to the positive control. Phage therapy decreased alpha diversity and altered the microbiota composition during the challenge, increasing V. parahaemolyticus. The Vibrio AHPND pathogen produces a potent PirAB toxin, making this disease difficult to manage. Further studies are needed to explore synergistic approaches as effective therapeutic tools.},
}
@article {pmid39899931,
year = {2025},
author = {Wang, Y and Chen, C and Zhou, B and Zhang, Y and Qin, J and Huang, J and Li, X},
title = {Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137435},
doi = {10.1016/j.jhazmat.2025.137435},
pmid = {39899931},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.},
}
@article {pmid39899597,
year = {2024},
author = {Tibiri, EB and Boua, PR and Soulama, I and Dubreuil-Tranchant, C and Tando, N and Tollenaere, C and Brugidou, C and Nanema, RK and Tiendrebeogo, F},
title = {Challenges and opportunities of developing bioinformatics platforms in Africa: the case of BurkinaBioinfo at Joseph Ki-Zerbo University, Burkina Faso.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39899597},
issn = {1477-4054},
support = {2012PASS019//Green Revolution in Africa/ ; },
mesh = {Burkina Faso ; *Computational Biology/methods/education ; Universities ; Humans ; },
abstract = {Bioinformatics, an interdisciplinary field combining biology and computer science, enables meaningful information to be extracted from complex biological data. The exponential growth of biological data, driven by high-throughput omics technologies and advanced sequencing methods, requires robust computational resources. Worldwide, bioinformatics skills and computational clusters are essential for managing and analysing large-scale biological datasets across health, agriculture, and environmental science, which are crucial for the African continent. In Burkina Faso, the establishment of bioinformatics infrastructure has been a gradual process. Initial training initiatives between 2015-2016, including bioinformatics courses and the establishment of the BurkinaBioinfo (BBi) platform, marked significant progress. Over 250 scientists have been trained at diverse levels in bioinformatics, 105 user accounts have been created for high-performance computing access. Operational since 2019, this platform has significantly facilitated training programs for scientists and system administrators in west Africa, covering data production, introductory bioinformatics, phylogenetic analysis, and metagenomics. Financial and technical support from various sources has facilitated the rapid development of the platform to meet the growing need for bioinformatics analysis, particularly in conjunction with local 'wet labs'. Establishing a bioinformatics cluster in Burkina Faso involved identifying the needs of researchers, selecting appropriate hardware and installing the necessary bioinformatics tools. At present, the main challenges for the BBi platform include ongoing staff training in bioinformatics skills and high-level IT infrastructure management in the face of growing infrastructure demands. Despite these challenges, the establishment of a bioinformatics platform in Burkina Faso offers significant opportunities for scientific research and economic development in the country.},
}
@article {pmid39898908,
year = {2025},
author = {Navia, JC and Alfonso, A and Miller, D and Maestre-Mesa, J and Durkee, H and Sepulveda-Beltran, PA and Echeverri-Tribin, F and Merikansky, S and Martinez, JD and Flynn, HW and Alfonso, EC and Parel, JM and Amescua, G},
title = {Prevalence of HSV Genomic Signatures Among Acanthamoeba Hosts and Contaminated Lens Cases: A Molecular and Clinical Study.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {66},
number = {2},
pages = {4},
pmid = {39898908},
issn = {1552-5783},
support = {P30 EY014801/EY/NEI NIH HHS/United States ; },
mesh = {Humans ; Male ; *Acanthamoeba/genetics/isolation &amp; purification ; Female ; Adult ; *Acanthamoeba Keratitis/epidemiology/diagnosis/parasitology ; Prevalence ; Middle Aged ; DNA, Viral/genetics/analysis ; Young Adult ; Polymerase Chain Reaction ; Genome, Viral/genetics ; Contact Lenses/parasitology ; Keratitis, Herpetic/epidemiology/virology/diagnosis ; Adolescent ; Herpesvirus 1, Human/genetics/isolation &amp; purification ; Visual Acuity ; Metagenomics ; Simplexvirus/genetics ; Aged ; },
abstract = {PURPOSE: To document the presence of herpes simplex virus (HSV) genomic signatures among Acanthamoeba hosts recovered from patients with Acanthamoeba keratitis (AK) and in contaminated lens cases.<br><br>METHODS: We used a combination of PCR sequencing and shotgun metagenomics to detect and confirm the presence of HSV genomic signatures in Acanthamoeba hosts and lens cases. Clinical outcomes were correlated with the prevalence of host HSV signatures.<br><br>RESULTS: HSV genomic signatures were detected in 26% (n = 6) of Acanthamoeba hosts recovered from patients with culture confirmed AK. HSV-1 and HSV-2 or both were identified in 33%, 50%, and 17% of isolates, respectively. Fifty-two percent of patients (12/23) were misdiagnosed initially as presenting with HSV keratitis. Patients with HSV-positive Acanthamoeba isolates had a mean best-corrected visual acuity of 1.43 LogMAR at diagnosis and 0.53 LogMAR at follow-up, compared with 1.85 and 0.92 LogMAR, respectively, in HSV-negative cases. Contact lens use was identified as a risk factor in 83% of 18 patients. We detected 46,597 viral signatures in 5 of 14 contaminated lens cases (35.7%). Distribution included 33% bacteriophages, 8.2% giant viruses, 4.1% nonhuman Herpesviridae, and 0.39% human Herpesviridae. Among the 184 human Herpesviridae genomic signatures, HSV types 1 or 2 or both were documented in 5.7%, VZV in 39.7%, HHV7 in 38.6%, HHV6 in 15.0%, and Epstein-Barr virus in 0.5%.<br><br>CONCLUSIONS: This study is the first to identify HSV-positive genomic signatures in clinical AK isolates and/or contact lens cases. Taken together, the high prevalence of HSV genomic signatures in both amebic hosts and lens cases, might signal an unrecognized Acanthamoeba-HSV association and the need for reassessing current management.},
}
@article {pmid39898315,
year = {2025},
author = {Walker, JR and Bente, DA and Burch, MT and Cerqueira, FM and Ren, P and Labonté, JM},
title = {Molecular assessment of oyster microbiomes and viromes reveals their potential as pathogen and ecological sentinels.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {100973},
pmid = {39898315},
issn = {2352-7714},
support = {UL1 TR001439/TR/NCATS NIH HHS/United States ; },
abstract = {Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.},
}
@article {pmid39897886,
year = {2025},
author = {Qayyum, H and Talib, MS and Ali, A and Kayani, MUR},
title = {Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41938},
pmid = {39897886},
issn = {2405-8440},
abstract = {Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (<1 %) and strains, we lack comprehensive insight into these communities. Although many bioinformatics approaches are available for recovering metagenome-assembled genomes, their effectiveness in recovering low-abundance species and strains is often questioned. Moreover, each tool has its trade-offs, making selecting the right tools challenging. In this study, we investigated the combinatory effect of various assemblers and binning tools on the recovery of low-abundance species and strain-resolved genomes from real and simulated human metagenomes. We evaluated the performance of nine combinations of metagenome assemblers and genome binning tools for their potential to recover genomes of useable quality. Our results revealed that the metaSPAdes-MetaBAT2 combination is highly effective in recovering low-abundance species, while MEGAHIT-MetaBAT2 excels in recovering strain-resolved genomes. These findings highlight the significant variation in the performance of different combinations, even when aiming for the same objective. This suggests the profound impact of selecting the right assembler-binner combination for metagenome analyses. We believe this study will be a cornerstone for the scientific community, guiding the choice of tools by highlighting their complementary effects. Furthermore, it underscores the potential of existing tools to address the current challenges in the field improving the recovery of information from metagenomes.},
}
@article {pmid39897789,
year = {2025},
author = {Schmidt, JE and Lewis, CA and Firl, AJ and Umaharan, P},
title = {Microbial bioindicators associated with cadmium uptake in sixteen genotypes of Theobroma cacao.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41890},
pmid = {39897789},
issn = {2405-8440},
abstract = {Recent regulatory limits on concentrations of cadmium (Cd), an element of concern for human health, have made Cd reduction a key issue in the global chocolate industry. Research into Cd minimization has investigated soil management, cacao genetic variation, and postharvest processing, but has overlooked the cacao-associated microbiome despite promising evidence in other crops that root-associated microorganisms could help reduce Cd uptake. A novel approach combining both amplicon and metagenomic sequencing identified microbial bioindicators associated with leaf and stem Cd accumulation in sixteen field-grown genotypes of Theobroma cacao. Sequencing highlighted over 200 amplicon sequence variants (ASVs) whose relative abundance was related to cacao leaf and stem Cd content or concentration. The two highest-accumulating genotypes, PA 32 and TRD 94, showed enrichment of four ASVs belonging to the genus Haliangium, the family Gemmataceae, and the order Polyporales. ASVs whose relative abundance was most negatively associated with plant Cd were identified as Paenibacillus sp. (β = -2.21), Candidatus Koribacter (β = -2.17), and Candidatus Solibacter (β = -2.03) for prokaryotes, and Eurotiomycetes (β = -4.58) and two unidentified ASVs (β = -4.32, β = -3.43) for fungi. Only two ASVs were associated with both leaf and stem Cd, both belonging to the Ktedonobacterales. Of 5543 C d-associated gene families, 478 could be assigned to GO terms, including 68 genes related to binding and transport of divalent heavy metals. Screening for Cd-related bioindicators prior to planting or developing microbial bioamendments could complement existing strategies to minimize the presence of Cd in the global cacao supply.},
}
@article {pmid39897560,
year = {2025},
author = {Zhang, P and Guo, R and Ma, S and Jiang, H and Yan, Q and Li, S and Wang, K and Deng, J and Zhang, Y and Zhang, Y and Wang, G and Chen, L and Li, L and Guo, X and Zhao, G and Yang, L and Wang, Y and Kang, J and Sha, S and Fan, S and Cheng, L and Meng, J and Yu, H and Chen, F and He, D and Wang, J and Liu, S and Shi, H},
title = {A metagenome-wide study of the gut virome in chronic kidney disease.},
journal = {Theranostics},
volume = {15},
number = {5},
pages = {1642-1661},
pmid = {39897560},
issn = {1838-7640},
mesh = {Humans ; *Renal Insufficiency, Chronic/virology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology/microbiology ; Middle Aged ; Male ; Female ; Aged ; Dysbiosis/virology/microbiology ; Adult ; Viruses/genetics/classification/isolation &amp; purification ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD[+]) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.},
}
@article {pmid39897495,
year = {2025},
author = {Solymosi, N and Tóth, AG and Nagy, S&#xc1; and Csabai, I and Feczkó, C and Reibling, T and Németh, T},
title = {Clinical considerations on antimicrobial resistance potential of complex microbiological samples.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18802},
pmid = {39897495},
issn = {2167-8359},
mesh = {*Escherichia coli/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Microbial Sensitivity Tests ; Genotype ; Metagenomics/methods ; Phenotype ; Genes, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.},
}
@article {pmid39896983,
year = {2025},
author = {Sayyad, LE and Smith, KL and Sadigh, KS and Cossaboom, CM and Choi, MJ and Whitmer, S and Cannon, D and Krapiunaya, I and Morales-Betoulle, M and Annambhotla, P and Basavaraju, SV and Ruberto, I and Kretschmer, M and Gutierrez, N and Zabel, K and Austin, C and Sandoval, E and Servellita, V and Foresythe, A and Sumimoto, N and Aqel, BA and Khamash, HA and Jadlowiec, CC and Grys, TE and Jaramillo, A and Grill, MF and Montgomery, JM and Shoemaker, T and Klena, JD and Chiu, CY and Vikram, HR},
title = {Severe Non-Donor-Derived Lymphocytic Choriomeningitis Virus Infection in 2 Solid Organ Transplant Recipients.},
journal = {Open forum infectious diseases},
volume = {12},
number = {2},
pages = {ofaf002},
pmid = {39896983},
issn = {2328-8957},
abstract = {BACKGROUND: Lymphocytic choriomeningitis virus (LCMV) infection in immunocompromised hosts can result in disseminated disease, meningoencephalitis, and death. Published cases in transplant recipients have been traced to transmission from infected donors. We report 2 cases of serious, non-donor-derived LCMV infection in solid organ transplant recipients.<br><br>METHODS: Initial identification of LCMV infection was done by using metagenomic next-generation sequencing (mNGS). Subsequent evaluations and confirmatory testing involved molecular diagnostics, serology, and phylogenetic analysis. A detailed epidemiologic investigation was conducted.<br><br>RESULTS: LCMV was detected by mNGS in 2 solid organ transplant recipients from distinct donors. A heart transplant recipient (from donor 1) died of progressive, disseminated LCMV infection, while a kidney transplant recipient (from donor 2) with LCMV meningoencephalitis survived. A multistate laboratory and epidemiologic investigation of both donors and all their organ recipients was initiated. Postmortem samples were obtained from both donors, and pretransplant and/or posttransplant samples were obtained from 5 of the 6 organ recipients. mNGS, serologic, and real-time reverse-transcription polymerase chain reaction testing confirmed LCMV infection in both solid organ transplant recipients. Epidemiologic investigation revealed significant pretransplant rodent exposures for both LCMV-infected recipients. Laboratory studies for the other organ recipients from both donors were negative for LCMV infection.<br><br>CONCLUSIONS: Our investigations suggest that LCMV infection in 2 solid organ transplant recipients originated from rodent exposure preceding transplantation and were not donor derived. Although uncommon, healthcare providers should be aware of LCMV-associated serious and life-threatening illness in immunocompromised hosts. Diagnostic modalities are limited to reference laboratories.},
}
@article {pmid39896720,
year = {2024},
author = {Coltro, EP and Cafferati Beltrame, L and da Cunha, CR and Zamparette, CP and Feltrin, C and Benetti Filho, V and Vanny, PA and Beduschi Filho, S and Klein, TCR and Scheffer, MC and Palmeiro, JK and Wagner, G and Sincero, TCM and Zárate-Bladés, CR},
title = {Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region.},
journal = {Frontiers in antibiotics},
volume = {3},
number = {},
pages = {1489356},
pmid = {39896720},
issn = {2813-2467},
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state.<br><br>METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed.<br><br>RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases.<br><br>DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.},
}
@article {pmid39896099,
year = {2025},
author = {Iwami, N and Komiya, S and Asada, Y and Tatsumi, K and Habara, T and Kuramoto, T and Seki, M and Yoshida, H and Takeuchi, K and Shiotani, M and Mukaida, T and Odawara, Y and Mio, Y and Kamiya, H},
title = {"Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma &amp; Alice: A multicenter prospective study".},
journal = {Reproductive medicine and biology},
volume = {24},
number = {1},
pages = {e12634},
pmid = {39896099},
issn = {1445-5781},
abstract = {PURPOSE: To evaluate the impact of Endometrial Microbiome Metagenomic Analysis and Analysis of Infectious Chronic Endometritis (EMMA &amp; ALICE) on pregnancy outcomes following recommended treatments in women with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL).<br><br>METHODS: This prospective, multicenter cohort study included 527 women under 42&#x2009;years old with RIF or RPL across 14 IVF centers in Japan. Endometrial samples were analyzed using EMMA &amp; ALICE, and patients received antibiotics, probiotics, or no treatment based on test results. Pregnancy outcomes were assessed using Kaplan-Meier survival analysis and multivariate generalized linear models.<br><br>RESULTS: Amongst participants, 43.4% had a normal Lactobacillus-dominated microbiota, 20.9% had dysbiosis, and 35.7% had mild dysbiosis or ultralow biomass. Kaplan-Meier analysis revealed significantly higher ongoing pregnancy rates in the dysbiosis group treated with antibiotics and probiotics compared to other groups (p&#x2009;=&#x2009;0.031). Post-treatment, ongoing pregnancy rates in the dysbiosis and mild dysbiosis groups were comparable to the normal group.<br><br>CONCLUSIONS: EMMA &amp; ALICE-guided antimicrobial and probiotic treatments improved pregnancy outcomes, enabling the dysbiosis group to achieve pregnancy earlier than the normal group. Addressing uterine dysbiosis may reduce the time to pregnancy in patients with RIF and RPL.<br><br>TRIAL REGISTRATION: University Hospital Medical Information Network (UMIN), UMIN000036917.},
}
@article {pmid39895875,
year = {2025},
author = {Esparteiro, D and Fouquet, G and Courtois, A and Naassila, M and Nguyen-Khac, E and Marcq, I},
title = {Shotgun Metagenomics Reveals Bacteroides stercoris as a Fecal Biomarker Depleted in Late-Stage Hepatocellular Carcinoma.},
journal = {Gastro hep advances},
volume = {4},
number = {1},
pages = {100539},
pmid = {39895875},
issn = {2772-5723},
}
@article {pmid39895797,
year = {2025},
author = {Gao, Y and Zheng, H and Ye, M and Zhou, G and Chen, J and Qiang, X and Bai, J and Lu, X and Tang, Q},
title = {Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.},
journal = {Journal of Cancer},
volume = {16},
number = {4},
pages = {1040-1050},
pmid = {39895797},
issn = {1837-9664},
abstract = {The gut microbiota plays a significant role in the initiation and progression of tumors, but its role in rectal neuroendocrine tumors (rNETs) remains unclear. Fecal samples were collected from 19 healthy individuals and 21 rNET patients,with the rNET cohort further divided into metastatic (rNETs-M) and non-metastatic (rNETs-nM) groups. Using metagenomic high-throughput sequencing, we analyzed the diversity, species composition, and functional characteristics of the gut microbiota. We applied a random forest model to identify potential microbial biomarkers for predicting rNET and specifically distinguishing rNETs-M cases. Alpha diversity analysis revealed that species diversity was lower in the rNETs group than in the control group. In contrast, the rNETs-M group exhibited higher species diversity than the rNETs-nM group. Beta diversity analysis demonstrated significant differences in community structure between the rNETs and control groups between the rNET-M and rNETs-nM groups. Notably, in the rNETs group, the abundance of potential pathogens such as Escherichia coli and Shigella was elevated.Furthermore, the rNETs-M group exhibited an increased abundance of potential pathogens such as Alistipes. KEGG enrichment analysis indicated that these distinct microbiota play a significant role in environmental information processing, genetic information processing, and metabolic pathways. Random forest analysis and ROC curve results identified Lachnospira pectinoschiza (AUC=0.885), Parasutterella muris (AUC=0.862), Sodaliphilus pleomorphus(AUC=0.956), Methylobacterium iners (AUC=0.971) as biomarkers with significant discriminatory value.},
}
@article {pmid39895693,
year = {2025},
author = {Zhou, CY and Dai, K and Lin, YP and Huang, XC and Hu, YL and Chen, XX and Yang, XF and Sun, QY and Zhang, Y and van Loosdrecht, MCM and Zeng, RJ and Zhang, F},
title = {Elucidating the complex hydrolysis and conversion network of xanthan-like extracellular heteropolysaccharides in waste activated sludge fermentation.},
journal = {Water research X},
volume = {27},
number = {},
pages = {100303},
pmid = {39895693},
issn = {2589-9147},
abstract = {The hydrolysis of structural extracellular polymeric substances (St-EPS) is considered a major limiting step in the anaerobic fermentation of waste activated sludge (WAS). However, the degradation of heteropolysaccharides, characterized by complex monomers of uronic acids and neutral saccharides in St-EPS, has rarely been reported. In this study, microbial-produced xanthan-like heteropolysaccharides, characterized by a blue filamentary film, were identified. The xanthan-producing bacteria comprised ∼7.2% of total genera present in WAS. An xanthan-degrading consortium (XDC) was enriched in an anaerobic batch reactor. This consortium could degrade Xanthan for over 90% and disrupt the gel structure of xanthan while promoting methane production from WAS by 29%. The xanthan degradation network consisting of extracellular enzymes and bacteria was elucidated by combining high-throughput sequencing, metagenomic, and metaproteomic analyses. Five enzymes were identified as responsible for hydrolyzing xanthan to monomers, including xanthan lyase, β-d-glucosidase, β-d-glucanase, α-d-mannosidase, and unsaturated glucuronyl hydrolase. Seven genera, including Paenibacillus (0.2%) and Clostridium (3.1%), were identified as key bacteria excreting one to five of the aforementioned enzymes. This study thus provides insights into the complex conversions in anaerobic digestion of WAS and gives a foundation for future optimization of this process.},
}
@article {pmid39895114,
year = {2025},
author = {Di Simone, SK and Forster, SC},
title = {Sputum Metagenomics Reveals Multidrug-Resistant Pseudomonas-Dominant Communities in Severe Asthma.},
journal = {Respirology (Carlton, Vic.)},
volume = {},
number = {},
pages = {},
doi = {10.1111/resp.14890},
pmid = {39895114},
issn = {1440-1843},
support = {//CSL Centenary Fellowship/ ; },
}
@article {pmid39895074,
year = {2025},
author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS},
title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {1},
pages = {e.2409018},
doi = {10.71150/jm.2409018},
pmid = {39895074},
issn = {1976-3794},
support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; },
abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.},
}
@article {pmid39894814,
year = {2025},
author = {El Leithy, AA and Youssef, ASE and Nassar, A and Aziz, RK and Khaled, NM and Mahrous, MT and Farahat, GN and Mohamed, AH and Bakr, YM},
title = {Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {8},
pmid = {39894814},
issn = {1757-4749},
abstract = {BACKGROUND: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.<br><br>AIM: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.<br><br>MATERIALS AND METHODS: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.<br><br>RESULTS: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value&#x2009;=&#x2009;0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value&#x2009;=&#x2009;0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value&#x2009;=&#x2009;0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.<br><br>CONCLUSION: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.},
}
@article {pmid39894607,
year = {2025},
author = {Gong, JC and Li, BH and Liu, CY and Li, PF and Hu, JW and Yang, GP},
title = {Impact of salinity gradients on nitric oxide emissions and functional microbes in estuarine wetland sediments.},
journal = {Water research},
volume = {273},
number = {},
pages = {123046},
doi = {10.1016/j.watres.2024.123046},
pmid = {39894607},
issn = {1879-2448},
mesh = {*Wetlands ; *Salinity ; *Nitric Oxide/metabolism ; *Geologic Sediments/microbiology ; Estuaries ; China ; },
abstract = {Estuarine wetland sediments are hotspots for nitrogen cycling and critical sources of atmospheric nitric oxide (NO). Yet studies on the impact of sediment salinity gradients on NO emissions and associated functional microbes at the land-ocean interface remain limited. Here, we measured sediment NO emission rates from incubated sediment samples that were collected from an estuarine wetland in Qingdao, China. Our findings indicate that sediment salinity is a pivotal factor shaping NO emission rates, by altering the community composition and gene abundance of functional microbes involved in NO emissions, with rates ranging from 0.04 to 0.25 μg N kg[-1] dry soil h[-1]. Metagenomic analysis of the sediment samples reveals that greater NO emission rates (+486 %) under salinity changes are linked to a higher abundance of the nirS gene (+26 %) responsible for NO formation and a lower abundance of norBC genes (-23 %) responsible for NO consumption. Accordingly, the increase of NO emissions may be attributed to the accumulation of denitrifying NO, which could improve plant salt tolerance through co-evolutionary interactions between plants and sediment-dwelling microbes. Taken together, these findings contribute to a richer understanding of how biochemical NO emissions in estuarine wetland sediments respond to salinity gradients.},
}
@article {pmid39894448,
year = {2025},
author = {Zhu, Y and Miao, H and Zhang, J and Jiang, Z and Chu, X and Xu, Y and Tian, W and Gao, H and Zhu, Y and Li, L and Yang, Q},
title = {Role of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis, a prospective cohort study in sepsis patients.},
journal = {The Journal of infection},
volume = {90},
number = {3},
pages = {106434},
doi = {10.1016/j.jinf.2025.106434},
pmid = {39894448},
issn = {1532-2742},
abstract = {PURPOSES: Sepsis caused great clinical burden all over the world. This study clarified the value of plasma metagenomic next-generation sequencing (p-mNGS) and blood cell mNGS (bc-mNGS) in sepsis diagnosis and evaluation.<br><br>METHODS: One hundred and fourty-seven blood samples were collected from sepsis patients who met sepsis 3.0 criteria. Blood culture (BC), qPCR, p-mNGS, bc-mNGS and necessary routine assays were conducted. Taking BC and qPCR as reference, diagnosis performance of p-mNGS and bc-mNGS was analyzed. Blood transcriptome was conducted to evaluate the immunological response of patients in groups with different p/bc-mNGS results. Impact of antibiotic use on different methods was also analyzed.<br><br>RESULTS: The p-mNGS demonstrated a sensitivity of 100% for bacteria/fungi and 97% for viruses, which was higher than bc-mNGS (88% for bacteria and fungi, 71% for viruses). However, bc-mNGS showed higher concordance with BC results, which indicated that co-mNGS (p-mNGS plus bc-mNGS) protocol increased sensitivity and was helpful to justify viable blood pathogens in sepsis patients. This study showed that p-mNGS(+) &amp; bc-mNGS(+) samples represented more activated immunity response (low expression of interferon-induced genes and high expression of JAK-STAT pathway genes), poorer clinical laboratory indicators (higher Sequential Organ Failure Assessment, higher procalcitonin and higher C-reactive protein) and lower survival rate. This study also proved that the use of broad-spectrum antibiotics affected much less on p/bc-mNGS diagnostic ability than on BC.<br><br>CONCLUSIONS: This research highlighted the potential value of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis patients, which will benefit the management of sepsis patients.},
}
@article {pmid39894225,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HL and Chang, Y and Ryu, S and Kim, HN},
title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.},
journal = {Journal of affective disorders},
volume = {376},
number = {},
pages = {26-35},
doi = {10.1016/j.jad.2025.01.149},
pmid = {39894225},
issn = {1573-2517},
abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.<br><br>METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.<br><br>RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.<br><br>CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.},
}
@article {pmid39894202,
year = {2025},
author = {Ladjouzi, R and Taminiau, B and Daube, G and Lucau-Danila, A and Drider, D},
title = {The efficacy of the bacteriocinogenic Enterococcus faecalis 14 in the control of induced necrotic enteritis in broilers.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105477},
doi = {10.1016/j.micinf.2025.105477},
pmid = {39894202},
issn = {1769-714X},
abstract = {PURPOSE: To demonstrate the efficacy of the bacteriocinogenic Enterococcus faecalis 14 (E. faecalis 14) in the control of induced necrotic enteritis (NE) in broilers.<br><br>METHODS: Six groups of 504 broilers consisting of an infected untreated control (IUC) group, an infected and amoxicillin treated control (ITC) group, and groups receiving prophylactically (2 groups) or therapeutically (2 groups) E. faecalis 14 or its &#x394;bac mutant were used. All groups were challenged with Clostridium perfringens 56 to induce NE. To predispose the boilers to develop subclinical NE, a high protein grower diet containing 15% fishmeal and a coccidial inoculum were administered.<br><br>RESULTS: NE lesions were observed on D26 in all groups except ITC and those receiving prophylactically and therapeutically E. faecalis 14. On D27, only ITC and the group prophylactically treated with E. faecalis 14 (T03 T03) were without lesions. Average body weight and daily weight gain remained lower in the treated groups compared to the ITC group, but there was a clear improvement in the period between D21 to D27, especially in the group prophylactically treated with E. faecalis 14. Specifically, the daily weight gain (DWG) in this period for group T03, was second highest after the group ITC. Metataxonomic analyses showed a positive effect of E. faecalis 14 in maintaining the diversity and richness of the intestinal microbiota, in contrast to ITC group and other conditions.<br><br>CONCLUSIONS: The results of this in vivo study demonstrated the efficacy of the prophylactic administration of the bacteriocinogenic E. faecalis 14 in preventing of the NE lesions caused by C. perfringens.},
}
@article {pmid39893982,
year = {2025},
author = {Zhong, YQ and He, XL and Li, YH and Zhu, H and Li, JW and Xu, H and Liu, C and Lin, LC and Wang, JF},
title = {Enhancing antibiotic removal in constructed wetlands: A MgFe-LDHs-based strategy for optimizing microbial communities and metabolic functions.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137412},
doi = {10.1016/j.jhazmat.2025.137412},
pmid = {39893982},
issn = {1873-3336},
abstract = {To efficiently remove antibiotics from domestic and livestock wastewater in southern China, vertical flow constructed wetlands (CWs) were designed with and without magnesium-iron layered double hydroxides (MgFe-LDHs). Their removal efficiencies for three typical antibiotics (tetracycline, oxytetracycline, and ofloxacin) were evaluated. Results showed that MgFe-LDHs significantly improved nitrogen and phosphorus removal (18.7 %-25.6 %) and enhanced the degradation of tetracycline, oxytetracycline, and ofloxacin (13.1 %-17.8 %). High-resolution LC-MS analysis indicated significant biodegradation through various pathways, such as oxidation, hydrolysis, and dealkylation. Analysis of the Shannon diversity index demonstrated that the introduction of novel MgFe-LDHs enhanced microbial diversity and evenness at the phylum, class, and genus levels. The introduction of MgFe-LDHs increased microbial diversity and enriched antibiotic-degrading genera like Xanthobacter, Ochrobactrum, and Stenotrophomonas. Moreover, MgFe-LDHs may have enhanced the metabolic pathways of glycolysis and the tricarboxylic acid cycle, thereby improving the microbial degradation of organic matter. In summary, MgFe-LDHs exhibited a multifaceted role in enhancing antibiotic removal in CWs by inducing the enrichment of antibiotic-degrading bacteria and regulating the metabolic functions of the microbial community, while also ensuring higher nitrogen and phosphorus removal efficiency.},
}
@article {pmid39893935,
year = {2025},
author = {Luo, Y and Gao, J and Su, X and Li, H and Li, Y and Qi, W and Han, X and Han, J and Zhao, Y and Zhang, A and Zheng, Y and Qian, F and He, H},
title = {Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis.},
journal = {EBioMedicine},
volume = {113},
number = {},
pages = {105586},
doi = {10.1016/j.ebiom.2025.105586},
pmid = {39893935},
issn = {2352-3964},
abstract = {BACKGROUND: Comprehensive and in-depth research on the immunophenotype of septic patients remains limited, and effective biomarkers for the diagnosis and treatment of sepsis are urgently needed in clinical practice.<br><br>METHODS: Blood samples from 31 septic patients in the Intensive Care Unit (ICU), 25 non-septic ICU patients, and 18&#xa0;healthy controls were analyzed using flow cytometry for deep immunophenotyping. Metagenomic sequencing was performed in 41 fecal samples, including 13 septic patients, 10 non-septic ICU patients, and 18 healthy controls. Immunophenotype shifts were evaluated using differential expression sliding window analysis, and random forest models were developed for sepsis diagnosis or prognosis prediction.<br><br>FINDINGS: Septic patients exhibited decreased proportions of natural killer (NK) cells and plasmacytoid dendritic cells (pDCs) in CD45[+] leukocytes compared with non-septic ICU patients and healthy controls. These changes statistically mediated the association of Bacteroides salyersiae with sepsis, suggesting a potential underlying mechanism. A&#xa0;combined diagnostic model incorporating B.salyersia, NK cells in CD45[+] leukocytes, and C-reactive protein (CRP) demonstrated high accuracy in distinguishing sepsis from non-sepsis (area under the receiver operating characteristic curve, AUC&#xa0;=&#xa0;0.950, 95% CI: 0.811-1.000). Immunophenotyping and disease severity analysis identified an Acute Physiology and Chronic Health Evaluation (APACHE) II score threshold of 21, effectively distinguishing mild (n&#xa0;=&#xa0;19) from severe (n&#xa0;=&#xa0;12) sepsis. A prognostic model based on the proportion of total lymphocytes, Helper T (Th) 17&#xa0;cells, CD4[+] effector memory T (TEM) cells, and Th1 cells in CD45[+] leukocytes achieved robust outcome prediction (AUC&#xa0;=&#xa0;0.906, 95% CI: 0.732-1.000), with further accuracy improvement when combined with clinical scores (AUC&#xa0;=&#xa0;0.938, 95% CI: 0.796-1.000).<br><br>INTERPRETATION: NK cell subsets within innate immunity exhibit significant diagnostic value for sepsis, particularly when combined with B.&#xa0;salyersiae and CRP. In addition, T cell phenotypes within adaptive immunity are correlated with sepsis severity and may serve as reliable prognostic markers.<br><br>FUNDING: This project was supported by the National Key R&amp;D Program of China (2023YFC2307600, 2021YFA1301000), Shanghai Municipal Science and Technology Major Project (2023SHZDZX02, 2017SHZDZX01), Shanghai Municipal Technology Standards Project (23DZ2202600).},
}
@article {pmid39893934,
year = {2025},
author = {Zeng, S and Mo, S and Wu, X and Meng, C and Peng, P and Kashif, M and Li, J and He, S and Jiang, C},
title = {Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge.},
journal = {Marine environmental research},
volume = {205},
number = {},
pages = {106980},
doi = {10.1016/j.marenvres.2025.106980},
pmid = {39893934},
issn = {1879-0291},
abstract = {Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.},
}
@article {pmid39893570,
year = {2025},
author = {Zampieri, G and Santinello, D and Palù, M and Orellana, E and Costantini, P and Favaro, L and Campanaro, S and Treu, L},
title = {Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf017},
pmid = {39893570},
issn = {1751-7370},
abstract = {Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by S. thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.},
}
@article {pmid39893166,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ},
title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1264},
pmid = {39893166},
issn = {2041-1723},
mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; },
abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.},
}
@article {pmid39893159,
year = {2025},
author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS},
title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4014},
pmid = {39893159},
issn = {2045-2322},
support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; },
mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; },
abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.},
}
@article {pmid39892935,
year = {2025},
author = {Hannaford, A and Hernandez-Acosta, RA and Little, JS and Campbell, JI and Weiss, ZF and Sherman, AC},
title = {Molecular Diagnostics for Invasive Molds: From Lab to Bedside.},
journal = {Clinics in laboratory medicine},
volume = {45},
number = {1},
pages = {27-40},
doi = {10.1016/j.cll.2024.10.009},
pmid = {39892935},
issn = {1557-9832},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis ; *Molecular Diagnostic Techniques ; Fungi/isolation &amp; purification ; Immunocompromised Host ; Mycoses/diagnosis ; },
abstract = {This review highlights the current state of molecular diagnostic modalities to detect invasive fungal infections, with a focus on molds in immunocompromised children and adults. Molecular diagnostics may also be utilized to detect antifungal drug resistance. Although both pathogen-specific and pathogen-agnostic assays may be beneficial in more rapidly identifying fungal infection with less invasive sampling in high-risk populations, the clinical implementation and interpretation of these tests must consider several important factors, including anatomic site and type of specimen, host characteristics, use of antifungal prophylaxis, and timing of specimen collection.},
}
@article {pmid39892320,
year = {2025},
author = {Huang, L and Dai, W and Sun, X and Pu, Y and Feng, J and Jin, L and Sun, K},
title = {Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128086},
doi = {10.1016/j.micres.2025.128086},
pmid = {39892320},
issn = {1618-0623},
abstract = {Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.},
}
@article {pmid39892190,
year = {2025},
author = {Su, R and Shi, L and Wei, Y and Ma, B},
title = {Comammox and AOA responses to ammonia loading rate in oligotrophic environments.},
journal = {Water research},
volume = {275},
number = {},
pages = {123191},
doi = {10.1016/j.watres.2025.123191},
pmid = {39892190},
issn = {1879-2448},
abstract = {Nitrification is a central process in the global nitrogen cycle, yet the ecological niches and growth strategies of ammonia-oxidizing microorganisms in oligotrophic environments remain poorly understood. To investigate the ecological responses of complete ammonia oxidizers (Comammox) and ammonia-oxidizing archaea (AOA), a membrane bioreactor (MBR) system with two distinct ammonia loading rates (ALRs) was employed in this study. Metagenomic and meta-transcriptomic analyses showed that Comammox species-including Candidatus Nitrospira nitrosa and Candidatus Nitrospira inopinata-underwent a pronounced "bloom" only at high ALR, where their DNA and mRNA relative abundances reached 4.7 % and 5.63 %, respectively. Meanwhile, AOA steadily increased under both high and low ALR in oligotrophic environments. Network analysis further indicated stronger cooperative interactions between Comammox and AOA in higher ALR, highlighting distinct ecological strategies that underpin ammonia oxidation in oligotrophic environments. These findings not only support the development of low-carbon nitrogen removal processes in wastewater treatment but also clarify the impact of nitrogen loading on the distribution of ammonia-oxidizing microorganisms in natural ecosystems and provide insights into the origin and evolutionary pathways of these essential microbes.},
}
@article {pmid39891257,
year = {2025},
author = {Elrashedy, A and Mousa, W and Nayel, M and Salama, A and Zaghawa, A and Elsify, A and Hasan, ME},
title = {Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {22},
pmid = {39891257},
issn = {1743-422X},
mesh = {Animals ; *Computational Biology/methods ; *Veterinary Medicine/methods ; *Virus Diseases/veterinary/virology ; Genomics/methods ; Proteomics ; Multiomics ; },
abstract = {The world is changing due to factors like bioterrorism, massive environmental changes, globalization of trade and commerce, growing urbanization, changing climate, and pollution. Numerous diseases have emerged because of these factors, especially in companion and food-producing animals. Numerous pathogens have established themselves in naïve populations, harming reproduction, productivity, and health. Bioinformatics is considered a valuable tool in infectious disease research, as it provides a comprehensive overview of the identification of pathogens, their genetic makeup, and their evolutionary relationship. Therefore, there is an urgent need for a novel bioinformatics approach to help decipher and model viral epidemiology and informatics on domestic animals and livestock. With significant advancements in bioinformatics and NGS, researchers can now identify contigs, which are contiguous sequences of DNA that are assembled from overlapping fragments, assemble a complete genome, perform phylogenetic analysis to diagnose, investigate the risk of viral diseases in animals, handle and share large biological datasets across various species. Additionally, multi-omics data integration further deepens our understanding of homology, divergence, mutations, and evolutionary relationships, providing a comprehensive perspective on the molecular mechanisms driving animal pathogens infections. This review aims to reveal the importance of utilizing the multidisciplinary areas of bioinformatics, genomics, proteomics, transcriptomics, metabolomics, and metagenomics and their roles in studying viral infectious diseases in veterinary medicine that will eventually improve the health of animals.},
}
@article {pmid39891205,
year = {2025},
author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P},
title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {34},
pmid = {39891205},
issn = {2049-2618},
support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; },
mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; },
abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.<br><br>RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.<br><br>CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.},
}
@article {pmid39891076,
year = {2025},
author = {Jia, Q and Sun, J and Wang, D and Xu, J and Li, X and Zhang, S and Wang, L and Liu, S and Tong, X and Fan, H},
title = {Clinical features and prognostic predictors of C. Psittaci Pneumonia: a systematic review and individual patient meta-analysis.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {55},
pmid = {39891076},
issn = {1471-2466},
mesh = {Humans ; *Psittacosis/diagnosis ; Prognosis ; *Chlamydophila psittaci/isolation &amp; purification ; Risk Factors ; Pneumonia/diagnosis ; Severity of Illness Index ; },
abstract = {BACKGROUND: The clinical presentations and prognostic indicators of C. psittaci pneumonia are inadequately investigated currently. The objective of the study was to assess the clinical presentation of C. psittaci pneumonia and the risk factors for severe pneumonia, within a systematic review and individual patient meta-analysis.<br><br>METHODS: We searched PubMed, CNKI, and Wanfang databases for case reports/series of proven/probable psittacosis published between 1st January 2000 and 28th February 2023, including all hospitalized individuals aged&#x2009;&#x2265;&#x2009;18 years. Patient demographics, manifestations, diagnostic methods, and outcomes were summarized descriptively. Patients were divided into severe or non-severe pneumonia groups mainly according to the ATS/IDSA 2007 criteria. Prognostic predictors for severe C. psittaci pneumonia were identified using multivariate logistic regression.<br><br>RESULTS: 3062 articles of 196 (566 individual patient cases) were included in the final analysis. Patients with chronic cardiovascular disease face a significantly elevated risk of developing severe C. psittaci pneumonia (adjusted odds ratio (aOR) 2.63; 95% confidence interval (CI) 1.05-6.59; P&#x2009;=&#x2009;0.039). Symptoms including dyspnea (aOR 4.88; 95% CI 3.19-7.46; P&#x2009;<&#x2009;0.001), neuropsychiatric symptoms (aOR 3.58; 95% CI 2.05-6.28; P&#x2009;<&#x2009;0.001), gastrointestinal symptoms (aOR 1.76; 95% CI 1.10-2.80; P&#x2009;=&#x2009;0.018), or the presence of multilobar infiltrates on imaging (aOR 3.27; 95% CI 2.11-5.06; P&#x2009;<&#x2009;0.001) upon admission frequently serve as indicators of severe pneumonia.<br><br>CONCLUSIONS: Chronic cardiovascular disease increases susceptibility to severe C. psittaci pneumonia. The presence of dyspnea, neuropsychiatric symptoms, gastrointestinal symptoms, and multilobar infiltrates upon admission merits clinicians' attention, advocating for timely sample submission for metagenomic next-generation sequencing (mNGS) to ascertain the etiology.},
}
@article {pmid39890997,
year = {2025},
author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J},
title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70066},
pmid = {39890997},
issn = {1758-2229},
support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation &amp; purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; },
abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.},
}
@article {pmid39890137,
year = {2025},
author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP},
title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089206},
pmid = {39890137},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; },
abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.<br><br>METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.<br><br>ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.<br><br>TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.},
}
@article {pmid39889699,
year = {2025},
author = {Tagirdzhanova, G and Scharnagl, K and Sahu, N and Yan, X and Bucknell, A and Bentham, AR and Jégousse, C and Ament-Velásquez, SL and Onuț-Brännström, I and Johannesson, H and MacLean, D and Talbot, NJ},
title = {Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.12.041},
pmid = {39889699},
issn = {1879-0445},
abstract = {Lichens are composite, symbiotic associations of fungi, algae, and bacteria that result in large, anatomically complex organisms adapted to many of the world's most challenging environments. How such intricate, self-replicating lichen architectures develop from simple microbial components remains unknown because of their recalcitrance to experimental manipulation. Here, we report a metagenomic and metatranscriptomic analysis of the lichen Xanthoria parietina at different developmental stages. We identified 168 genomes of symbionts and lichen-associated microbes across the sampled thalli, including representatives of green algae, three different classes of fungi, and 14 bacterial phyla. By analyzing the occurrence of individual species across lichen thalli from diverse environments, we defined both substrate-specific and core microbial components of the lichen. Metatranscriptomic analysis of the principal fungal symbiont from three different developmental stages of a lichen, compared with axenically grown fungus, revealed differential gene expression profiles indicative of lichen-specific transporter functions, specific cell signaling, transcriptional regulation, and secondary metabolic capacity. Putative immunity-related proteins and lichen-specific structurally conserved secreted proteins resembling fungal pathogen effectors were also identified, consistent with a role for immunity modulation in lichen morphogenesis.},
}
@article {pmid39889605,
year = {2025},
author = {Gong, X and Peng, Q and Jiang, R and Yang, N and Xing, C and Wang, R},
title = {Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137383},
doi = {10.1016/j.jhazmat.2025.137383},
pmid = {39889605},
issn = {1873-3336},
abstract = {Excess manganese (Mn) and NH4[+]-N emissions from electrolytic manganese metal industrial tailwater may harm the environment. However, previous studies have not combined Mn-oxidizing microalgae to reclaim Mn with woodchip substrates for nitrogen removal from tailwater. Here, a two-stage bioreactor system was constructed to recover Mn by microalgal-mediated bio-oxidation in an algae reactor (AR) and remove nitrogen by denitrification in a woodchip reactor (WR). The results showed that up to 100 % of Mn[2+] in the tailwater was removed after a 3-day incubation period. The maximum amount of biogenerated Mn oxide nanoparticles reached 13.34 mg/L with Mn[4+] as the main Mn valence. Mn recovery reached 65.69 % through precipitate collection, and the NH4[+]-N removal efficiency reached 97 % in the AR. Mn oxidation by algae might promote oxidative removal of NH4[+]-N. NO3[-]-N and total nitrogen removal efficiencies in the WR reached 82-90 % and 65-87 %, respectively, which was attributed to denitrification. The predominance of the denitrification gene narG in the WR may have driven the efficient nitrate removal. Flavobacterium, Acidovora, Massilia, Arcticibacter, and Acinetobacter were the most abundant genera in the WR and represented dominant denitrifying bacteria in the woodchip microbiome, indicating their important contribution to denitrification. Overall, the combined application of Mn-oxidizing algae and woodchip-denitrifying bioreactors may represent an efficient treatment technology for electrolytic manganese wastewater remediation.},
}
@article {pmid39889194,
year = {2025},
author = {Zhong, Y and Cai, ZY and Wang, JR and Qi, QG and Hao, J},
title = {Peritoneal dialysis-associated peritonitis caused by Coxiella Burnetii: A case report.},
journal = {Medicine},
volume = {104},
number = {5},
pages = {e41407},
pmid = {39889194},
issn = {1536-5964},
support = {2022MS08036//Inner Mongolia Natural Science Foundation/ ; NJYT- 23-068//Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; 202201253//Medical and Health Science and Technology Plan of Health Commission of Inner Mongolia Autonomous Region/ ; YKD2021MS034//Inner Mongolia Medical University General program/ ; },
mesh = {Female ; Humans ; *Peritonitis/microbiology/drug therapy/diagnosis ; Middle Aged ; *Coxiella burnetii/isolation &amp; purification ; *Peritoneal Dialysis/adverse effects ; *Q Fever/diagnosis/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Kidney Failure, Chronic/therapy ; Animals ; China ; },
abstract = {RATIONALE: Peritoneal dialysis (PD)-associated peritonitis (PDAP) is the leading cause of PD failure and discontinuation of PD. Several zoonotic pathogens could lead to the development of PDAP. Coxiella burnetii (C. burnetii) was a zoonotic pathogen and the cause of Q fever. However, reports of PDAP caused by C. burnetii are rare. We herein report the first case of PDAP caused by C. burnetii in mainland China.<br><br>PATIENTS CONCERNS: A 45-year-old woman was admitted to our hospital with chief complaint of yellow and cloudy PD effluent for 2 days. She had undergone PD for 5 years due to end-stage renal disease. She was engaged in cattle and sheep breeding. The culture of PD effluent was negative, even for specific species, such as Mycobacteria and fungi.<br><br>DIAGNOSES: The culture from the PD effluent tested positive for C. burnetii by adopting metagenomic next-generation sequencing on day 37. We diagnosed her as PDAP caused by C. burnetii.<br><br>INTERVENTIONS: Empirical treatment with multiple broad-spectrum antibiotics (including vancomycin, etimicin, piperacillin) was initially adopted. After identifying C. burnetii as the culprint as the PDAP, the regimen was changed to doxycycline (100&#x2009;mg twice daily) and moxifloxacin (400&#x2009;mg once daily) orally, leading to clinical improvement.<br><br>OUTCOMES: The white blood cell count of the PD effluent decreased to within the normal range and the culture of PD effluent was negative for C. burnetii at the visit of 4 months after discharge. Also, there was no sign for recurrence.<br><br>LESSONS: Vigilance should be heightened for PDAP cases with negative culture of PD fluid and poor response to standard broad-spectrum antibiotic treatment, along with a history of cattle and sheep breeding. In such conditions, PD effluent should be tested to detect possible peritonitis caused by C. burnetii, even in patients without symptoms of fever. Prompt pathogen identification and appropriate treatment are crucial for clinical improvement of such cases.},
}
@article {pmid39888330,
year = {2025},
author = {Thompson, JR and Canto, T and Carr, JP and Pallás, V and Šafářová, D},
title = {ICTV Virus Taxonomy Profile: Bromoviridae 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {1},
pages = {},
pmid = {39888330},
issn = {1465-2099},
mesh = {*Genome, Viral ; *Plant Diseases/virology ; *Bromoviridae/genetics/classification ; RNA, Viral/genetics ; Virion/ultrastructure/genetics ; Phylogeny ; },
abstract = {Bromoviridae is a family of plant viruses with tripartite, positive-sense RNA genomes of about 8 kb in total. Genomic RNAs are packaged in separate virions that may also contain sub-genomic, defective or satellite RNAs. Virions are variable in morphology (spherical or bacilliform) and may be transmitted between hosts mechanically, via pollen, or non-persistently by insect vectors. Members of the family are responsible for major disease epidemics in fruit, vegetable and fodder crops such as tomatoes, cucurbits, bananas, fruit trees, common beans and alfalfa. Since the adoption of metagenomic high-throughput sequencing methodologies, there has been a notable increase in the number of species in the genus Ilarvirus. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Bromoviridae, which is available at ictv.global/report/bromoviridae.},
}
@article {pmid39887801,
year = {2025},
author = {Tonoli, A and Anselmi, S and Ward, JM and Hailes, HC and Jeffries, J},
title = {Expanding the Enzymatic Toolbox for Carboligation: Increasing the Diversity of the 'Split' Transketolase Sequence Space.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {},
number = {},
pages = {e202401028},
doi = {10.1002/cbic.202401028},
pmid = {39887801},
issn = {1439-7633},
abstract = {Transketolases (TKs) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the transfer of two-carbon units in a stereoselective manner, making them valuable biocatalysts for sustainable processes. Most known TKs are about 650 amino acids long; however, a second type found in Archaea and many Bacteria consists of two proteins, each of about 300 amino acids. Exploring the unique features and differences of split TKs may help in assessing their potential use in biocatalysis and for uncovering new reactivities. Additionally, it could provide valuable information on how their structure relates to their function, especially compared to full-length TKs. In this study, we significantly expanded the known repertoire of split TKs approximately 14-fold to the best of our knowledge, by identifying and providing accessions of nearly 500 putative split-TK subunit pairs. Moreover, we doubled the number of experimentally produced and tested split TKs by cloning, purifying, and testing ten candidates retrieved from genomes and in-house metagenomes. Interestingly, pQR2809 and pQR2812, derived from hyperthermophilic organisms, showed enhanced thermostability compared to other TK examples in the literature, maintaining partial activity after heating at 90 °C or 100 °C for 1 hour, respectively.},
}
@article {pmid39887373,
year = {2025},
author = {Byrd, DA and Damerell, V and Gomez Morales, MF and Hogue, SR and Lin, T and Ose, J and Himbert, C and Ilozumba, MN and Kahlert, C and Shibata, D and Toriola, AT and Li, CI and Figueiredo, J and Stephens, WZ and Warby, CA and Hardikar, S and Siegel, EM and Round, J and Ulrich, CM and Gigic, B},
title = {The gut microbiome is associated with disease-free survival in stage I-III colorectal cancer patients.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35342},
pmid = {39887373},
issn = {1097-0215},
support = {//ERA-NET on Translational Cancer Research (TRANSCAN)/ ; //Heidelberger Stiftung Chirurgie, Heidelberg University Hospital/ ; //Medizinische Fakult&#xe4;t Heidelberg, Universit&#xe4;t Heidelberg/ ; //Matthias-Lackas Foundations/ ; //Stiftung LebensBlicke/ ; R01 CA189184/NH/NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; //Rahel Goitein-Straus-Program/ ; 01KD2101D//German Federal Ministry of Education and Research/ ; 01KT1503//German Federal Ministry of Education and Research/ ; },
abstract = {Colorectal cancer (CRC) is the second overall leading cause of cancer death in the United States, with recurrence being a frequent cause of mortality. Approaches to improve disease-free survival (DFS) are urgently needed. The gut microbiome, reflected in fecal samples, is likely mechanistically linked to CRC progression and may serve as a non-invasive biomarker. Accordingly, we leveraged baseline fecal samples from N = 166 stage I-III CRC patients in the ColoCare Study, a prospective cohort of newly diagnosed CRC patients. We sequenced the V3 and V4 regions of the 16S rRNA gene to characterize fecal bacteria. We calculated estimates of alpha diversity, beta diversity, and a priori- and exploratory-selected bacterial presence/absence and relative abundance. Associations of microbial metrics with DFS were estimated using multivariable Cox proportional hazards models. We found that alpha diversity was strongly associated with improved DFS, most strongly among rectal cancer patients (Shannon HRrectum = 0.40 95% CI = 0.19, 0.87; p = .02). Overall microbiome composition differences (beta diversity), as characterized by principal coordinate axes, were statistically significantly associated with DFS. Peptostreptococcus was statistically significantly associated with worse DFS (HR = 1.62, 95% CI = 1.13, 2.31; p = .01 per 1-SD) and Order Clostridiales was associated with improved DFS (HR = 0.62, 95% CI = 0.43-0.88; p = .01 per 1-SD). In exploratory analyses, Coprococcus and Roseburia were strongly associated with improved DFS. Overall, higher bacterial diversity and multiple bacteria were strongly associated with DFS. Metagenomic sequencing to elucidate species, gene, and functional level details among larger, diverse patient populations are critically needed to support the microbiome as a biomarker of CRC outcomes.},
}
@article {pmid39887237,
year = {2025},
author = {Stewart, AG and Fishman, JA},
title = {Surveillance and prevention of infection in clinical xenotransplantation.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0015023},
doi = {10.1128/cmr.00150-23},
pmid = {39887237},
issn = {1098-6618},
abstract = {SUMMARYXenotransplantation, the transplantation of living organs, tissues, or cells between species, carries the potential to address the global shortage of human organs for patients with end-stage organ failure. Recent advances in genetic engineering have improved prospects for clinical xenotransplantation by reducing immune and inflammatory responses to grafts, controlling coagulation on endothelial surfaces, and modifying viral risks, including the porcine endogenous retrovirus (PERV). Management of infectious risks posed by clinical xenotransplantation requires meticulous attention to the biosecure breeding and microbiological surveillance of source animals and recipients and consideration of novel infection control requirements. Infectious risks in xenotransplantation stem from both known human pathogens in immunosuppressed transplant recipients and from porcine organisms for which the clinical manifestations, microbial assays, and therapies are generally limited. Both known and unknown zoonoses may be transmitted from pigs to humans. Some pig-specific pathogens do not infect human cells but have systemic manifestations when active within the xenograft, including porcine cytomegalovirus/porcine roseolovirus (PCMV/PRV), which contributes to graft rejection and consumptive coagulopathy. The role of porcine endogenous retrovirus (PERV) in humans remains uncertain despite the absence of documented transmissions and the availability of swine with inactivated genomic PERV. New technologies, such as metagenomic sequencing and multi-omics approaches, will be essential for detection of novel infections and for understanding interactions between the xenograft, the host's immune system, and potential pathogens. These approaches will allow development of infection control protocols, pathogen surveillance requirements, and tailored antimicrobial therapies to enhance the safety and success of clinical xenotransplantation.},
}
@article {pmid39887086,
year = {2025},
author = {Breton, J and Tu, V and Tanes, C and Wilson, N and Quinn, R and Kachelries, K and Friedman, ES and Bittinger, K and Baldassano, RN and Compher, C and Albenberg, L},
title = {A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.},
journal = {Journal of Crohn's &amp; colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf018},
pmid = {39887086},
issn = {1876-4479},
abstract = {BACKGROUND &amp; AIMS: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.<br><br>METHODS: A cross-sectional study including 51 children with CD between 6 and 18 years of age and 50 healthy controls was conducted. Dietary inflammatory potential was measured using the modified Children-Dietary Inflammatory Index (mC-DII) and diet quality assessed by the Healthy Eating Index (HEI)-2015 and alternate Mediterranean eating index (aMed). Microbiome was analysed using shotgun metagenomic sequencing and untargeted metabolomic analysis.<br><br>RESULTS: A poor-quality, pro-inflammatory diet with similar mC-DII, HEI-2015 and aMed scores was found across healthy children and children with CD. In children with active disease, a pro-inflammatory diet was associated with decreased diversity, increased virulence potential and expansion of the Proteobacteria phylum dominated by Escherichia coli (E. coli) spp. Positive correlation between E. coli relative abundance and mC-DII was associated with a low intake of a cluster composed of fibers, vitamins and minerals with anti-inflammatory potential. A negative association between metabolites of fatty acid metabolism and HEI was found.<br><br>CONCLUSIONS: In total, our results suggest that a pro-inflammatory diet may potentiate hallmarks of the inflammation-associated dysbiosis in CD and highlight the need for microbiome-targeted dietary interventions optimizing the anti-inflammatory potential of habitual diet in the management of pediatric CD.},
}
@article {pmid39886930,
year = {2025},
author = {Zhang, W and Feng, J and Tan, K and Jiang, J and Deng, J},
title = {Bordetella pertussis Detected in Blood Samples From Neonatal Twins via Metagenomic Next-generation Sequencing.},
journal = {The Pediatric infectious disease journal},
volume = {44},
number = {2},
pages = {e71-e72},
pmid = {39886930},
issn = {1532-0987},
}
@article {pmid39885140,
year = {2025},
author = {Shao, B and Xie, YG and Zhang, L and Ruan, Y and Liang, B and Zhang, R and Xu, X and Wang, W and Lin, Z and Pei, X and Wang, X and Zhao, L and Zhou, X and Wu, X and Xing, D and Wang, A and Lee, DJ and Ren, N and Canfield, DE and Hedlund, BP and Hua, ZS and Chen, C},
title = {Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1202},
pmid = {39885140},
issn = {2041-1723},
support = {52076063//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52100035//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52400025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52300155//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52321005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023DX04//State Key Laboratory of Urban Water Resource and Environment (SKLUWRE)/ ; 2024M754204//China Postdoctoral Science Foundation/ ; 2023M740917//China Postdoctoral Science Foundation/ ; },
mesh = {*Sulfur/metabolism ; *Nitrates/metabolism ; *Heterotrophic Processes ; *Denitrification ; *Oxidation-Reduction ; Bacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Nitrous Oxide/metabolism ; Microbiota ; Sulfides/metabolism ; Metagenomics ; Greenhouse Gases/metabolism ; },
abstract = {Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.},
}
@article {pmid39885121,
year = {2025},
author = {Nooij, S and Plomp, N and Sanders, IMJG and Schout, L and van der Meulen, AE and Terveer, EM and Norman, JM and Karcher, N and Larralde, MF and Vossen, RHAM and Kloet, SL and Faber, KN and Harmsen, HJM and Zeller, GF and Kuijper, EJ and Smits, WK and Ducarmon, QR},
title = {Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1182},
pmid = {39885121},
issn = {2041-1723},
mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Metagenomics/methods ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Health Status ; Genome-Wide Association Study ; Clostridiales/genetics/isolation &amp; purification ; Life Style ; Phylogeny ; Infant, Newborn ; Genomics ; Female ; Male ; Adult ; Virulence Factors/genetics ; },
abstract = {Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.},
}
@article {pmid39884534,
year = {2025},
author = {Zhou, M and Luo, C and Zhang, J and Li, R and Chen, J and Ren, P and Tang, Y and Suo, Z and Chen, K},
title = {Potential risk of microplastics in plateau karst lakes: Insights from metagenomic analysis.},
journal = {Environmental research},
volume = {270},
number = {},
pages = {120984},
doi = {10.1016/j.envres.2025.120984},
pmid = {39884534},
issn = {1096-0953},
abstract = {Microplastic (MP) pollution has become one of global concern. While MP pollution in lakes has been well studied, research on MP sources, distribution, and ecological risks in the Tibetan Plateau is limited. We systematically investigated the MP abundance and distribution in alpine travertine lakes in Jiuzhai nature reserve located in east edge of Qinghai-Tibetan Plateau and assessed the distributions of microbiomes, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in water, sediments, and MPs, using macrogenomics. MP abundance was 20.27-58.80 n/L in water and 583.33-996.67 n/kg in sediments. MPs were dominantly fibrous and transparent. The particle size distribution was 0.1-0.5 mm for MPs in water, and 0.5-1 mm in sediments. MPs were mainly composed of polyethylene and polyethylene terephthalate. The microbial community of MP biofilms differed from that in the surrounding environmental medium, and Proteobacteria were more abundant in biofilm than in water and sediment. MP biofilms exhibited more cooperative behavior with microorganisms in water than with those in sediments. MPs were selectively enriched for ARGs and VFGs, and MP biofilms had a higher diversity of ARGs, the most abundant isoform being msbA, which is a multidrug resistance gene. VFGs were more abundant in MP biofilms than in water and sediment. The study results are useful for understanding MP sources and ecological risks in plateau karst lakes and provide a valuable dataset and theoretical basis for studies on MP pollution in other alpine calcareous lakes.},
}
@article {pmid39884152,
year = {2025},
author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128076},
doi = {10.1016/j.micres.2025.128076},
pmid = {39884152},
issn = {1618-0623},
abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.},
}
@article {pmid39884010,
year = {2025},
author = {Peng, Y and Lu, J and Fan, L and Zhou, J and Dong, W and Jiang, M},
title = {Enzymes offer a promising avenue for enhancing the competitiveness of biodegradable plastics in environmental restoration and the circular economy.},
journal = {Waste management (New York, N.Y.)},
volume = {195},
number = {},
pages = {32-43},
doi = {10.1016/j.wasman.2025.01.040},
pmid = {39884010},
issn = {1879-2456},
abstract = {As a promising alternative to traditional plastics, the widespread application of biodegradable plastic (BP) will help solve worsening environmental problems. Enzymes such as cutinase, lipase, protease and esterase produced by bacteria and fungi in the environment play a crucial role in the degradation, recycling and valorization of BP by degrading them into low-molecular-weight oligomers or small monomers. These enzymes offering advantages such as high efficiency, cleanliness, safety and environmental friendliness, making them more competitive in environmental restoration and circular economy. This review describes in detail the occurrence and distribution of enzymes involved in the degradation of BPs (represented by PHB, PLA and PCL). Omics methods (metagenomic and proteomic) combined with high-throughput platforms can screen out BP-degrading enzymes in different environments, and then use protein engineering to optimize the degrading enzymes to improve enzymatic degradation efficiency. Finally, we focus on the methods and strategies for the commercialization of degrading enzymes, future research prospects and challenges are also discussed. This review highlights the importance of BP-degrading enzymes in the bio-cycling of BP, and expected to drive the widespread use of BP.},
}
@article {pmid39883852,
year = {2025},
author = {Monpierre, L and Angebault, C and Hua, C and Merio, L and Ortonne, N and Lafont, E and Foulet, F and Botterel, F},
title = {Contribution of shotgun metagenomics in the diagnosis of a subcutaneous phaeohyphomycosis caused by Parathyridaria percutanea.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf018},
pmid = {39883852},
issn = {1365-2133},
}
@article {pmid39883300,
year = {2024},
author = {Zhang, D and Yu, H and Yu, X and Yang, Y and Wang, C and Wu, K and Niu, M and He, J and He, Z and Yan, Q},
title = {Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments.},
journal = {Advanced biotechnology},
volume = {2},
number = {3},
pages = {21},
pmid = {39883300},
issn = {2948-2801},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory/ ; },
abstract = {Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing. We found that the N removal activities could be affected through potential competition and inhibition among microbial metabolic pathways. High-diversity microbial communities generally increased the abundance and expression of N removal functional genes. Further enrichment experiments showed that the enrichment of N removal microorganisms led to a development of simplified but more stable microbial communities, characterized by similar evolutionary patterns among N removal microorganisms, tighter interactions, and increased adaptability. Notably, the sustained provision of NH4[+] and NO2[-] during the enrichment could potentially strengthen the interconnections among denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) processes. Moreover, the identification of shared metabolic traits among denitrification, anammox and DNRA implies important cooperative associations and adaptability of N removal microorganisms. Our findings highlight the microbial interactions affect the adaptive strategies of key microbial taxa involved in N removal.},
}
@article {pmid39882903,
year = {2025},
author = {Huang, X and Yao, X and Song, W and Zhao, M and Zhu, Z and Liu, H and Song, X and Huang, J and Chen, Y and Wang, Z and Peng, C and Wu, W and Yang, H and Hua, L and Chen, H and Wu, B and Peng, Z},
title = {Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002525},
doi = {10.1128/msystems.00025-25},
pmid = {39882903},
issn = {2379-5077},
abstract = {Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with Streptococcus suis, Mycoplasma hyorhinis, Mycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida being frequently detected in high abundances. Notably, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, and Klebsiella pneumoniae were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were significantly associated with a substantial number of mobile genetic elements, including transposons (e.g., tnpAIS1, tnpA1353, int3, and ISCau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.IMPORTANCEIn this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.},
}
@article {pmid39882902,
year = {2025},
author = {Zhu, D and Wozniak, KJ and Midani, F and Wang, S and Sun, X and Britton, RA},
title = {Control of Clostridioides difficile virulence and physiology by the flagellin homeostasis checkpoint FliC-FliW-CsrA in the absence of motility.},
journal = {mBio},
volume = {},
number = {},
pages = {e0380124},
doi = {10.1128/mbio.03801-24},
pmid = {39882902},
issn = {2150-7511},
abstract = {UNLABELLED: Mutations affecting Clostridioides difficile flagellin (FliC) have been shown to be hypervirulent in animal models and display increased toxin production and alterations in central metabolism. The regulation of flagellin levels in bacteria is governed by a tripartite regulatory network involving fliC, fliW, and csrA, which creates a feedback system to regulate flagella production. Through genomic analysis of C. difficile clade 5 strains (non-motile), we identified they have jettisoned many of the genes required for flagellum biosynthesis yet retain the major flagellin gene fliC and regulatory gene fliW. We therefore investigated the roles of fliC, fliW, and csrA in the clade 5 ribotype 078 strain C. difficile 1015, which lacks flagella and is non-motile. Analysis of mutations in fliC, fliW, and csrA (and all combinations) on C. difficile pathogenesis indicated that FliW plays a central role in C. difficile virulence as animals infected with strains carrying a deletion of fliW showed decreased survival and increased disease severity. These in vivo findings were supported by in vitro studies showing that mutations impacting the activity of FliW showed increased toxin production. We further identified that FliW can interact with the toxin-positive regulator TcdR, indicating that modulation of toxin production via FliW occurs by sequestering TcdR from activating toxin transcription. Furthermore, disruption of the fliC-fliW-csrA network results in significant changes in carbon source utilization and sporulation. This work highlights that key proteins involved in flagellar biosynthesis retain their regulatory roles in C. difficile pathogenesis and physiology independent of their functions in motility.<br><br>IMPORTANCE: Clostridioides difficile is a leading cause of nosocomial antibiotic-associated diarrhea in developed countries with many known virulence factors. In several pathogens, motility and virulence are intimately linked by regulatory networks that allow coordination of these processes in pathogenesis and physiology. Regulation of C. difficile toxin production by FliC has been demonstrated in vitro and in vivo and has been proposed to link motility and virulence. Here, we show that clinically important, non-motile C. difficile strains have conserved FliC and regulatory partners FliW and CsrA, despite lacking the rest of the machinery to produce functional flagella. Our work highlights a novel role for flagellin outside of its role in motility and FliW in the pathogenesis and physiology of C. difficile.},
}
@article {pmid39882857,
year = {2025},
author = {Grettenberger, C and Gold, DA and Brown, CT},
title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0101324},
doi = {10.1128/msphere.01013-24},
pmid = {39882857},
issn = {2379-5042},
abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.},
}
@article {pmid39882224,
year = {2025},
author = {Takamaru, H and Tsay, C and Shiba, S and Yachida, S and Saito, Y},
title = {Microbiome and Colorectal Cancer in Humans: A Review of Recent Studies.},
journal = {Journal of the anus, rectum and colon},
volume = {9},
number = {1},
pages = {20-24},
pmid = {39882224},
issn = {2432-3853},
abstract = {The tumor microenvironment has recently been well-studied in various gastrointestinal cancers, including colorectal cancer (CRC). The gut microbiota, a collection of microorganisms in the human gastrointestinal tract, is one of the microenvironments associated with colon carcinogenesis. It has been challenging to elucidate the mechanisms by which gut microbiota contributes to carcinogenesis and cancer progression due to complex interactions with the host, including its metabolites and immune and inflammatory responses. Various studies described the influence of diet on reported changes in the composition and microbiota of gut bacteria and its association with CRC. In recent years, metagenomic techniques such as shotgun sequencing and genome-wide association studies focused on understanding the role of the microbiota and the metabolome on early CRCs and colon carcinogenesis to determine if there are modifiable or intervenable targets for CRC. In this review, we will attempt to provide an overview of gut microbiota related to CRC, with particular attention to the findings of recent studies.},
}
@article {pmid39881980,
year = {2024},
author = {Renk, H and Schoppmeier, U and Müller, J and Kuger, V and Neunhoeffer, F and Gille, C and Peter, S},
title = {Oxygenation and intestinal perfusion and its association with perturbations of the early life gut microbiota composition of children with congenital heart disease.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1468842},
pmid = {39881980},
issn = {1664-302X},
abstract = {BACKGROUND: Early life gut microbiota is known to shape the immune system and has a crucial role in immune homeostasis. Only little is known about composition and dynamics of the intestinal microbiota in infants with congenital heart disease (CHD) and potential influencing factors.<br><br>METHODS: We evaluated the intestinal microbial composition of neonates with CHD (n&#x202f;=&#x202f;13) compared to healthy controls (HC, n&#x202f;=&#x202f;30). Fecal samples were analyzed by shotgun metagenomics. Different approaches of statistical modeling were applied to assess the impact of influencing factors on variation in species composition. Unsupervised hierarchical clustering of the microbial composition of neonates with CHD was used to detect associations of distinct clusters with intestinal tissue oxygenation and perfusion parameters, obtained by the "oxygen to see" (O2C) method.<br><br>RESULTS: Overall, neonates with CHD showed an intestinal core microbiota dominated by the genera Enterococcus (27%) and Staphylococcus (20%). Furthermore, a lower abundance of the genera Bacteroides (8% vs. 14%), Parabacteroides (1% vs. 3%), Bifidobacterium (4% vs. 12%), and Escherichia (8% vs. 23%) was observed in CHD compared to HCs. CHD patients that were born by vaginal delivery showed a lower fraction of the genera Bacteroides (15% vs. 21%) and Bifidobacterium (7% vs. 22%) compared to HCs and in those born by cesarean section, these genera were not found at all. In infants with CHD, we found a significant impact of oxygen saturation (SpO2) on relative abundances of the intestinal core microbiota by multivariate analysis of variance (F[8,2]&#x202f;=&#x202f;24.9, p&#x202f;=&#x202f;0.04). Statistical modeling suggested a large proportional shift from a microbiota dominated by the genus Streptococcus (50%) in conditions with low SpO2 towards the genus Enterococcus (61%) in conditions with high SpO2. We identified three distinct compositional microbial clusters, corresponding neonates differed significantly in intestinal blood flow and global gut perfusion.<br><br>CONCLUSION: Early life differences in gut microbiota of CHD neonates versus HCs are possibly linked to oxygen levels. Delivery method may affect microbiota stability. However, further studies are needed to assess the effect of potential interventions including probiotics or fecal transplants on early life microbiota perturbations in neonates with CHD.},
}
@article {pmid39881594,
year = {2025},
author = {Kaur, I and Shaw, B and Multani, A and Pham, C and Malhotra, S and Smith, E and Adachi, K and Allyn, P and Bango, Z and Beaird, OE and Caldera, JR and Chandrasekaran, S and Chan, L and Cheema, R and Daouk, S and Deville, J and Dong, HV and Fan, A and Garner, O and Gaynor, P and Gray, H and Gorin, A and Kalava, S and Kanatani, M and Karnaze, A and Saleh, T and Sharma, Y and Stauber, S and Vargas, M and Veral, M and Winston, D and Yanagimoto-Ogawa, L and Aldrovandi, G and Nielsen-Saines, K and Fuller, T and Jackson, N and Uslan, D and Schaenman, J and Vijayan, T and Sakona, A and Yang, S},
title = {Real-world clinical impact of plasma cell-free DNA metagenomic next-generation sequencing assay.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/ice.2024.242},
pmid = {39881594},
issn = {1559-6834},
abstract = {OBJECTIVE: To describe the real-world clinical impact of a commercially available plasma cell-free DNA metagenomic next-generation sequencing assay, the Karius test (KT).<br><br>METHODS: We retrospectively evaluated the clinical impact of KT by clinical panel adjudication. Descriptive statistics were used to study associations of diagnostic indications, host characteristics, and KT-generated microbiologic patterns with the clinical impact of KT. Multivariable logistic regression modeling was used to further characterize predictors of higher positive clinical impact.<br><br>RESULTS: We evaluated 1000 unique clinical cases of KT from 941 patients between January 1, 2017-August 31, 2023. The cohort included adult (70%) and pediatric (30%) patients. The overall clinical impact of KT was positive in 16%, negative in 2%, and no clinical impact in 82% of the cases. Among adult patients, multivariable logistic regression modeling showed that culture-negative endocarditis (OR 2.3; 95% CI, 1.11-4.53; P .022) and concern for fastidious/zoonotic/vector-borne pathogens (OR 2.1; 95% CI, 1.11-3.76; P .019) were associated with positive clinical impact of KT. Host immunocompromised status was not reliably associated with a positive clinical impact of KT (OR 1.03; 95% CI, 0.83-1.29; P .7806). No significant predictors of KT clinical impact were found in pediatric patients. Microbiologic result pattern was also a significant predictor of impact.<br><br>CONCLUSIONS: Our study highlights that despite the positive clinical impact of KT in select situations, most testing results had no clinical impact. We also confirm diagnostic indications where KT may have the highest yield, thereby generating tools for diagnostic stewardship.},
}
@article {pmid39881417,
year = {2025},
author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD},
title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {130},
pmid = {39881417},
issn = {1479-5876},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; },
abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.<br><br>METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.<br><br>RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.<br><br>CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.},
}
@article {pmid39881387,
year = {2025},
author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O},
title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {30},
pmid = {39881387},
issn = {2049-2618},
support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Metagenome ; *Probiotics/administration &amp; dosage ; Prebiotics ; Bacteria/classification/genetics/isolation &amp; purification ; Animal Feed/microbiology ; Vaccination/veterinary ; Dietary Supplements ; },
abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.<br><br>RESULTS: Using a binning strategy, 84 (&#x2265;&#x2009;75% completeness,&#x2009;&#x2264;&#x2009;5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n&#x2009;=&#x2009;52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.<br><br>CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.},
}
@article {pmid39881253,
year = {2025},
author = {Garcia, I and Riis, RK and Moen, LV and Rohringer, A and Madslien, EH and Bragstad, K},
title = {Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {87},
pmid = {39881253},
issn = {1471-2164},
mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *COVID-19/virology/epidemiology ; Humans ; *Mutation ; *High-Throughput Nucleotide Sequencing/methods ; Spike Glycoprotein, Coronavirus/genetics ; Wastewater-Based Epidemiological Monitoring ; },
abstract = {The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, current variant surveillance methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive and representative as clinical testing and sequencing efforts decline.In this paper, we introduce HERCULES (High-throughput Epidemiological Reconstruction and Clustering for Uncovering Lineages from Environmental SARS-CoV-2), an unsupervised method that uses long-read sequencing of a single 1 Kb fragment of the Spike gene. HERCULES identifies and quantifies mutations and lineages without requiring database-guided deconvolution, enhancing the detection of novel variants.We evaluated HERCULES on Norwegian wastewater samples collected from July 2022 to October 2023 as part of a national pilot on WBE of SARS-CoV-2. Strong correlations were observed between wastewater and clinical sample data in terms of prevalence of mutations and lineages. Furthermore, we found that SARS-CoV-2 trends in wastewater samples were identified one week earlier than in clinical data.Our results demonstrate HERCULES' capability to identify new lineages before their detection in clinical samples, providing early warnings of potential outbreaks. The methodology described in this paper is easily adaptable to other pathogens, offering a versatile tool for environmental surveillance of new emerging pathogens.},
}
@article {pmid39881163,
year = {2025},
author = {Dash, M and Thiyageshwari, S and Selvi, D and Johnson, HKV and Ariyan, M and Rajan, K and Anandham, R},
title = {Unveiling microbial diversity in slightly and moderately magnesium deficient acidic soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3696},
pmid = {39881163},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Magnesium/metabolism/analysis ; *RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Biodiversity ; Magnesium Deficiency/genetics ; Phosphorus/deficiency/metabolism ; Microbiota/genetics ; },
abstract = {Magnesium (Mg) an essential plant nutrient is widespread deficient in the acidic soils of Nilgiris of Tamil nadu, India. The vegetable yield and quality is especially affected due to deficiency of nutrients like Mg. This study investigates soil characteristics and bacterial diversity in the Nilgiris district of Tamil Nadu, India, with respect to Mg deficiency. The soil samples were collected from different vegetable growing regions of the Nilgiris to assess soil physiocochemical parameters, soil enzymes and soil Mg status. 16S rRNA gene-based metagenomic analysis used to investigate the functional potential and structural diversity of the bacterial communities in high Mg and low Mg deficiency soil. Results indicated mildly acidic soils with a sandy loam texture and high organic carbon content. While nitrogen (N), phosphorus (P), and potassium (K) levels were adequate, Mg deficiency was consistent. Soil enzymes such as dehydrogenase, acid phosphatase, urease and aryl sulfatase, varied across the soil samples. Additionally, 16S rRNA gene-based metagenomics analysis revealed the bacterial diversity and functional pathways in soils with high and low Mg deficiency. Low Mg levels were associated with increased bacterial richness, dominated by Proteobacteria, Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Acidobacteria. Functional pathways related to carbon metabolism, amino acid biosynthesis, and various metabolic processes were more abundant in low Mg deficient soils. This research highlights the significant influence of Mg levels on bacterial diversity and functional potentials in acidic soils, providing insights into soil management strategies in Mg-deficient regions.},
}
@article {pmid39880958,
year = {2025},
author = {Maghini, DG and Oduaran, OH and Olubayo, LAI and Cook, JA and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SSR and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Wirbel, J and , and Bhatt, AS and Hazelhurst, S},
title = {Expanding the human gut microbiome atlas of Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39880958},
issn = {1476-4687},
support = {R01 AI148623/AI/NIAID NIH HHS/United States ; D43 TW010540/TW/FIC NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; U54 HG006938/HG/NHGRI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; },
abstract = {Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives[1], are not equitably represented in large-scale gut microbiome research[2-4]. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.},
}
@article {pmid39880818,
year = {2025},
author = {Jiang, ZJ and Hong, JC and Lin, BW and Zhang, WQ and Fan, QC and Yang, BH and Yao, XP},
title = {Comparison of mNGS with conventional methods for diagnosis of cryptococcal meningitis: a retrospective study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3656},
pmid = {39880818},
issn = {2045-2322},
support = {2019XQ1079//Startup Fund for Scientific Research of Fujian Medical University/ ; 82171841//National Natural Science Foundation of China/ ; 2020Y93010140//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; },
mesh = {*Meningitis, Cryptococcal/diagnosis/cerebrospinal fluid/microbiology ; Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Sensitivity and Specificity ; Metagenomics/methods ; Antigens, Fungal/cerebrospinal fluid/analysis ; Young Adult ; },
abstract = {The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of cryptococcal meningitis is relatively under characterized. Here, we retrospectively evaluated data from cryptococcal meningitis patients who were tested using mNGS and/or routine testing, including fungal culture, India ink staining, and cryptococcal antigen (CrAg) testing. The performance of mNGS was then assessed. Initial cerebrospinal fluid (CSF) samples were collected from 65 patients with suspected central nervous system (CNS) infection and tested using conventional tests and/or mNGS. mNGS offers a culture-independent approach, facilitating a rapid and unbiased detection of a broad spectrum of pathogens. Patients with bacterial tuberculous or viral meningitis were used as mNGS-positive controls and one autoimmune encephalitis patient was used as an mNGS-negative control. In the 45 patients diagnosed with cryptococcal meningitis, the sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 92%, 100%, 100%, 90.9%, and 95.6%, respectively. Compared to conventional methods, the sensitivity of mNGS was slightly lower than CrAg tests (96.7%) but higher than India ink (79.5%) and culturing (63.4%). Of the two negative mNGS cases (2/25, 8.0%), one was positive by India ink staining, culture, and CrAg testing, while the other was positive only by CrAg testing. A combination of mNGS and conventional methods enhanced the detection rate to 100%. Our study demonstrates that both CrAg and mNGS offer excellent diagnostic accuracy for cryptococcal meningitis, and utilizing both tests can enhance clinical assessment and patient management.},
}
@article {pmid39880110,
year = {2025},
author = {Chen, N and Wang, L and Zhao, Z and Zhu, M and Li, Y},
title = {Impacts of aquaculture on nitrogen cycling and microbial community dynamics in coastal tidal flats.},
journal = {Environmental research},
volume = {270},
number = {},
pages = {120973},
doi = {10.1016/j.envres.2025.120973},
pmid = {39880110},
issn = {1096-0953},
abstract = {The expansion of aquaculture areas has encroached upon vast areas of coastal wetlands and introduced excessive nitrogen inputs, disrupting microbial communities and contributing to various environmental issues. However, investigations on how aquaculture affects microbial communities and nitrogen metabolism mechanisms in coastal tidal flats remain scarce. Hence, we explored the composition, diversity, and assembly processes of nitrogen-cycling (N-cycling) microbial communities in tidal flats in Jiangsu using metagenomic assembly methods. Our study further delved into the seasonal variations of these microbial characteristics to better explore the effects of seasonal changes in aquaculture areas on microbial community. Nitrogen metabolism-related processes and functional genes were identified through the KEGG and NCyc databases. The results revealed significant seasonal variation in the relative abundance and composition of microbial communities. Higher diversity was observed in winter, while the co-occurrence network of microbial communities was more complex in summer. Pseudomonadota emerged as the most abundant phylum in the N-cycling community. Furthermore, pH and NO3-N were identified as the primary factors influencing bacterial community composition, whereas NO2-N was more strongly associated with the N-cycling community. Regarding the nitrogen metabolism processes, nitrogen mineralization and nitrification were predominant in the tidal flat regions. NO2-N and NO3-N exhibited significant effects on several N-cycling functional genes (e.g., nirB, hao, and narG). Finally, neutral and null modeling analyses indicated that bacterial communities were predominantly shaped by stochastic processes, whereas N-cycling communities were largely driven by deterministic processes. These findings highlighted the significant role that aquaculture pollution plays in shaping the N-cycling communities in tidal flats. This underscored the importance of understanding microbial community dynamics and nitrogen metabolism in tidal flats to improve environmental management in coastal aquaculture areas.},
}
@article {pmid39879767,
year = {2025},
author = {Li, S and Bai, Y and Li, Z and Wang, A and Ren, NQ and Ho, SH},
title = {Overlooked role of extracellular polymeric substances in antibiotic-resistance gene transfer within microalgae-bacteria system.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137206},
doi = {10.1016/j.jhazmat.2025.137206},
pmid = {39879767},
issn = {1873-3336},
abstract = {Controlling the spread of antibiotic-resistance genes (ARGs) under antibiotic stress has become an increasingly urgent issue. Microalgae possess the capability to remove antibiotics while concurrently inhibiting ARGs. Microalgae-bacteria systems can produce significant quantities of extracellular polymeric substances (EPS). However, the roles of EPS in the spread of ARGs have not been sufficiently explored, resulting in an insufficient understanding of the contribution of each EPS component and a lack of analysis on the complex interactions between EPS and ARGs. This study systematically explored the overlooked role of EPS in the transmission of ARGs within microalgae-bacteria systems. The current results showed that the potential of the microalgae-bacteria system for treating antibiotic wastewater. The tightly bound-EPS (TB-EPS) can acquire the higher absolute abundances of ARGs compared with the loosely bound-EPS (LB-EPS). The correlation coefficient between polysaccharides and TB-EPS ARGs was higher than that between polysaccharides and LB-EPS ARGs. The gene patterns of LB-EPS closely clustered with those of TB-EPS, while intracellular ARG gene patterns differed from both TB-EPS and LB-EPS. Metagenomic analyses indicated that the relative abundances of sul1 and sul2 were considerably higher at the beginning stage compared to the end stage. The abundance of Achromobacter, increased by the end stage, aligning with its potential to produce exopolysaccharide. Additionally, the absolute abundance of genes encoding exopolysaccharides (nagB and galE) and conjugative transfer transcription regulator (traF), increased over time. These findings enhanced our comprehension of the significance of EPS on the fate of ARGs in microalgae-bacteria systems during the treatment of antibiotic-contaminated wastewater.},
}
@article {pmid39879766,
year = {2025},
author = {Liu, X and Li, H and Yang, J and Yan, S and Zhou, Y and Jiang, R and Li, R and Wang, M and Ren, P},
title = {Different effects of bio/non-degradable microplastics on sewage sludge compost performance: Focusing on antibiotic resistance genes, virulence factors and key metabolic functions.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137329},
doi = {10.1016/j.jhazmat.2025.137329},
pmid = {39879766},
issn = {1873-3336},
abstract = {Microplastics (MP) have aroused increasing concern due to the negative environmental impact. However, the impact of bio/non-biodegradable MPs on the sludge composting process has not been thoroughly investigated. This study examined antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial community functions in sludge compost with the application of polylactic acid (PLA) and polypropylene (PP), using metagenomic sequencing. The findings indicated that both types of MPs could extend the thermophilic phase, enhance microbial activity, and inhibit the formation of humic acids. Compared to CK, the subtypes of ARGs decreased 4.22 % and 13.11 % in PLA and PP groups, respectively. But new ARGs emerged, particularly in the PLA group. The proportions of ARGs related to efflux and VFs associated with the adhesion system increased 1.62 %-2.27 % and 55.56 %-60.00 %, respectively, in MPs-added composts. The relative abundance of potential bacterial hosts (e.g., Psychrobacter) carrying multiple ARGs and VFs was much higher in PLA-added compost than in the other two. Moreover, PP facilitated denitrification process and PLA enhanced dissimilatory nitrate reduction to ammonium. Both types of MPs inhibited assimilatory nitrate reduction to ammonia but promoted inorganic nitrogen assimilation. This study broadens our understanding of the potential environmental risks posed by biodegradable and non-biodegradable microplastics on sludge compost and offers valuable insights for the management and application of compost products.},
}
@article {pmid39879090,
year = {2025},
author = {McReynolds, E and Elshahed, MS and Youssef, NH},
title = {An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota.},
journal = {Microbial genomics},
volume = {11},
number = {1},
pages = {},
pmid = {39879090},
issn = {2057-5858},
support = {P20 GM152333/GM/NIGMS NIH HHS/United States ; },
mesh = {*Phylogeny ; *Ecosystem ; *Soil Microbiology ; *Acidobacteria/genetics/classification ; Genome, Bacterial ; Evolution, Molecular ; Metagenomics ; Genetic Variation ; },
abstract = {Members of the phylum Acidobacteriota inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various Acidobacteriota lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes Terriglobia, Vicinamibacteria, Blastocatellia and Thermoanaerobaculia were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes Aminicenantia and Holophagae showed preferences to non-soil habitats. However, while specific preferences were observed, most Acidobacteriota lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of the Acidobacteriota. The observed lack of strong habitat specialization and habitat-transition-driven lineage evolution in the Acidobacteriota suggest ready cross-colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of Acidobacteriota as a major component in soil microbiomes post-ecosystem disturbance events or during pedogenesis.},
}
@article {pmid39878481,
year = {2025},
author = {Ragupathy, V and Kelley, K and Hewlett, I},
title = {Identification of near full-length human pegivirus type 2 (HPgV-2) genomes in blood donor samples co-infected with hepatitis C virus (HCV).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0117924},
doi = {10.1128/mra.01179-24},
pmid = {39878481},
issn = {2576-098X},
abstract = {Human pegivirus (HPgV) identified from an HCV-infected plasma sample through nanopore metagenomics. The analysis revealed a nearly complete HPgV-2 genome. Phylogenetic analysis confirmed its classification within the HPgV-2 genotype, providing insights into viral co-infection dynamics. The metagenomics approach advances the understanding of viral diversity and supports the development of accurate diagnostics.},
}
@article {pmid39878462,
year = {2025},
author = {Ho, JY and Hu, D and Case, RJ and Boucher, YF},
title = {Metagenome-assembled genomes (MAGs) of the emerging pathogen Shewanella algae from enrichment of coastal seawater, sediment, and algae at St. John's Island, Singapore.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0084624},
doi = {10.1128/mra.00846-24},
pmid = {39878462},
issn = {2576-098X},
abstract = {Coastal water, sediment, and algae samples were collected from St. John's Island, Singapore, and enriched in either broth or agar. Metagenomic sequencing was carried out on DNA from these enrichments and analyzed. A total of 29 metagenome-assembled genomes had been successfully asserted to be a close representation of Shewanella algae.},
}
@article {pmid39877883,
year = {2024},
author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Sowa, K and Kitazumi, Y and Shirai, O},
title = {A suitable solvent for adsorption of poorly water-soluble substances onto silica gel in a ready biodegradability test.},
journal = {Journal of pesticide science},
volume = {49},
number = {4},
pages = {271-276},
pmid = {39877883},
issn = {1348-589X},
abstract = {When a test substance is poorly water-soluble, it can be adsorbed onto silica gel to facilitate dispersibility in a ready biodegradability test. To uniformly adsorb the test substance onto silica gel, the substance is dissolved in a solvent and then mixed with the silica gel. It is desirable for the solvent to completely evaporate afterward. In this study, we identified n-hexane as a suitable solvent for this purpose. Furthermore, through fluorescence observation, we revealed that the test substance adsorbed onto the silica gel adhered to activated sludge flocs. This is thought to improve contact between the test substance and microorganisms, thereby accelerating biodegradation.},
}
@article {pmid39877881,
year = {2024},
author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Sowa, K and Kitazumi, Y and Shirai, O},
title = {Comparative evaluation of trimethylated α-, β-, and γ-cyclodextrins as optimal dispersants for ready biodegradability testing of poorly water-soluble substances.},
journal = {Journal of pesticide science},
volume = {49},
number = {4},
pages = {210-223},
pmid = {39877881},
issn = {1348-589X},
abstract = {We investigated whether various modified cyclodextrins (CDs) and emulsifiers could be applied as dispersing agents in ready biodegradability tests of poorly water-soluble substances. Trimethylated α-, β-, and γ-CDs and partially methylated β-CD were not biodegraded in the test period but accelerated the biodegradation of octabenzone and anthraquinone. The process by which trimethylated α-, β-, and γ-CDs enhance the biodegradation of test substances has been partially uncovered. These CDs create inclusion complexes with the substances, which then coalesce into larger aggregates. These aggregates disperse throughout the testing medium and attach to clusters of activated sludge, known as flocs. This close contact with the sludge speeds up the breakdown of the hydrophobic substances being tested.},
}
@article {pmid39877811,
year = {2025},
author = {Latif, S and Kousar, R and Fatima, A and Khan, N and Fatimah, H},
title = {Internal transcribed spacer metagenomics data unravelling the core fungal community structure residing the wheat and maize rhizosphere.},
journal = {Data in brief},
volume = {58},
number = {},
pages = {111269},
pmid = {39877811},
issn = {2352-3409},
abstract = {Plants are colonized by a vast array of microorganisms that outstrip plant cell densities and genes, thus referred to as plant's second genome or extended genome. The microbial communities exert a significant influence on the vigor, growth, development and productivity of plants by supporting nutrient acquisition, organic matter decomposition and tolerance against biotic and abiotic stresses such as heat, high salt, drought and disease, by regulating plant defense responses. The rhizosphere is a complex micro-ecological zone in the direct vicinity of plant roots and is considered a hotspot of microbial diversity. The exploration and understanding of the rhizosphere microbes can be valuable in sustainable agriculture. The present dataset aimed to reveal the core fungal community residing in the rhizosphere of wheat (Triticum aestivum L.) and maize (Zea mays L.). The rhizosphere fungal communities were explored via amplicon sequencing of the Internal Transcribed Spacer (ITS) region using the IonS5[TM]XL sequencing platform. The data obtained were filtered and the high-quality reads were clustered into Microbial Operational Taxonomic Units (OTUs) at 97 % similarity. Further, the data were subjected to alpha and beta diversity analysis. The OTUs obtained from the wheat rhizosphere soils of Kallar Syedian (TA.KS), Islamabad (TA.ISB) and Mirpur Azad Kashmir (TA.MAK) were 603, 513 and 424, respectively, whereas 616 OTUs were found in the maize rhizosphere soil of Kallar Syedian (ZM.KS). The major fungal phyla inhabiting the rhizosphere soils were Ascomycota, accounting for 94 %, 97 %, 95 % and 90 % of the fungal community in ZM.KS, TA.KS, TA.MAK and TA.ISB, respectively. Alpha and beta diversity analysis depicted the presence of considerable variations in the relative abundance of fungal groups residing in the rhizosphere soils. The dataset obtained can be employed in meta-analysis studies that will pave the way toward understanding the core fungal community structure and will directly aid in enhancing crop productivity through rhizosphere engineering.},
}
@article {pmid39877399,
year = {2025},
author = {Park, SY and Goldman, JD and Levine, DJ and Haidar, G},
title = {A Systematic Literature Review to Determine Gaps in Diagnosing Suspected Infection in Solid Organ Transplant Recipients.},
journal = {Open forum infectious diseases},
volume = {12},
number = {1},
pages = {ofaf001},
pmid = {39877399},
issn = {2328-8957},
abstract = {BACKGROUND: Improved diagnostic testing (DT) of infections may optimize outcomes for solid organ transplant recipients (SOTR), but a comprehensive analysis is lacking.<br><br>METHODS: We conducted a systematic literature review across multiple databases, including EMBASE and MEDLINE(R), of studies published between 1 January 2012-11 June 2022, to examine the evidence behind DT in SOTR. Eligibility criteria included the use of conventional diagnostic methods (culture, biomarkers, directed-polymerase chain reaction [PCR]) or advanced molecular diagnostics (broad-range PCR, metagenomics) to diagnose infections in hospitalized SOTR. Bias was assessed using tools such as the Cochrane Handbook and PRISMA 2020.<br><br>RESULTS: Of 2362 studies, 72 were eligible and evaluated heterogeneous SOT populations, infections, biospecimens, DT, and outcomes. All studies exhibited bias, mainly in reporting quality. Median study sample size was 102 (range, 11-1307). Culture was the most common DT studied (N = 45 studies, 62.5%), with positive results in a median of 27.7% (range, 0%-88.3%). Biomarkers, PCR, and metagenomics were evaluated in 7, 19, and 3 studies, respectively; only 6 reported sensitivity, specificity, and positive/negative predictive values. Directed-PCR performed well for targeted pathogens, but only 1 study evaluated broad-range PCR. Metagenomics approaches detected numerous organisms but required clinical adjudication, with too few studies (N = 3) to draw conclusions. Turnaround time was shorter for PCR/metagenomics than conventional diagnostic methods (N = 4 studies, 5.6%). Only 6 studies reported the impact of DT on outcomes like antimicrobial use and length of stay.<br><br>CONCLUSIONS: We identified considerable evidence gaps in infection-related DT among SOT, particularly molecular DT, highlighting the need for further research.},
}
@article {pmid39877321,
year = {2025},
author = {Ito, E and Ohki, T and Toya, N and Emoto, T and Yamashita, T and Sugiyama, T and Yamada, T and Mori, H and Toyoda, A and Hirata, KI},
title = {Metagenomic Analysis of Gut Microbiota for Abdominal Aortic Aneurysm.},
journal = {Annals of vascular diseases},
volume = {18},
number = {1},
pages = {},
pmid = {39877321},
issn = {1881-641X},
abstract = {Objectives: The pathophysiological mechanism of abdominal aortic aneurysm (AAA) remains unclear. We previously reported that Bifidobacterium adolescentis levels were reduced in the feces of patients with AAA by 16S ribosomal ribonucleic acid (RNA) gene sequencing. In this study, we increased the number of cases and conducted metagenomic analyses to examine bacterial genes associated with the pathophysiology of AAA. Methods: For gut microbiota data, feces from 55 patients with AAA and 52 patients with no history of AAA, lower extremity artery disease, or coronary artery disease (control group) were collected. Metagenomic analysis was performed by collecting raw stool samples from patients. For intestinal microbiota analysis, metagenomic analysis of the fecal samples was performed. Results: Oral bacteria, including Actinomyces oris (p <0.0001), Streptococcus salivarius (p <0.001), Lactobacillus salivarius (p <0.001), and Streptococcus sp. (p <0.001), were increased in the feces of patients with AAA. In addition, bacterial genes related to alpha lipoic acid (ALA) biosynthesis (M00882, M00883, and M00884, p <0.0001) were decreased in patients with AAA. Conclusions: In the feces of patients with AAA, there was an increase in oral bacteria, and the expression of bacterial genes related to ALA biosynthesis was reduced. The results suggest the possibility of developing gut microbial drug treatments for AAA.},
}
@article {pmid39877152,
year = {2025},
author = {Plewka, J and Alibrandi, A and Bornemann, TLV and Esser, SP and Stach, TL and Sures, K and Becker, J and Moraru, C and Soares, A and di Primio, R and Kallmeyer, J and Probst, AJ},
title = {Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqae027},
pmid = {39877152},
issn = {2633-6693},
abstract = {Oil reservoirs are society's primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, n-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.},
}
@article {pmid39876557,
year = {2025},
author = {Morsink, MC and van Schaik, EN and Bossers, K and Duijker, DA and Speksnijder, AGCL},
title = {Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bmb.21888},
pmid = {39876557},
issn = {1539-3429},
abstract = {Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.},
}
@article {pmid39876003,
year = {2025},
author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M},
title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {28},
pmid = {39876003},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; },
abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.<br><br>RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.<br><br>CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.},
}
@article {pmid39875829,
year = {2025},
author = {Zhang, Z and Zong, X and Liu, Z and Dong, X and Bai, H and Fan, L and Li, T},
title = {Comprehensive analysis of vaginal microbiota in Chinese women with genital tuberculosis: implications for diagnosis and treatment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {52},
pmid = {39875829},
issn = {1471-2180},
support = {2024-4-2119//Capital's Funds for Health Improvement and Research/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; YQRC201906//"Excellent young Talents" project of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Tuberculosis, Female Genital/microbiology/diagnosis ; *Microbiota ; China ; Middle Aged ; Young Adult ; Antitubercular Agents/therapeutic use ; Lactobacillus/isolation &amp; purification/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; East Asian People ; },
abstract = {BACKGROUND: Tuberculosis remains an infectious disease of global concern, with potential impacts on respiratory and intestinal microbiota owing to prolonged broad-spectrum antibiotic therapy. Despite its potential to cause infertility, the vaginal microbiota of women with genital tuberculosis remains poorly understood. We comprehensively analyzed the vaginal microbiota in Chinese women with genital tuberculosis.<br><br>RESULTS: We recruited women with pelvic (n&#x2009;=&#x2009;28), endometrial (n&#x2009;=&#x2009;16), and pulmonary (n&#x2009;=&#x2009;12) tuberculosis as the research group, and healthy women (n&#x2009;=&#x2009;11) as the control group. Vaginal discharges were collected for metagenomic analysis of its microbiota. The alpha diversity of the vaginal microbiota in women with genital tuberculosis was slightly higher than that in healthy women, though the difference was not statistically significant (P&#x2009;=&#x2009;0.23). Similarly, no significant differences in alpha diversity were observed between women with genital and pulmonary tuberculosis (P&#x2009;=&#x2009;0.82) or between those with pelvic and endometrial tuberculosis (P&#x2009;=&#x2009;0.82). Notably, the lowest alpha diversity was recorded six months to one year after initiating anti-tuberculosis treatment, with this decline being statistically significant (P&#x2009;=&#x2009;0.023). The dominance of Lactobacillus iners in the vaginal microbiota was more common in women with genital tuberculosis than that of Lactobacillus crispatus. Furthermore, the abundance of short-chain fatty acid -producing anaerobes, such as Actinomycetes, Streptococcus, and Finegoldia, were significantly increased. Short-chain fatty acid precursor pathways, including the ko03010 ribosome pathway, ko00970 aminoacyl-tRNA synthesis, ko00230 purine metabolism, ko00240 pyrimidine metabolism, and ko00010 glycolysis gluconeogenesis pathway, were significantly upregulated in women with endometrial tuberculosis.<br><br>CONCLUSIONS: Extrapulmonary tuberculosis, particularly genital tuberculosis and its associated vaginal dysbiosis impacts female fecundity. Vaginal dysbiosis is more pronounced when M. tuberculosis invades the endometrium. Given the effect of antibiotics on vaginal flora, probiotic combined interventions could be used as a future research direction.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid39875797,
year = {2025},
author = {Sung, YH and Ju, YK and Lee, HJ and Park, SM and Suh, JW and Kim, JY and Sohn, JW and Yoon, YK},
title = {Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3493},
pmid = {39875797},
issn = {2045-2322},
support = {Q2021541//Yuhan/ ; HI23C1297//Ministry of Health and Welfare/ ; },
mesh = {Humans ; Pilot Projects ; Female ; Male ; *Meningitis, Bacterial/cerebrospinal fluid/diagnosis/microbiology ; *Metagenomics/methods ; Middle Aged ; *Nanopore Sequencing/methods ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/genetics/isolation &amp; purification/classification ; Aged ; Nanopores ; Cerebrospinal Fluid/microbiology ; Young Adult ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis.},
}
@article {pmid39875095,
year = {2025},
author = {Moeller, AH},
title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240454},
pmid = {39875095},
issn = {1744-957X},
support = {/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Genome, Bacterial ; Geography ; },
abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.},
}
@article {pmid39875062,
year = {2025},
author = {Zhan, M and Li, Z and Chen, J and Zhao, Y and Bai, Z and Lu, B and Chen, H and Liu, Y},
title = {Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110430},
doi = {10.1016/j.clim.2025.110430},
pmid = {39875062},
issn = {1521-7035},
abstract = {OBJECT: Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.<br><br>METHOD: A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.<br><br>RESULT: Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.<br><br>CONCLUSIONS: Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.},
}
@article {pmid39874761,
year = {2025},
author = {Wang, R and Chen, J and Chen, H},
title = {Metagenomic insights into efficiency and mechanism of antibiotic resistome reduction by electronic mediators-enhanced microbial electrochemical system.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137350},
doi = {10.1016/j.jhazmat.2025.137350},
pmid = {39874761},
issn = {1873-3336},
abstract = {Electronic mediators are an effective means of enhancing the efficiency of microbial electrochemical electron transfer; however, there are still gaps in understanding the strengthening mechanisms and the efficiency of removing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study systematically elucidates the effects of various electron mediators on bioelectrochemical processes, electron transfer efficiency, and the underlying mechanisms that inhibit ARG propagation within sediment microbial fuel cell systems (SMFCs). The results indicate that the addition of electron mediators significantly increased the output voltage (33.3 %-61.1 %) and maximum power density (14 %-106 %) of SMFCs, while also reducing ARB abundance and transmission risk. The enhancement effect follows the order of biochar, nanoscale zero-valent iron, graphene, and carbon nanotubes, with biochar emerging as the most economical and efficient choice for generating electricity and removing human pathogenic bacteria carrying ARGs. Procrustes analysis revealed that electron mediators facilitated the removal of ARGs by altering the structure of the microbiome, particularly the electricity-generating microorganisms (EGMs). Voltage and mobile genetic elements were the primary drivers of ARGs in the SMFCs. The network analysis results show that multiple carbohydrate-active enzymes, cluster of orthologous groups, and EGMs were negatively correlated with ARGs, indicating that the electron mediator-enhanced SMFCs mainly inhibit the spread of ARGs by promoting cell division, carbohydrate metabolism, and electricity generation. This study provides novel insights into how electron mediators affect ARG removal in microbial electrochemistry, which can inform economically viable strategies for sustainable environmental remediation.},
}
@article {pmid39874694,
year = {2025},
author = {Wang, H and Dai, H and Jiang, D and Cao, X and Wang, R and Dai, Z and Zhang, W and Abbasi, HN and Li, B and Zhu, G and Wang, X},
title = {Screening, identification, and application of anaerobic ammonia oxidizing bacteria in activated sludge systems: A comprehensive review.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124272},
doi = {10.1016/j.jenvman.2025.124272},
pmid = {39874694},
issn = {1095-8630},
mesh = {*Sewage/microbiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; Bacteria, Anaerobic/metabolism ; Nitrogen/metabolism ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; },
abstract = {Anaerobic ammonium oxidation (Anammox) has garnered significant attention due to its ability to eliminate the need for aeration and supplementary carbon sources in biological nitrogen removal process, relying on the capacity of anaerobic ammonium oxidizing bacteria (AnAOB) to directly convert ammonium and nitrite nitrogen into nitrogen gas. This review consolidates the latest advancements in AnAOB research, outlining the mechanisms and enzymatic processes of Anammox, and summarizing the molecular biological techniques used for studying AnAOB, such as 16s rRNA sequencing, qPCR, and metagenomic sequencing. Additionally, it also overviews the currently identified AnAOB species and their distinct metabolic traits, while consolidating strategies to improve their performance. It further delineates coupled processes that utilize Anammox technology, offering practical insights for process selection. Eventually, the review concludes by suggesting future research directions and highlighting critical areas for further investigation. This review serves as a theoretical reference for the enrichment and cultivation of AnAOB, environmental impact management, and the selection of effective treatment processes.},
}
@article {pmid39874239,
year = {2025},
author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I},
title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.},
journal = {Annals of the rheumatic diseases},
volume = {84},
number = {1},
pages = {93-105},
doi = {10.1136/ard-2024-225829},
pmid = {39874239},
issn = {1468-2060},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; },
abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.<br><br>METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.<br><br>RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.<br><br>CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.<br><br>TRIAL REGISTRATION NUMBER: NCT02394964.},
}
@article {pmid39873828,
year = {2025},
author = {Pal, S and Biswas, R and Sar, A and Misra, A and Dam, S and Dam, B},
title = {ABC-type salt tolerance transporter genes are abundant and mutually shared among the microorganisms of the hypersaline Sambhar Lake.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {1},
pages = {14},
pmid = {39873828},
issn = {1433-4909},
mesh = {*Salt Tolerance ; *Lakes/microbiology ; *ATP-Binding Cassette Transporters/genetics/metabolism ; Metagenome ; India ; Bacterial Proteins/genetics/metabolism ; },
abstract = {To fish-out novel salt-tolerance genes, metagenomic DNA of moderately saline sediments of India's largest hypersaline Sambhar Lake was cloned in fosmid. Two functionally-picked clones helped the Escherichia coli host to tolerate 0.6 M NaCl. Deep sequencing of their fosmid DNA insert revealed 32-37% of genes to encode transporters, mostly belonging to ABC (ATP-Binding Cassette)-type, but none specific to channel Na[+]. The complete metagenome sequence of Sambhar Lake brines, and reanalysed data of twelve other hypersaline metagenome sequences, however, have only around 5% transporter genes, suggesting metagenomic DNA fragments being biasedly-cloned during functional screening. Almost half of the ~ 40 Kb inserts in the two clones was shared, and encode several transporters, and some transposase. This advocates that these transporter-loaded DNA lengths are shuttled among microorganisms of hypersaline environments. Interestingly, one clone showed retarded growth with prominent cell disruptions in scanning electron microscopic images, when fosmid copy number was increased or transporters were NaCl-induced. Its cloned insert exclusively has three genes, encoding a structurally functional ATP-binding protein and its efflux component, whose possible overexpression led to membrane crowding and cell rupture. Thus, microorganisms thriving in hypersaline lakes have plentiful ABC transporters that are mutually shared among themselves. These novel salt tolerance genes have future agricultural biotechnological potential.},
}
@article {pmid39873521,
year = {2025},
author = {Pu, G and Hou, L and Zhao, Q and Liu, G and Wang, Z and Zhou, W and Niu, P and Wu, C and Li, P and Huang, R},
title = {Interactions between gut microbes and host promote degradation of various fiber components in Meishan pigs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150024},
doi = {10.1128/msystems.01500-24},
pmid = {39873521},
issn = {2379-5077},
abstract = {UNLABELLED: Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with GPR183 and GPR174 exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, GPR174 and SLC2A4 were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs.<br><br>IMPORTANCE: Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA absorption in cecum. By integrating multi-omics data, we constructed a framework outlining host-microbiota interactions that control dietary fiber utilization in pigs. Our data provide novel insights into host-microbiota interactions regulating fiber degradation and lay some theoretical foundations for improving the utilization efficiency of high-fiber cereal feed in pigs through targeted modulation of gut microbial function.},
}
@article {pmid39873074,
year = {2025},
author = {Yang, YH and Yu, JJ and Han, HY and Chang, WM and Wang, CW},
title = {Ex-vivo investigation of human salivary microbial growth with lysogeny broth for translational research-A pilot study.},
journal = {Journal of dental sciences},
volume = {20},
number = {1},
pages = {437-443},
pmid = {39873074},
issn = {2213-8862},
abstract = {BACKGROUND/PURPOSE: Salivary microbiome has become a surrogate indicator of oral disease due to its collective reservoirs and convenience in sampling. However, failed clinical trials often lead to wastes of resources, indicating a need for preclinical models. In this pilot study, we aimed to compare the salivary microbiome by metagenomics analysis before and after lysogeny broth culture for prospective translational studies.<br><br>MATERIALS AND METHODS: The study cohort included seven patients with severe periodontitis (Stage III/IV, Grade C), from whom unstimulated saliva was collected. The salivary microbiome was sequenced over the 16S rRNA gene V3-V4 hypervariable regions at baseline and after 6&#xa0;hours of lysogeny broth culture.<br><br>RESULTS: The results revealed changes in salivary microbiome and reduced bacterial diversity after culture, mainly due to the expansion of genera Neisseria (Median (Mdn) 15.95% to 37.52%, P&#xa0;<&#xa0;0.05), Rothia (Mdn 10.21% to 16.32%, P&#xa0;<&#xa0;0.05), and Haemophilus (Mdn 5.88% to 13.25%, P&#xa0;<&#xa0;0.05). Periodontitis-related pathogens such as phyla Bacteroidetes, Fusobacteria and Spirochaetes were identified, while genera Porphyromonas, Parvimonas, Peptostreptococcus, and Campylobacter showed a decrease after lysogeny broth culture. Caries-related pathogens, including genera Veillonella, Leptotrichia, and species Haemophilus parainfluenzae and Streptococcus salivarius, were also detected.<br><br>CONCLUSION: This pilot study revealed that periodontitis- and caries-related bacteria could be identified in the saliva at baseline and after 6&#xa0;hours ex-vivo culture with lysogeny broth. Our findings also suggested that lysogeny broth favored the growth of specific genera and may serve as a reference to monitor short-term modulation of these bacteria in salivary microbiome.},
}
@article {pmid39872816,
year = {2024},
author = {Gu, G and Zeeshan Ul Haq, M and Sun, X and Zhou, J and Liu, Y and Yu, J and Yang, D and Yang, H and Wu, Y},
title = {Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1482904},
pmid = {39872816},
issn = {1664-302X},
abstract = {Continuous cropping (CC) profoundly impacts soil ecosystems, including changes in soil factors and the structure and stability of microbial communities. These factors are interrelated and together affect soil health and plant growth. In this research, metagenomic sequencing was used to explore the effects of CC on physicochemical properties, enzyme activities, microbial community composition, and functional genes of the rhizosphere soil of patchouli. We found that this can lead to changes in various soil factors, including the continuous reduction of pH and NH 4 + -N and the unstable changes of many factors. In addition, S-PPO enzyme activity increased significantly with the cropping years, but S-NAG increased in the first 2 years and decreased in the third cropping year. Metagenomic sequencing results showed that CC significantly changed the diversity and composition of rhizosphere microbial communities. The relative abundance of Pseudomonas and Bacteroides decreased substantially from the phylum level. At the genus level, the number of microbial genera specific to the zero-year cropping (CK) and first (T1), second (T2), and third (T3) years decreased significantly, to 1798, 172, 42, and 44, respectively. The abundance of many functional genes changed, among which COG0823, a gene with the cellular process and signaling functions, significantly increased after CC. In addition, NH 4 + -N, S-CAT, S-LAP, and SOC were the main environmental factors affecting rhizosphere-dominant microbial communities at the phylum level, while pH, SOC, and AK were the key environmental factors affecting rhizosphere functional genes of Pogostemon cablin. In summary, this study showed the dynamic changes of soil factors and rhizosphere microorganisms during CC, providing a theoretical basis for understanding the formation mechanism and prevention of CC obstacles and contributing to the formulation of scientific soil management and fertilization strategies.},
}
@article {pmid39872134,
year = {2025},
author = {Li, Y and Ren, X and Wang, Q and Shen, S and Li, Y and Qian, X and Tang, Y and Jia, J and Zhang, H and Ding, J and Song, Y and Zhang, S and Wang, S and Xu, Y and Jiang, Y and He, X and Dai, M and Zhong, L and Xiong, Y and Pan, Y and Wang, M and Shao, H and Cai, H and Huang, L and Wang, H},
title = {A Predictive Model for Pulmonary Aspergillosis in ICU Patients: A Multicenter Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {441-454},
pmid = {39872134},
issn = {1178-6973},
abstract = {BACKGROUND: Several predictive models for invasive pulmonary aspergillosis (IPA) based on clinical characteristics have been reported. Nevertheless, the significance of other concurrently detected microorganisms in IPA patients is equally noteworthy. This study aimed to develop a risk prediction model for IPA by integrating clinical and microbiological characteristics.<br><br>METHODS: This retrospective study was conducted in adult intensive care units (ICUs) of 17 medical centers in China. Clinical data were collected from patients with severe pneumonia who underwent clinical metagenomics of bronchoalveolar lavage fluid between January 1, 2019, and June 30, 2023. Subsequently, patients were randomly assigned to training and validation cohorts in a 7:3 ratio. In the training cohort, potential influencing factors were identified through univariate analysis, clinical practice, and existing literature, and a risk prediction model was constructed using multivariate logistic regression analysis. The performance of this model was then assessed and validated in the validation cohort.<br><br>RESULTS: Out of 1737 patients initially included in the study, 898 were ultimately analyzed, of which 100 (11%) were diagnosed with IPA. The risk prediction model for IPA, incorporating microbiological characteristics, identified six independent risk factors, namely age, immunosuppression, chronic kidney disease, connective tissue disease, liver failure, and cytomegalovirus positivity. The model demonstrated a superior discriminative ability, with area under the curve (AUC) values of 0.791 and 0.792 in the training and validation cohorts, respectively. Sensitivity and specificity reached 73.1% and 74.9%, respectively, and the model demonstrated good calibration.<br><br>CONCLUSION: This study developed a novel risk prediction model for IPA incorporating microbiological characteristics based on clinical metagenomics. The model exhibited good discriminative ability and calibration.},
}
@article {pmid39872133,
year = {2025},
author = {Liu, B and Bao, Z and Chen, W and Xi, X and Ge, X and Zhou, J and Zheng, X and Zhang, P and Deng, W and Ding, R and Zhou, M and Fang, J},
title = {Targeted Next-Generation Sequencing in Pneumonia: Applications in the Detection of Responsible Pathogens, Antimicrobial Resistance, and Virulence.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {407-418},
pmid = {39872133},
issn = {1178-6973},
abstract = {BACKGROUND: Targeted next-generation sequencing (tNGS) is a high-throughput and cost-effective diagnostic alternative for pneumonia, with the ability to simultaneously detect pathogens, antimicrobial resistance genes, and virulence genes. We aimed to explore the applicability of tNGS in the co-detection of the responsible pathogens, antimicrobial resistance (AMR) genes, and virulence genes in patients with pneumonia.<br><br>METHODS: A prospective study was conducted among patients with suspected pneumonia at Ruijin Hospital from March 1 to May 31, 2023. Bronchoalveolar lavage fluid (BALF) or sputum samples were collected and sent for tNGS, metagenomic next-generation sequencing (mNGS), and conventional microbiological tests (CMTs).<br><br>RESULTS: In total, 67 BALF and 11 sputum samples from 78 patients were included in the analyses. According to the composite reference standards, the accuracy of tNGS in the detection of responsible pathogens was 0.852 (95% confidence interval 0.786-0.918), which resembled that of mNGS and remarkably exceeded that of CMTs. In addition, 81 AMR genes associated with responsible pathogens were reported, and 75.8% (25/33) priority drug-resistant pathogens could be directly identified. A total of 144 virulence genes were detected for four common pathogens. And patients with virulence genes detected were of higher proportions of severe pneumonia (95.0% vs 42.9%, P = 0.009), acute respiratory distress syndrome (55.0% vs 0%, P = 0.022), and neutrophils (82.3% vs 62.2%, P = 0.026) than those not.<br><br>CONCLUSION: In patients with pneumonia, tNGS could detect the responsible pathogens, AMR genes, and virulence genes simultaneously, serving as an efficient and cost-effective tool for the diagnosis, treatment, and severity indication of pneumonia.},
}
@article {pmid39872132,
year = {2025},
author = {Jia, Q and Wang, L and Tong, X and Sun, J and Fan, H},
title = {Coexistence of Asymptomatic Allergic Bronchopulmonary Aspergillosis and Active Pulmonary Tuberculosis: Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {401-405},
pmid = {39872132},
issn = {1178-6973},
abstract = {We present a rare case of asymptomatic allergic bronchopulmonary aspergillosis (ABPA) concurrent with active pulmonary tuberculosis. Allergic bronchopulmonary aspergillosis is an immunological pulmonary disorder characterized by hypersensitivity to Aspergillus fumigatus, while pulmonary tuberculosis (PTB) is a complex infection caused by Mycobacterium tuberculosis (MTB). The association between pulmonary tuberculosis infections and Aspergillus infections remains a fascinating area of inquiry. A 26-year-old female patient exhibited no symptoms. However, her initial chest computed tomography revealed bronchiectasis with high-attenuation mucus plugs in the upper lobes, peripheral lung atelectasis, and a tree-in-bud pattern. To obtain a clear diagnosis, she visited multiple hospitals and incurred substantial time and financial costs. Active tuberculosis was initially confirmed using specialized detection methods, including metagenomic next-generation sequencing and Xpert MTB/RIF analysis of bronchoalveolar lavage fluid. Subsequent pathological biopsy and Aspergillus-specific antibody tests further confirmed the diagnosis of allergic bronchopulmonary aspergillosis combined with active tuberculosis. Following twelve months of antituberculosis therapy, an avoidable surgery, and three months of oral glucocorticoid treatment, the patient's lung lesions showed significant resolution. This case provides valuable insights into the clinical diagnosis and management of these two distinct infectious diseases.},
}
@article {pmid39871844,
year = {2024},
author = {Zhang, Y and Yin, M and Wen, H},
title = {VV-ECMO adjuvant therapy for Leptospira complicated with H1N1 infection: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1495324},
pmid = {39871844},
issn = {2296-858X},
abstract = {BACKGROUND: Leptospirosis is an acute infectious disease that occurs by infection, progresses rapidly, and has a high mortality rate, with an estimated 1.2 million new cases and nearly 59,000 deaths each year. Due to its diverse clinical manifestations, diagnosis is often delayed. Therefore, it is necessary to pay attention to its clinical manifestations, diagnostic techniques, and treatment methods.<br><br>CASE REPORT: A 51-year-old male patient from the Han ethnic group experienced fever, chills, headache, and overall fatigue after being exposed to rain, followed by yellowing of the skin and worsening of breathing difficulties. Metagenomic next-generation sequencing (mNGS) indicates infection with leptospirosis and influenza A. After 5&#x202f;days of treatment with venovenous extracorporeal membrane oxygenation (VV-ECMO), Penicillium, and Oseltamivir, the condition improved.<br><br>CONCLUSION: Leptospirosis improves with VV-ECMO support and anti-infective treatment with penicillin and oseltamivir. VV-ECMO provides a therapeutic time window for rescue, and mNGS lays a foundation for early detection of etiology of leptospirosis.},
}
@article {pmid39871406,
year = {2025},
author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR},
title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.},
}
@article {pmid39871128,
year = {2025},
author = {Roy, S and Dawson, RA and Bradley, JA and Hernández, M},
title = {Prevalence and dynamics of antimicrobial resistance in pioneer and developing Arctic soils.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {50},
pmid = {39871128},
issn = {1471-2180},
support = {NE/X018180/1//Natural Environment Research Council/ ; NE/X018180/1//Natural Environment Research Council/ ; 730938//HORIZON EUROPE European Research Council/ ; RF\ERE\210050//Royal Society/ ; },
mesh = {*Soil Microbiology ; Arctic Regions ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Interspersed Repetitive Sequences ; Ecosystem ; },
abstract = {Antimicrobial resistance (AMR) in soil is an ancient phenomenon with widespread spatial presence in terrestrial ecosystems. However, the natural processes shaping the temporal dissemination of AMR in soils are not well understood. We aimed to determine whether, how, and why AMR varies with soil age in recently deglaciated pioneer and developing Arctic soils using a space-for-time approach. Specifically, we assess how the magnitude and spread of AMR changes with soil development stages, including antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). We showed that ARGs, MGEs, and ARB are present, and exhibit a non-uniform distribution in the developing soils. Their abundance generally increases with soil age but at different rates overall and across different glacier forefields. Our analyses suggest a strong positive relationship between soil age and ARGs and ARB, which we attribute to increased competition between microbes in older soils. We also observed a strong negative relationship between soil age and ARG diversity mediated by soil organic matter - suggesting facilitation due to the alleviation of nutrient limitation. These contrasting results suggest that both competition and facilitation can regulate AMR spread through time in the Arctic, but competition might be the stronger determinant of AMR spread.},
}
@article {pmid39870396,
year = {2025},
author = {Rytter, H and Naimi, S and Wu, G and Lewis, J and Duquesnoy, M and Vigué, L and Tenaillon, O and Belda, E and Vazquez-Gomez, M and Touly, N and Arnone, D and Hao, F and Ley, RE and Clément, K and Peyrin-Biroulet, L and Patterson, AD and Gewirtz, AT and Chassaing, B},
title = {In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333925},
pmid = {39870396},
issn = {1468-3288},
abstract = {BACKGROUND: Non-absorbed dietary emulsifiers, including carboxymethylcellulose (CMC), directly disturb intestinal microbiota, thereby promoting chronic intestinal inflammation in mice. A randomised controlled-feeding study (Functional Research on Emulsifiers in Humans, FRESH) found that CMC also detrimentally impacts intestinal microbiota in some, but not all, healthy individuals.<br><br>OBJECTIVES: This study aimed to establish an approach for predicting an individual's sensitivity to dietary emulsifiers via their baseline microbiota.<br><br>DESIGN: We evaluated the ability of an in vitro microbiota model (MiniBioReactor Arrray, MBRA) to reproduce and predict an individual donor's sensitivity to emulsifiers. Metagenomes were analysed to identify signatures of emulsifier sensitivity.<br><br>RESULTS: Exposure of human microbiotas, maintained in the MBRA, to CMC recapitulated the differential CMC sensitivity previously observed in FRESH subjects. Furthermore, select FRESH control subjects (ie, not fed CMC) had microbiotas that were highly perturbed by CMC exposure in the MBRA model. CMC-induced microbiota perturbability was associated with a baseline metagenomic signature, suggesting the possibility of using one's metagenome to predict sensitivity to dietary emulsifiers. Transplant of human microbiotas that the MBRA model deemed CMC-sensitive, but not those deemed insensitive, into IL-10[-/-] germfree mice resulted in overt colitis following CMC feeding.<br><br>CONCLUSION: These results suggest that an individual's sensitivity to emulsifier is a consequence of, and can thus be predicted by, examining their baseline microbiota, paving the way to microbiota-based personalised nutrition.},
}
@article {pmid39870395,
year = {2025},
author = {Nan, K and Zhong, Z and Yue, Y and Shen, Y and Zhang, H and Wang, Z and Zhuma, K and Yu, B and Fu, Y and Wang, L and Sun, X and Qu, M and Chen, Z and Guo, M and Zhang, J and Chu, Y and Liu, R and Miao, C},
title = {Fasting-mimicking diet-enriched Bifidobacterium pseudolongum suppresses colorectal cancer by inducing memory CD8[+] T cells.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333020},
pmid = {39870395},
issn = {1468-3288},
abstract = {BACKGROUND: Fasting-mimicking diet (FMD) boosts the antitumour immune response in patients with colorectal cancer (CRC). The gut microbiota is a key host immunity regulator, affecting physiological homeostasis and disease pathogenesis.<br><br>OBJECTIVE: We aimed to investigate how FMD protects against CRC via gut microbiota modulation.<br><br>DESIGN: We assessed probiotic species enrichment in FMD-treated CRC mice using faecal metagenomic sequencing. The candidate species were verified in antibiotic-treated conventional and germ-free mouse models. Immune landscape alterations were evaluated using single-cell RNA sequencing and multicolour flow cytometry. The microbiota-derived antitumour metabolites were identified using metabolomic profiling.<br><br>RESULTS: Faecal metagenomic profiling revealed Bifidobacterium pseudolongum enrichment in FMD-treated CRC mice. B. pseudolongum mediates the FMD antitumour effects by increasing the tissue-resident memory CD8[+] T-cell (TRM) population in CRC mice. The level of L-arginine, a B. pseudolongum functional metabolite, increased in FMD-treated CRC mice; furthermore, L-arginine induced the TRM phenotype in vivo and in vitro. Mechanistically, L-arginine is transported by the solute carrier family 7-member 1 (SLC7A1) receptor in CD8[+] T cells. Both FMD and B. pseudolongum improved anti-CTLA-4 efficacy in the orthotopic mouse CRC model. In FMD-treated patients with CRC, the CD8[+] TRM cell number increased as B. pseudolongum and L-arginine accumulated. The abundance of CD8[+] TRM cells and B. pseudolongum was associated with a better prognosis in patients with CRC.<br><br>CONCLUSION: B. pseudolongum contributes to the FMD antitumour effects in CRC by producing L-arginine. This promotes CD8[+] T-cell differentiation into memory cells. B. pseudolongum administration is a potential CRC therapeutic strategy.},
}
@article {pmid39869988,
year = {2025},
author = {Pietilä, S and Suomi, T and Paulin, N and Laiho, A and Sclivagnotis, YS and Elo, LL},
title = {Adaptive sequence alignment for metagenomic data analysis.},
journal = {Computers in biology and medicine},
volume = {186},
number = {},
pages = {109743},
doi = {10.1016/j.compbiomed.2025.109743},
pmid = {39869988},
issn = {1879-0534},
abstract = {With advances in sequencing technologies, the use of high-throughput sequencing to characterize microbial communities is becoming increasingly feasible. However, metagenomic assembly poses computational challenges in reconstructing genes and organisms from complex samples. To address this issue, we introduce a new concept called Adaptive Sequence Alignment (ASA) for analyzing metagenomic DNA sequence data. By iteratively adapting a set of partial alignments of reference sequences to match the sample data, the approach can be applied in multiple scenarios, from taxonomic identification to assembly of target regions of interest. To demonstrate the benefits of ASA, we present two application scenarios and compare the results with state-of-the-art methods conventionally used for the same tasks. In the first, ASA accurately detected microorganisms from a sequenced metagenomic sample with a known composition. The second illustrated the utility of ASA in assembling target genetic regions of the microorganisms. An example implementation of the ASA concept is available at https://github.com/elolab/ASA.},
}
@article {pmid39869787,
year = {2025},
author = {Lin, C and Li, LJ and Yang, K and Xu, JY and Fan, XT and Chen, QL and Zhu, YG},
title = {Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf009},
pmid = {39869787},
issn = {1751-7370},
abstract = {Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes. However, the effects of protozoan predation on antibiotic resistance genes dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of antibiotic resistance genes to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with antibiotic resistance genes and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of antibiotic resistance genes, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.},
}
@article {pmid39869311,
year = {2025},
author = {Li, R and Xu, M and Xu, M and Zhou, Y and Wen, T and Liu, Q and Yi, D and Wang, H and Wei, D},
title = {Semirational Engineering of a Distal Loop Region to Enhance the Catalytic Activity and Stability of Leucine Dehydrogenase.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {5},
pages = {2961-2969},
doi = {10.1021/acs.jafc.4c06915},
pmid = {39869311},
issn = {1520-5118},
mesh = {*Leucine Dehydrogenase/genetics/chemistry/metabolism ; *Protein Engineering ; Enzyme Stability ; Biocatalysis ; Molecular Dynamics Simulation ; Bacterial Proteins/genetics/chemistry/metabolism ; Kinetics ; Substrate Specificity ; Catalysis ; },
abstract = {Enzymatic asymmetric synthesis of l-phenylglycine by amino acid dehydrogenases has potential for industrial applications; however, this is hindered by their low catalytic efficiency toward high-concentration substrates. We identified and characterized a novel leucine dehydrogenase (MsLeuDH) with a high catalytic efficiency for benzoylformic acid via directed metagenomic approaches. Further, we obtained a triple-point mutant MsLeuDH-EER (D332E/G333E/L334R) with improved stability and catalytic efficiency through the rational design of distal loop 13. A coexpression system of MsLeuDH-EER and formate dehydrogenase completely converted a 300 mM substrate within 4 h with >99.9% enantiomeric excess. Molecular dynamics simulations revealed that mutations on loop 13 enhanced the overall structural rigidity of the protein to improve its stability but also stabilized the "closed" conformation through rigidifying the hinge region loop by distant modulation. Our results show that distal loop 13 can serve as a new hotspot region for enhancing the catalytic performance of leucine dehydrogenases.},
}
@article {pmid39868792,
year = {2025},
author = {Zhou, Z and Yang, M and Fang, H and Niu, Y and Lu, J and Ma, Y and Zhang, B and Zhu, H and Chen, P},
title = {Interspecies interactions mediated by arginine metabolism enhance the stress tolerance of Fusobacterium nucleatum against Bifidobacterium animalis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0223524},
doi = {10.1128/spectrum.02235-24},
pmid = {39868792},
issn = {2165-0497},
abstract = {Colorectal cancer (CRC) is a common cancer accompanied by microbiome dysbiosis. Exploration of probiotics against oncogenic microorganisms is promising for CRC treatment. Here, differential microorganisms between CRC and healthy control were analyzed. Antibacterial experiments, whole-genome sequencing, and metabolic network reconstruction were combined to reveal the anti-Fusobacterium nucleatum mechanism, which was verified by co-culture assay and mendelian randomization analysis. Sequencing results showed that F. nucleatum was enriched in CRC, yet Bifidobacterium animalis decreased gradually from healthy to CRC. Additionally, F. nucleatum could be inhibited by B. animalis. Whole-genome sequencing of B. animalis showed high phylogenetic similarity with known probiotic strains and highlighted its functions for amino acid and carbohydrate metabolism. Metabolic network reconstruction demonstrated that cross-feeding and specific metabolites (acidic molecules, arginine) had a great influence on the coexistence relationship. Finally, the arginine supplement enhanced the competitive ability of F. nucleatum against B. animalis, and the mendelian randomization and metagenomic sequencing analysis confirmed the positive relationship among F. nucleatum, arginine metabolism, and CRC. Thus, whole-genome sequencing and metabolic network reconstruction are valuable for probiotic mining and patient dietary guidance.IMPORTANCEUsing probiotics to inhibit oncogenic microorganisms (Fusobacterium nucleatum) is promising for colorectal cancer (CRC) treatment. In this study, whole-genome sequencing and metabolic network reconstruction were combined to reveal the anti-F. nucleatum mechanism of Bifidobacterium animalis, which was verified by co-culture assay and mendelian randomization analysis. The result indicated that the arginine supplement enhanced the competitive ability of F. nucleatum, which may be harmful to F. nucleatum-infected CRC patients. B. animalis is a potential probiotic to relieve this dilemma. Thus, using in silico simulation methods based on flux balance analysis, such as genome-scale metabolic reconstruction, provides valuable insights for probiotic mining and dietary guidance for cancer patients.},
}
@article {pmid39868304,
year = {2025},
author = {Choi, JM and Rumi, MA and Vikesland, PJ and Pruden, A and Zhang, L},
title = {ARGfore: A multivariate framework for forecasting antibiotic resistance gene abundances using time-series metagenomic datasets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.13.632008},
pmid = {39868304},
issn = {2692-8205},
abstract = {BACKGROUND: The global spread of antibiotic resistance presents a significant threat to human, animal, and plant health. Metagenomic sequencing is increasingly being utilized to profile antibiotic resistance genes (ARGs) in various environments, but presently a mechanism for predicting future trends in ARG occurrence patterns is lacking. Capability of forecasting ARG abundance trends could be extremely valuable towards informing policy and practice aimed at mitigating the evolution and spread of ARGs.<br><br>RESULTS: Here we propose ARGfore, a multivariate forecasting model for predicting ARG abundances from time-series metagenomic data. ARGfore extracts features that capture inherent relationships among ARGs and is trained to recognize patterns in ARG trends and seasonality.<br><br>CONCLUSION: ARGfore outperformed standard time-series forecasting methods, such as N-HiTS, LSTM, and ARIMA, exhibiting the lowest mean absolute percentage error when applied to different wastewater datasets. Additionally, ARGfore demonstrated enhanced computational efficiency, making it a promising candidate for a variety of ARG surveillance applications. The rapid prediction of future trends can facilitate early detection and deployment of mitigation efforts if necessary. ARGfore is publicly available at https://github.com/joungmin-choi/ARGfore .},
}
@article {pmid39868213,
year = {2025},
author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM},
title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39868213},
issn = {2692-8205},
support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; },
abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.},
}
@article {pmid39868175,
year = {2025},
author = {Simmonds, P and Butković, A and Grove, J and Mayne, R and Mifsud, JCO and Beer, M and Bukh, J and Drexler, JF and Kapoor, A and Lohmann, V and Smith, DB and Stapleton, JT and Vasilakis, N and Kuhn, JH},
title = {Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the Flaviviridae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39868175},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; HHSN272201800013C/AI/NIAID NIH HHS/United States ; I01 BX000207/BX/BLRD VA/United States ; U01 AI151807/AI/NIAID NIH HHS/United States ; },
abstract = {The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and 'flavi-like' viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2. These results support their classification into the established order, Amarillovirales, in three families (Flaviviridae, Pestiviridae, and Hepaciviridae), and 14 genera. This taxonomic framework informed by RdRP hallmark gene evolutionary relationships provides a stable reference from which major genome re-organisational events can be understood.},
}
@article {pmid39868118,
year = {2025},
author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT},
title = {Microbiota assembly of specific pathogen-free neonatal mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39868118},
issn = {2692-8205},
support = {F31 AI167499/AI/NIAID NIH HHS/United States ; R01 AI139314/AI/NIAID NIH HHS/United States ; R01 AI173360/AI/NIAID NIH HHS/United States ; T32 AI007163/AI/NIAID NIH HHS/United States ; T32 AI007172/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.<br><br>RESULTS: The fecal microbiome of young pups is simple, dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after fourteen days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.<br><br>CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome.},
}
@article {pmid39867878,
year = {2024},
author = {Lin, F},
title = {Tuberculous meningitis diagnosis and treatment: classic approaches and high-throughput pathways.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1543009},
pmid = {39867878},
issn = {1664-3224},
mesh = {*Tuberculosis, Meningeal/diagnosis ; Humans ; *Mycobacterium tuberculosis ; *High-Throughput Nucleotide Sequencing ; Biomarkers ; Proteomics/methods ; Metagenomics/methods ; Metabolomics/methods ; Antitubercular Agents/therapeutic use ; },
abstract = {Tuberculous meningitis (TBM), a severe form of non-purulent meningitis caused by Mycobacterium tuberculosis (Mtb), is the most critical extrapulmonary tuberculosis (TB) manifestation, with a 30-40% mortality rate despite available treatment. The absence of distinctive clinical symptoms and effective diagnostic tools complicates early detection. Recent advancements in nucleic acid detection, genomics, metabolomics, and proteomics have led to novel diagnostic approaches, improving sensitivity and specificity. This review focuses on nucleic acid-based methods, including Xpert Ultra, metagenomic next-generation sequencing (mNGS), and single-cell sequencing of whole brain Tissue, alongside the diagnostic potential of metabolomic and proteomic biomarkers. By evaluating the technical features, diagnostic accuracy, and clinical applicability, this review aims to inform the optimization of TBM diagnostic strategies and explores the integration and clinical translation of multi-omics technologies.},
}
@article {pmid39867819,
year = {2025},
author = {Zhang, Y and Wu, J and Lin, Q and Ou, J and Qi, X and Zheng, Y and Li, F and Weng, Y},
title = {Infection Tracing and Virus Genomic Analysis of Two Cases of Human Infection with Avian Influenza A(H5N6) - Fujian Province, China, April-May 2024.},
journal = {China CDC weekly},
volume = {7},
number = {3},
pages = {107-112},
pmid = {39867819},
issn = {2096-7071},
abstract = {Global human cases of zoonotic influenza A(H5N6) have increased significantly in recent years, primarily due to widespread circulation of clade 2.3.4.4b virus since 2020. Concurrent with this trend, sporadic human infections with clade 2.3.4.4h H5N6 avian influenza virus continue to occur. The high mortality rate associated with H5N6 virus infections has emerged as a critical public health concern.<br><br>WHAT IS ADDED BY THIS REPORT?: Through comprehensive field epidemiological investigations and laboratory analyses, we identified the infection sources for these cases and conclusively ruled out human-to-human transmission. Genetic analyses revealed that while the virus maintains its avian host tropism, it has acquired mutations that may enhance human receptor binding affinity, viral replication capacity, pathogenicity, and neuraminidase inhibitor resistance.<br><br>The ongoing viral mutations increase the potential for H5 subtype avian influenza viruses to overcome species barriers and cause human epidemics. Enhanced surveillance strategies incorporating advanced technologies, such as metagenomic sequencing, are essential for early risk detection and management. Special attention should be directed toward cancer patients and immunocompromised individuals, who demonstrate increased susceptibility to avian influenza virus infections and require targeted prevention and control measures.},
}
@article {pmid39867343,
year = {2024},
author = {Guimarães, LO and Ribeiro, GO and da Couto, R and Ramos, EDSF and Morais, VDS and Telles-de-Deus, J and Helfstein, VC and Dos Santos, JM and Deng, X and Delwart, E and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, &#xc9;},
title = {Exploring mosquito virome dynamics within São Paulo Zoo: insights into mosquito-virus-environment interactions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1496126},
pmid = {39867343},
issn = {2235-2988},
mesh = {Animals ; Brazil ; *Virome ; *Mosquito Vectors/virology ; *Metagenomics ; Animals, Zoo/virology ; Arboviruses/genetics/classification/isolation &amp; purification ; Culicidae/virology ; Aedes/virology ; Anopheles/virology ; Culex/virology ; Ecosystem ; },
abstract = {BACKGROUND: Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the Aedes genus, such as dengue, Zika, and chikungunya. Against this background, the São Paulo Zoo is an intriguing ecological niche to explore the virome of mosquitoes, potentially shedding light on the dynamics of arbovirus transmission within a confined setting.<br><br>METHODS: In this study, we conducted a comprehensive metagenomic analysis of mosquitoes collected from diverse habitats within the zoo, focusing on the Aedes, Anopheles, and Culex genera. From 1,039 contigs of viral origin, we identified 229 viral species infecting mosquitoes, with the orders Picornavirales, Nodamuvirales and Sobelivirales being the most prevalent and abundant. The difference in virome composition was primarily driven by mosquito host species rather than specific collection sites or trap height.<br><br>RESULTS: Despite environmental disparities, the virome remained remarkably uniform across different areas of the zoo, emphasizing the strong association between mosquito species and their viral communities. Furthermore, we identified a core virome shared among mosquito species, highlighting potential cross-species transmission events and underscoring the need for targeted surveillance and control measures.<br><br>CONCLUSION: These results contribute to our understanding of the interplay between mosquitoes, the environment, and viruses, providing valuable insights for disease intervention strategies in mosquito-borne diseases.},
}
@article {pmid39867288,
year = {2025},
author = {Zhang, H and Zhang, X and Zheng, Y and Gu, X and Fu, Z and Gai, W and Wang, H},
title = {Impact of Herpesvirus Detection via Metagenomic Next-Generation Sequencing in Patients with Lower Respiratory Tract Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {377-389},
pmid = {39867288},
issn = {1178-6973},
abstract = {PURPOSE: This study aimed to investigate the impact of herpesvirus detection by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) on lower respiratory tract infections (LRTIs) patients' lung microbiome composition and prognosis.<br><br>PATIENTS AND METHODS: We initially enrolled 234&#xa0;hospitalized patients with LRTIs who underwent BALF mNGS between February 2022 and May 2023. The study analyzed the clinical manifestations and the pulmonary microbial composition between herpesvirus detection (HD) and non-herpesvirus detection (non-HD) group.<br><br>RESULTS: After exclusions, a total of 201 patients were included, out of which 73 patients had herpesvirus detections (HD). The most frequently detected herpesviruses were Human herpesvirus 7 (HHV-7) (19.4%), Epstein-Barr virus (EBV) (12.4%), and cytomegalovirus (CMV) (10.4%). The HD group had a higher proportion of male patients (78.08% vs 55.04%, P = 0.001) and a greater incidence of hemoptysis and multilobar infiltrates compared non-HD group. Additionally, the HD group tended to have longer hospital stays compared to non-HD group, especially in immunosuppressed patients. Furthermore, in immunocompetent patients, there were significant differences in &#x3b1; diversity and &#x3b2; diversity between the HD group and non-HD group, but such differences were not observed in immunosuppressed patients.<br><br>CONCLUSION: The presence of herpesvirus in patients with non-critical LRTI is associated with longer hospital stays and alterations in the lung's microbial composition. Additionally, the impacts of herpesvirus presence are influenced by the immune status of the patients.},
}
@article {pmid39866837,
year = {2025},
author = {Zhao, P and Jiang, Z and Li, X and Ainiwaer, M and Li, L and Wang, D and Fan, L and Chen, F and Liu, J},
title = {Airway stenosis: classification, pathogenesis, and clinical management.},
journal = {MedComm},
volume = {6},
number = {2},
pages = {e70076},
pmid = {39866837},
issn = {2688-2663},
abstract = {Airway stenosis (AS) is a fibroinflammatory disease characterized by abnormal activation of fibroblasts and excessive synthesis of extracellular matrix, which has puzzled many doctors despite its relatively low prevalence. Traditional treatment such as endoscopic surgery, open surgery, and adjuvant therapy have many disadvantages and are limited in the treatment of patients with recurrent AS. Therefore, it is urgent to reveal the pathogenesis of AS and accelerate its clinical transformation. Based on the discovered pathogenesis, including fibrosis, inflammation, epithelial-mesenchymal transition, metabolic reprogramming, microbiome, genetic susceptibility, and other mechanisms, researchers have developed a series of treatments, such as drug therapy, gene therapy, stem cell therapy, growth factor therapy, protein therapy, and photodynamic therapy. This review introduces the classification of AS, explores the existing pathogenesis and preclinical treatments developed based on the pathogenesis, and finally summarizes the current clinical management. In addition, the prospect of exploring the interaction between different types of cells and between microorganisms and cells to identify the intersection of multiple mechanisms based on single-cell RNA sequencing, 16S rRNA gene sequencing and shotgun metagenomic sequencing is worth looking forward to.},
}
@article {pmid39866751,
year = {2025},
author = {Ren, Z and Luo, W and Li, H and Ding, H and Zhang, Y},
title = {Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf003},
pmid = {39866751},
issn = {2730-6151},
abstract = {Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.},
}
@article {pmid39866677,
year = {2024},
author = {Violette, MJ and Hyland, E and Burgener, L and Ghosh, A and Montoya, BM and Kleiner, M},
title = {Meta-omics reveals role of photosynthesis in microbially induced carbonate precipitation at a CO2-rich geyser.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae139},
pmid = {39866677},
issn = {2730-6151},
abstract = {Microbially induced carbonate precipitation (MICP) is a natural process with potential biotechnological applications to address both carbon sequestration and sustainable construction needs. However, our understanding of the microbial processes involved in MICP is limited to a few well-researched pathways such as ureolytic hydrolysis. To expand our knowledge of MICP, we conducted an omics-based study on sedimentary communities from travertine around the CO2-driven Crystal Geyser near Green River, Utah. Using metagenomics and metaproteomics, we identified the community members and potential metabolic pathways involved in MICP. We found variations in microbial community composition between the two sites we sampled, but Rhodobacterales were consistently the most abundant order, including both chemoheterotrophs and anoxygenic phototrophs. We also identified several highly abundant genera of Cyanobacteriales. The dominance of these community members across both sites and the abundant presence of photosynthesis-related proteins suggest that photosynthesis could play a role in MICP at Crystal Geyser. We also found abundant bacterial proteins involved in phosphorous starvation response at both sites suggesting that P-limitation shapes both composition and function of the microbial community driving MICP.},
}
@article {pmid39866676,
year = {2024},
author = {Prabhu, A and Tule, S and Chuvochina, M and Bodén, M and McIlroy, SJ and Zaugg, J and Rinke, C},
title = {Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae067},
pmid = {39866676},
issn = {2730-6151},
abstract = {Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal-spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish to marine sites revealed that nutrient concentrations and salinity best explained spatial community variations, whereas temperature and dissolved oxygen likely drive seasonal shifts. By combining short and long read sequencing data, we recovered 2,459 metagenome-assembled genomes, proposed new taxon names for previously uncharacterised lineages, and created an extensive, habitat specific genome reference database. Community profiling based on this genome reference database revealed a diverse prokaryotic community comprising 61 bacterial and 18 archaeal phyla, and resulted in an improved taxonomic resolution at lower ranks down to genus level. We found that the vast majority (61 out of 73) of abundant genera (>1% average) represented unnamed and novel lineages, and that all genera could be clearly separated into brackish and marine ecotypes with inferred habitat specific functions. Applying supervised machine learning and metabolic reconstruction, we identified several microbial indicator taxa responding directly or indirectly to elevated nitrate and total phosphorus concentrations. In conclusion, our analysis highlights the importance of improved taxonomic resolution, sheds light on the role of previously uncharacterised lineages in estuarine nutrient cycling, and identifies microbial indicators for nutrient levels crucial in estuary health assessments.},
}
@article {pmid39866568,
year = {2025},
author = {Pucci, N and Ujčič-Voortman, J and Verhoeff, AP and Mende, DR},
title = {Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18602},
pmid = {39866568},
issn = {2167-8359},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Milk, Human/microbiology/chemistry/metabolism ; Infant ; *Bifidobacterium/metabolism/genetics ; *Bifidobacterium longum/metabolism ; Female ; *Polysaccharides/metabolism ; Infant, Newborn ; Feces/microbiology ; Metagenome ; Breast Feeding ; Male ; },
abstract = {BACKGROUND: The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.<br><br>METHODOLOGY: We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.<br><br>RESULTS: B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.<br><br>DISCUSSION: Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.},
}
@article {pmid39866262,
year = {2025},
author = {Liu, C and Wu, W and Wang, L and Li, J},
title = {Case report: co-infection of Scedosporium and Mycobacterium in lungs.},
journal = {AME case reports},
volume = {9},
number = {},
pages = {3},
pmid = {39866262},
issn = {2523-1995},
abstract = {BACKGROUND: There are hundreds of pathogens that cause lung infections. Compared to infections caused by a single pathogen, mixed infections account for a larger proportion of pulmonary infections and have a more severe clinical presentation, while treatment options differ between the two. We aimed to explore the advantages of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of mixed infections.<br><br>CASE DESCRIPTION: To investigate the specific pathogens in a 79-year-old male pneumonia patient who had recurrent cough with poor empirical treatment, we collected bronchoalveolar lavage fluid (BALF) from the patient and performed mNGS technology, along with Sanger sequencing and polymerase chain reaction (PCR) was carried out to confirm the authenticity of the pathogens detected by mNGS. The findings showed that rare pathogen Scedosporium boydii (S. boydii, reads: 18) and Mycobacterium avium complex (MAC, reads: 19) were detected, and the patient was subsequently transferred to another hospital for the same mNGS with the same results as the first detection. Therefore, combined treatment with voriconazole, ethambutol, azithromycin, and levofloxacin were given to the S. boydii and MAC for 1 week, and then patient's condition improved and discharged.<br><br>CONCLUSIONS: mNGS, a non-targeted sequencing technology, could improve the efficiency of clinical diagnosis for mixed infection of rare or atypical pathogens, bring new ideas for clinical pathogen diagnosis, and improve patient prognosis.},
}
@article {pmid39865210,
year = {2025},
author = {Dubovitskiy, N and Derko, A and Loginova, A and Khozyainova, A and Denisov, E and Apanasevich, M and Kokhanenko, A and Druzyaka, A and Shestopalov, A and Sharshov, K},
title = {Viral metagenomics in wild ducks reveals the presence of seadornaviruses in Siberia.},
journal = {Archives of virology},
volume = {170},
number = {2},
pages = {41},
pmid = {39865210},
issn = {1432-8798},
support = {122012400086-2//State funded budget projects (Russia)/ ; 23-44-00026//Russian Scientific Foundation/ ; },
mesh = {Animals ; Siberia ; *Ducks/virology ; *Metagenomics ; *Phylogeny ; Genome, Viral/genetics ; Bird Diseases/virology ; Animals, Wild/virology ; },
abstract = {Seadornavirus is a genus of mosquito-borne viruses that includes Banna virus, which was first discovered in human patients with encephalitis and fever, as well as Kadipiro virus and Liao ning virus. In this study, we used metagenomics to investigate the diversity of viruses in wild ducks and detected both Banna virus and Kadipiro virus in wild birds in Siberia. These data suggest that seadornaviruses, which were previously only found in South East Asia, are also circulating in Northern Eurasia.},
}
@article {pmid39865153,
year = {2025},
author = {Wu, Z and Jiang, M and Jia, M and Sang, J and Wang, Q and Xu, Y and Qi, L and Yang, W and Feng, L},
title = {The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {127},
pmid = {39865153},
issn = {2399-3642},
support = {2022-I2M-CoV19-006//Chinese Academy of Medical Sciences (CAMS)/ ; },
mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; Infant ; *Oropharynx/microbiology/virology ; *Microbiota ; Child, Preschool ; Male ; Female ; Child ; Acute Disease ; Virus Diseases/virology/microbiology/epidemiology ; },
abstract = {Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.},
}
@article {pmid39865091,
year = {2025},
author = {Qi, YL and Zhang, HT and Li, M and Li, WJ and Hua, ZS},
title = {Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {151},
pmid = {39865091},
issn = {2052-4463},
support = {32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42207145//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Hot Springs/microbiology ; *Genome, Archaeal ; *Archaea/genetics/classification ; *Metagenome ; China ; *Phylogeny ; },
abstract = {Terrestrial geothermal springs, reminiscent of early Earth conditions, host diverse and abundant populations of Archaea. In this study, we reconstructed 2,949 metagenome-assembled genomes (MAGs) from 152 metagenomes collected over six years from 48 geothermal springs in Tengchong, China. Among these MAGs, 1,431 (49%) were classified as high-quality, while 1,518 (51%) were considered as medium-quality. Phylogenomic analysis revealed that these MAGs spanned 12 phyla, 27 classes, 67 orders, 147 families, 265 genera, and 475 species. Notably, 575 (19%) MAGs represented new taxa at various taxonomic levels, and 2,075 (70%) lacked nomenclature and effective descriptions. The most abundant phyla of archaeal genomes were Thermoproteota, Thermoplasmatota, and Micrarchaeota. The DRTY, ZMQ, and ZZQ geothermal springs were predominated by Archaea, particularly by Thermoproteia and Thermoplasmata. These draft genomes provide new data for studying species diversity and function within terrestrial geothermal spring archaeal communities, thus contributing to the conservation and utilization of thermophilic and hyperthermophilic microbial resources.},
}
@article {pmid39864798,
year = {2025},
author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Bhure, M and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG},
title = {Ruminal microbial responses to Moringa oleifera feed in lactating goats (Capra hircus): A metagenomic exploration.},
journal = {New biotechnology},
volume = {86},
number = {},
pages = {87-96},
doi = {10.1016/j.nbt.2025.01.006},
pmid = {39864798},
issn = {1876-4347},
abstract = {The purpose of the current study was to explore the effects of Moringa oleifera feed on the taxonomy and function of the rumen microbial community, and further to evaluate its impact on milk yield and body weight in lactating goats. Nineteen goats were divided into moringa leaf diet (ML; n = 10) and masoor straw (MS; n = 9) groups. For each group fortnight milk yield and body weight was recorded. Rumen solid and liquid fraction samples were processed for metagenomic shotgun sequencing and further analysed. The pairwise comparison between the two groups showed a significant increase (p-value- <0.01) in milk yield of the ML goats after the 4th fortnight interval onwards. The metagenomic analysis revealed Bacteroidetes and Firmicutes are the most abundant phyla, with increased Bacteroidetes in response to the moringa diet. The ML group exhibited a reduction in microbial diversity, with an increase in Prevetolla and Bacteroidales populations which are positively associated with carbohydrate, protein, and VFA metabolism, and an increased proportions of Treponema sp., Ruminococcus sp., Ruminobacter amylophilus, and Aeromonas, indicating improved cellulose and nitrogen metabolism. KEGG analysis revealed significant changes in microbial gene pool and metabolic pathways, particularly in carbohydrate metabolism, propanoate metabolism, and fatty acid synthesis genes. These microbial and functional shifts are correlated with improvements in milk yield, growth rates, and potentially reduced methane emissions.This study highlighted the potential benefits of feeding moringa in the animal production system. However, furthermore experimental evidence including genetic and environmental effects is needed for a comprehensive understanding of moringa feed's impact on goat health and productivity.},
}
@article {pmid39864640,
year = {2025},
author = {Wang, BC and Jeng, ML and Tsai, JF and Wu, LW},
title = {Genome skimming for improved phylogenetics of Taiwanese phasmids (Insecta: Phasmatodea).},
journal = {Molecular phylogenetics and evolution},
volume = {205},
number = {},
pages = {108292},
doi = {10.1016/j.ympev.2025.108292},
pmid = {39864640},
issn = {1095-9513},
abstract = {Taiwan, a relatively young continental island, harbors a high proportion of endemic phasmids, reflecting its unique evolutionary history. However, a comprehensive phylogenetic framework to clarify these phasmids is still lacking. In this study, we sequenced ten of eleven valid genera and two undescribed species of Taiwanese phasmids (total 16 species) using the genome-skimming approach. We also integrated these sequences with public databases to create two aligned datasets: one comprising 92 taxa (mitogenomes) and the other 606 taxa (seven nuclear and mitochondrial genes), enabling us to examine their phylogenetic relationships using longer sequences and more samples. Our analyses show that Taiwanese phasmids should be categorized into six families, with a revised number of genera to 13. Furthermore, four species require taxonomic treatments: namely Micadina honei (Günther, 1940) comb. nov., Micadina truncatum (Shiraki, 1935) comb. nov., Otraleus okunii (Shiraki, 1935) comb. nov., and Ramulus granulatus (Shiraki, 1935) syn. nov. now recognized as Ramulus artemis (Westwood, 1859). While some Taiwanese genera exhibit polyphyletic relationships, our findings highlight the importance of taxon sampling, particularly for type species in resolving these systematic issues. The genome-skimming approach has proven to be an excellent method for producing comparable sequence datasets, facilitating the investigation of highly diverse insects, even when samples are old, small, or have highly fragmented DNAs.},
}
@article {pmid39864304,
year = {2025},
author = {Labarga, D and Mairata, A and Puelles, M and Wallner, A and Aziz, A and Alícia, P},
title = {Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128073},
doi = {10.1016/j.micres.2025.128073},
pmid = {39864304},
issn = {1618-0623},
abstract = {The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.},
}
@article {pmid39864165,
year = {2025},
author = {Wang, XP and Han, NN and Yang, JH and Fan, NS and Jin, RC},
title = {Metagenomic insight into the diffusion signal factor mediated social traits of anammox consortia after starvation.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124270},
doi = {10.1016/j.jenvman.2025.124270},
pmid = {39864165},
issn = {1095-8630},
mesh = {*Oxidation-Reduction ; Quorum Sensing ; Ammonium Compounds/metabolism ; Anaerobiosis ; Metagenomics ; Nitrogen/metabolism ; Microbial Consortia ; Wastewater/microbiology ; Geobacter/metabolism ; Bacteria/metabolism ; },
abstract = {Biomass starvation is common in biological wastewater treatment. As a social trait of microbial community, how quorum sensing (QS) regulated bacterial trade-off through interactions after starvation remains unclear. This study deciphered the mechanism of anaerobic ammonium oxidation (anammox) consortia in response to starvation, including reducing extracellular electron transfer (EET), adenosine 5'-triphosphate (ATP) content and amino acid metabolism. Metagenomic analysis has shown that the addition of the diffusion signal factor (DSF) resulted in a high abundance of antioxidant genes, which contributed to achieving redox balance in anammox bacteria. There was an enrichment of Geobacter and Methanosarcina, which were QS-responsive direct interspecific electron transfer participants. Furthermore, DSF stimulated the nitrogen and carbon metabolism of Ca. Kuenenia_stuttgartiensis, promoting syntrophy of metabolic intermediates within microbial community. This study highlighted the effect of DSF on the microbial interaction patterns and deciphered the QS-based social traits of anammox consortia after starvation, facilitating the stable operation of the anammox process.},
}
@article {pmid39862584,
year = {2025},
author = {Zheng, Z and Ji, W and Wang, X and Wang, X and Dai, S and Zhang, Z and Zhang, Y and Wang, X and Cao, S and Chen, M and Xie, B and Feng, J and Wu, D},
title = {Household waste-specific ambient air shows greater inhalable antimicrobial resistance risks in densely populated communities.},
journal = {Waste management (New York, N.Y.)},
volume = {194},
number = {},
pages = {309-317},
doi = {10.1016/j.wasman.2025.01.030},
pmid = {39862584},
issn = {1879-2456},
abstract = {Household waste is a hotspot of antibiotic resistance, which can be readily emitted to the ambient airborne inhalable particulate matters (PM10) during the day-long storage in communities. Nevertheless, whether these waste-specific inhalable antibiotic resistance genes (ARGs) are associated with pathogenic bacteria or pose hazards to local residents have yet to be explored. By high-throughput metagenomic sequencing and culture-based antibiotic resistance validation, we analyzed 108 airborne PM10 and nearby environmental samples collected across different types of residential communities in Shanghai, the most populous city in China. Compared to the cold-dry period, the warm-humid season had significantly larger PM10-associated antibiotic resistomes in all types of residential communities (T-test, P < 0.001), most of airborne ARGs in which were estimatedly originated from disposed household waste (∼ 30 %). In addition, the airborne bacteria were assembled in a deterministic approach (iCAMP, P < 0.01), where the waste-specific bacteria taxa including Acinetobacter, Pseudomonas, Rhodococcus, and Kocuria had the predominant niches in the airborne microbial assemblages. Notably, these waste-sourced bacteria were also identified as the primary airborne hosts of ARGs encoding the aminoglycoside resistances. Among them, some antibiotic resistant human pathogens, such as Pseudomonas aeruginosa and Acinetobacter baumannii, not only exhibited higher ARG horizontal gene transfer (HGT) potential across the microbial assemblages, but also imposed direct infection risks on the local residents by 2 min inhalation exposure per day. When the daily exposure duration increased to 11 min, the infection-induced illness burden became unignorably high, especially in densely populated urban communities, being twofold greater than rural areas.},
}
@article {pmid39862030,
year = {2025},
author = {Xie, J and Li, G and Lin, F and Bai, Z and Yu, L and Zhang, D and Zhang, B and Ye, J and Yu, R},
title = {Acute Q Fever after Kidney Transplantation: A Case Report.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {86},
number = {1},
pages = {1-10},
doi = {10.12968/hmed.2024.0604},
pmid = {39862030},
issn = {1750-8460},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Q Fever/diagnosis ; Male ; Middle Aged ; Immunocompromised Host ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Aims/Background Patients receiving kidney transplant experience immunosuppression, which increases the risk of bacterial, viral, fungal, and parasitic infections. Q fever is a potentially fatal infectious disease that affects immunocompromised renal transplant recipients and has implications in terms of severe consequences for the donor's kidney. Case Presentation A patient with acute Q fever infection following kidney transplantation was admitted to the Tsinghua Changgung Hospital in Beijing, China, in March 2021. Next-generation sequencing (NGS) was used to diagnose Q fever in the patient. Based on the patient's blood test, we detected Rickettsia, the causative agent of Q fever and a zoonotic disease that can manifest in acute or chronic forms in humans. Comprehensive data on clinical symptoms, blood tests, chest computed tomography (CT), NGS, Immunoglobulin G (IgG) antibody titer, and therapeutic efficacy associated with Q fever infection following renal transplantation in this patient were gathered. Conclusion This is the first reported case of acute Q fever occurring in a Chinese renal transplant recipient detected using metagenomic NGS. This case underscores the need to consider acute Q fever as a possible differential diagnosis in kidney transplant recipients with fever of unknown origin.},
}
@article {pmid39861970,
year = {2025},
author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I},
title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf014},
pmid = {39861970},
issn = {1751-7370},
abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.},
}
@article {pmid39861854,
year = {2025},
author = {Hyman, P},
title = {Are You My Host? An Overview of Methods Used to Link Bacteriophages with Hosts.},
journal = {Viruses},
volume = {17},
number = {1},
pages = {},
pmid = {39861854},
issn = {1999-4915},
mesh = {*Bacteriophages/genetics/physiology ; *Host Specificity ; *Bacteria/virology/genetics ; *Genome, Viral ; Metagenomics/methods ; },
abstract = {Until recently, the only methods for finding out if a particular strain or species of bacteria could be a host for a particular bacteriophage was to see if the bacteriophage could infect that bacterium and kill it, releasing progeny phages. Establishing the host range of a bacteriophage thus meant infecting many different bacteria and seeing if the phage could kill each one. Detection of bacterial killing can be achieved on solid media (plaques, spots) or broth (culture clearing). More recently, additional methods to link phages and hosts have been developed. These include methods to show phage genome entry into host cells (e.g., PhageFISH); proximity of phage and host genomes (e.g., proximity ligation, polonies, viral tagging); and analysis of genomes and metagenomes (e.g., CRISPR spacer analysis, metagenomic co-occurrence). These methods have advantages and disadvantages. They also are not measuring the same interactions. Host range can be divided into multiple host ranges, each defined by how far the phage can progress in the infection cycle. For example, the ability to effect genome entry (penetrative host range) is different than the ability to produce progeny (productive host range). These different host ranges reflect bacterial defense mechanisms that block phage growth and development at various stages in the infection cycle. Here, I present a comparison of the various methods used to identify bacteriophage-host relationships with a focus on what type of host range is being measured or predicted.},
}
@article {pmid39861802,
year = {2024},
author = {Musaeva, T and Fadeev, A and Pisareva, M and Eder, V and Ksenafontov, A and Korzhanova, M and Tsvetkov, V and Perederiy, A and Kiseleva, I and Danilenko, D and Lioznov, D and Komissarov, A},
title = {Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63.},
journal = {Viruses},
volume = {17},
number = {1},
pages = {},
pmid = {39861802},
issn = {1999-4915},
support = {#TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing"//Ministry of Health of the Russian Federation/ ; },
mesh = {Humans ; *Whole Genome Sequencing/methods ; *Seasons ; *Genome, Viral ; *Coronavirus/genetics/classification/isolation &amp; purification ; *Coronavirus Infections/virology/epidemiology ; *Phylogeny ; Russia/epidemiology ; Retrospective Studies ; Coronavirus OC43, Human/genetics/isolation &amp; purification/classification ; Coronavirus 229E, Human/genetics/isolation &amp; purification/classification ; Coronavirus NL63, Human/genetics/isolation &amp; purification ; Nasopharynx/virology ; Respiratory Tract Infections/virology/epidemiology ; },
abstract = {Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900-1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses.},
}
@article {pmid39861468,
year = {2025},
author = {Fricker, AD and Sejane, K and Desai, M and Snyder, MW and Duran, L and Mackelprang, R and Bode, L and Ross, MG and Flores, GE},
title = {A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.},
journal = {Nutrients},
volume = {17},
number = {2},
pages = {},
pmid = {39861468},
issn = {2072-6643},
support = {R21 HD104028/HD/NICHD NIH HHS/United States ; SC1GM136546/GM/NIGMS NIH HHS/United States ; R01 HD099813/HD/NICHD NIH HHS/United States ; SC1 GM136546/GM/NIGMS NIH HHS/United States ; R01HD099813/HD/NICHD NIH HHS/United States ; R21HD104028/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Pilot Projects ; Female ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; *Oligosaccharides/analysis ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; Male ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Overweight/microbiology ; Infant, Newborn ; Obesity/microbiology ; },
abstract = {BACKGROUND: Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome.<br><br>METHODS: Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively.<br><br>RESULTS: Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera.<br><br>CONCLUSIONS: These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.},
}
@article {pmid39860994,
year = {2025},
author = {Shringi, S and Shah, DH and Carney, K and Verma, A},
title = {Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39860994},
issn = {2076-0817},
support = {Grant#19KC001//an institutional research grant from Richard A. Gillespie College of Veterinary Medicine, Lincoln Memorial University/ ; },
mesh = {Animals ; Dogs/microbiology ; *Feces/microbiology ; *Metagenome ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/isolation &amp; purification ; Virginia/epidemiology ; Kentucky/epidemiology ; Tennessee/epidemiology ; Metagenomics/methods ; },
abstract = {According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses.},
}
@article {pmid39860966,
year = {2024},
author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Marchenko, A and Turgunov, Y and Kozhakhmetov, S and Suieubayev, M and Mukhanbetzhanov, N and Kabdulina, N},
title = {Interrelationships of the Intestinal Microbiome, Trimethylamine N-Oxide and Lipopolysaccharide-Binding Protein with Crohn's Disease Activity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39860966},
issn = {2076-0817},
support = {AP14871959//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Crohn Disease/microbiology/metabolism ; Female ; Male ; Adult ; *Acute-Phase Proteins/metabolism/analysis ; *Feces/microbiology/chemistry ; Middle Aged ; *Membrane Glycoproteins/metabolism ; Carrier Proteins/metabolism ; Young Adult ; Lipopolysaccharides/metabolism ; },
abstract = {UNLABELLED: Crohn's disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease's severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity.<br><br>METHODS: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed.<br><br>RESULTS: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species.<br><br>CONCLUSIONS: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.},
}
@article {pmid39860395,
year = {2025},
author = {Ullah, N and Fusco, L and Ametrano, L and Bartalucci, C and Giacobbe, DR and Vena, A and Mikulska, M and Bassetti, M},
title = {Diagnostic Approach to Pneumonia in Immunocompromised Hosts.},
journal = {Journal of clinical medicine},
volume = {14},
number = {2},
pages = {},
pmid = {39860395},
issn = {2077-0383},
abstract = {In immunocompromised patients, pneumonia presents a diagnostic challenge due to diverse etiologies, nonspecific symptoms, overlapping radiological presentation, frequent co-infections, and the potential for rapid progression to severe disease. Thus, timely and accurate diagnosis of all pathogens is crucial. This narrative review explores the latest advancements in microbiological diagnostic techniques for pneumonia in immunocompromised patients. It covers major available microbiological tools for diagnosing both community-acquired and hospital-acquired pneumonia, encompassing a wide spectrum of pathogens including bacterial, viral, fungal, and parasitic. While traditional culture methods remain pivotal in identifying many pneumonia-causing etiologies, their limitations in sensitivity and time to results have led to the rise of non-invasive antigen tests and molecular diagnostics. These are increasingly employed alongside cultures and microscopy for more efficient diagnosis, mainly in viral and fungal infections. Lastly, we report the future of pneumonia diagnostics, exploring the potential of metagenomics and CRISPR/Cas13a for more precise and rapid pathogen detection in immunocompromised populations.},
}
@article {pmid39859429,
year = {2025},
author = {Vicente-Valor, J and Tesolato, S and Paz-Cabezas, M and Gómez-Garre, D and Ortega-Hernández, A and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Jarabo, JR and Gómez-Martínez, AM and Hernando, F and Torres, A and Iniesta, P},
title = {Fecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859429},
issn = {1422-0067},
support = {PI19/00073//Carlos III Health Institute (Ministerio de Econom&#xed;a y Competitividad), Spain and co-funded by the European Union through the European Regional Development Fund (ERDF) 'A way to make Europe'/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology ; *Lung Neoplasms/microbiology ; Female ; Male ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Adult ; },
abstract = {Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC. Specifically, we investigated tumor and non-tumor tissues from 38 recruited patients with CRC and 19 with NSCLC. DNA from samples was submitted for 16S rDNA metagenomic sequencing, followed by data analysis through the QIIME2 pipeline and further statistical processing with STATA IC16. Tumor and non-tumor tissue selected genera were highly correlated in both CRC and NSCLC (100% and 81.25%). Following this, we established tissue-feces correlations, using selected genera from a LEfSe analysis previously published. In CRC, we found a strong correlation between the taxa detected in feces and those from colorectal tissues. However, our data do not demonstrate this correlation in NSCLC. In conclusion, our findings strongly reinforce the utility of fecal microbiota as a non-invasive biomarker for CRC diagnosis, while highlighting critical distinctions for NSCLC. Furthermore, our data demonstrate that the microbiota components of tumor and non-tumor tissues are similar, with only minor differences being detected.},
}
@article {pmid39859368,
year = {2025},
author = {Resman Rus, K and Bosilj, M and Triglav, T and Jereb, M and Zalaznik, M and Klešnik, M and Češljarac, D and Matičič, M and Avšič-Županc, T and Rus, T and Korva, M},
title = {Metagenomic Sequencing for Diagnosing Listeria-Induced Rhombencephalitis in Patient and Contaminated Cheese Samples: A Case Report.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859368},
issn = {1422-0067},
support = {P3-0083//The Slovenian Research and Innovation Agency/ ; J3-2515//The Slovenian Research and Innovation Agency/ ; },
mesh = {Humans ; *Cheese/microbiology ; Adult ; *Metagenomics/methods ; *Listeria monocytogenes/genetics/isolation &amp; purification ; *Listeriosis/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Hemolysin Proteins/genetics ; Heat-Shock Proteins/genetics ; Bacterial Toxins/genetics ; Encephalitis/diagnosis/microbiology ; Male ; Rhombencephalon/microbiology ; },
abstract = {Among the various causes of rhomboencephalitis, Listeria monocytogenes infection is the most common. However, conventional microbiological methods often yield negative results, making diagnosis challenging and leading to extensive, often inconclusive, diagnostics. Advanced molecular techniques like metagenomic next-generation sequencing (mNGS) offer a powerful and efficient approach to pathogen identification. We present a case of life-threatening rhomboencephalitis in a 32-year-old immunocompetent patient where extensive microbiological, immunological, and biochemical tests were inconclusive. Given the patient's consumption of unpasteurized homemade cheese, neurolisteriosis was suspected, and mNGS was employed on clinical samples (CSF, serum, urine) and the food source to identify the pathogen. mNGS detected L. monocytogenes in both patient samples and the cheese. Mapping reads were distributed across the genome, with 18.9% coverage in clinical samples and 11.8% in the cheese sample. Additionally, the Listeriolysin (hlyA) gene was detected with 22.3% coverage in clinical samples and 12.3% in the food source, confirming neurolisteriosis. The patient fully recovered following antibiotic treatment. This case underscores the importance of mNGS in diagnosing CNS infections when conventional methods yield negative results, and supports its inclusion in diagnostic protocols for suspected neurolisteriosis, particularly when traditional methods prove inadequate.},
}
@article {pmid39858934,
year = {2025},
author = {Wang, M and Valizadegan, N and Fields, CJ and Donovan, SM},
title = {Fecal Microbiome and Metabolomic Profiles of Mixed-Fed Infants Are More Similar to Formula-Fed than Breastfed Infants.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858934},
issn = {2076-2607},
support = {R01 DK107561/DK/NIDDK NIH HHS/United States ; R01 DK138032/DK/NIDDK NIH HHS/United States ; 1R01DK107561-05A1/NH/NIH HHS/United States ; 1R01DK138032-01A1/NH/NIH HHS/United States ; },
abstract = {Many infants consume both human milk and infant formula (mixed-fed); however, few studies have investigated how mixed feeding affects the gut microbiome composition and metabolic profiles compared to exclusive breastfeeding or formula feeding. Herein, how delivery mode and early nutrition affect the microbiome and metabolome of 6-week-old infants in the STRONG Kids2 cohort was investigated. Fecal samples were collected from exclusively breastfed (BF; n = 25), formula-fed (FF; n = 25) or mixed-fed (MF; n = 25) participants. Within each feeding group, infants were either delivered vaginally (VD; n = 13) or by Cesarean section (CS; n = 12). Feeding mode affects the fecal microbiome diversity, composition, and functional potential, as well as metabolomic profiles regardless of delivery mode. Alpha and beta diversity of MF differed from that of BF (p < 0.05) but were comparable to FF infants. Functional analyses have shown 117 potential metabolic pathways differed between BF and FF, 112 between BF and MF, and 8 between MF and FF infants (p < 0.05, q < 0.10). Fecal metabolomic profiles of MF and FF clustered together and separated from BF infants. In total, 543 metabolites differed between BF and FF, 517 between BF and MF, and 3 between MF and FF (p < 0.05, q < 0.10). Delivery mode affected overall microbial composition (p = 0.022) at the genus level and 24 potential functional pathways, with 16 pathways being higher in VD than CS infants (p < 0.05, q < 0.10). Metabolomic analysis identified 47 differential metabolites between CS and VD, with 39 being lower in CS than VD (p < 0.05, q < 0.10). In summary, fecal microbiota composition and function and metabolite profiles of 6-week-old MF infants are closer to FF than BF infants.},
}
@article {pmid39858902,
year = {2025},
author = {Bednarska, NG and Håberg, AK},
title = {Understanding Patterns of the Gut Microbiome May Contribute to the Early Detection and Prevention of Type 2 Diabetes Mellitus: A Systematic Review.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858902},
issn = {2076-2607},
abstract = {The rising burden of type 2 diabetes mellitus (T2DM) is a growing global public health problem, particularly prominent in developing countries. The early detection of T2DM and prediabetes is vital for reversing the outcome of disease, allowing early intervention. In the past decade, various microbiome-metabolome studies have attempted to address the question of whether there are any common microbial patterns that indicate either prediabetic or diabetic gut microbial signatures. Because current studies have a high methodological heterogeneity and risk of bias, we have selected studies that adhered to similar design and methodology. We performed a systematic review to assess if there were any common changes in microbiome belonging to diabetic, prediabetic and healthy individuals. The cross-sectional studies presented here collectively covered a population of 65,754 people, with 1800 in the 2TD group, 2770 in the prediabetic group and 61,184 in the control group. The overall microbial diversity scores were lower in the T2D and prediabetes cohorts in 86% of the analyzed studies. Re-programming of the microbiome is potentially one of the safest and long-lasting ways to eliminate diabetes in its early stages. The differences in the abundance of certain microbial species could serve as an early warning for a dysbiotic gut environment and could be easily modified before the onset of disease by changes in lifestyle, taking probiotics, introducing diet modifications or stimulating the vagal nerve. This review shows how metagenomic studies have and will continue to identify novel therapeutic targets (probiotics, prebiotics or targets for elimination from flora). This work clearly shows that gut microbiome intervention studies, if performed according to standard operating protocols using a predefined analytic framework (e.g., STORMS), could be combined with other similar studies, allowing broader conclusions from collating all global cohort studies efforts and eliminating the effect-size statistical insufficiency of a single study.},
}
@article {pmid39858899,
year = {2025},
author = {Fernández-Sánchez, V and Plascencia-Nieto, ES and Cureño-Díaz, MA and Durán-Manuel, EM and Rodríguez-Tovar, AV and Calzada-Mendoza, CC and Cruz-Cruz, C and Loyola-Cruz, M&#xc1; and Álvarez-Sánchez, ME and Bravata-Alcántara, JC and Vásquez-Jiménez, E and Gutiérrez-Muñoz, VH and Blanco-Hernández, DMR and Nicolás-Sayago, L and Rojas-Bernabé, A and García-Hernández, O and Gómez-Zamora, E and Ruíz-Valdés, M and Castro-Escarpulli, G and Bello-López, JM},
title = {Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858899},
issn = {2076-2607},
abstract = {Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens and highlight the shortcomings of traditional cultures. The aim of this work was to characterise the bacterial composition of PLAs through massive sequencing of the V3-V4 hypervariable region of the 16S rRNA gene in cases where conventional culture methods were negative. Purulent material was collected from three patients with PLAs at Hospital Juárez de México. Classical and molecular microbiological cultures were performed in parallel. Metagenomic DNA was extracted and massively sequenced (16S rRNA gene) using the Illumina MiSeq platform. A bioinformatic analysis was performed to determine the diversity at six different taxa levels and the relative abundances. The culture methods were not sufficient to detect the causative agent of the PLAs. However, the massive sequencing revealed the causative agents of the monomicrobial and polymicrobial infectious foci, with Gardnerella vaginalis, Lactobacillus iners, and Prevotella timonensis as the dominant bacteria. The massive sequencing revealed the presence of unusual pathogens that traditional culture failed to detect. There is an immediate need for molecular or comprehensive microbiological culture techniques to search for unusual bacteria in the diagnosis of PLAs.},
}
@article {pmid39858891,
year = {2025},
author = {Malik, PK and Kolte, AP and Trivedi, S and Tamilmani, G and Mohapatra, A and Vaswani, S and Belevendran, J and Sahoo, A and Gopalakrishnan, A and Bhatta, R},
title = {Anti-Methanogenic Potential of Seaweeds and Impact on Feed Fermentation and Rumen Microbiome In Vitro.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858891},
issn = {2076-2607},
support = {CRP D31031//IAEA/ ; },
abstract = {A series of in vitro studies were conducted to explore the anti-methanogenic potential of five seaweeds collected from the Indian sea and to optimize the level(s) of incorporation of the most promising seaweed(s) into a straw and concentrate diet to achieve a significant reduction in methane (CH4) production without disturbing rumen fermentation characteristics. A chemical composition analysis revealed a notable ash content varying between 55 and 70% in seaweeds. The crude protein content was highly variable and ranged between 3.25 and 15.3% of dry matter. Seaweeds contained appreciable concentrations of tannins and saponins. Among the seaweeds, Spyridia filamentosa exhibited significantly higher CH4 production, whereas the percentage of CH4 in total gas was significantly lower in the cases of Kappaphycus alvarezii and Sargassum wightii. The ranking of seaweeds in terms of CH4 production (mL/g OM) is as follows: Sargassum wightii < Kappaphycus alvarezii < Acanthophora specifera < Padina gymnospora < Spyridia filamentosa. A remarkable decrease of 31-42% in CH4 production was recorded with the incremental inclusion of Kappaphycus alvarezii at levels of 3-5% of the dry matter in the diet. The addition of Sargassum wightii led to a significant decrease of 36-48% in CH4 emissions when incorporated at levels of 4-5% of dry matter, respectively. The findings of this study revealed a significant decrease in the numbers of total protozoa and Entodinomorphs, coupled with increasing abundances of sulfate-reducing microbes and minor methanogens. Metagenome data revealed that irrespective of the seaweed and treatment, the predominant microbial phyla included Bacteroidota, Bacillota, Pseudomonadota, Actinomycetota, Fibrobacterota, and Euryarchaeota. The prevalence of Methanobrevibacter was similar across treatments, constituting the majority (~79%) of the archaeal community. The results also demonstrated that the supplementation of Kappaphycus alvarezii and Sargassum wightii did not alter the feed fermentation pattern, and therefore, the reduction in CH4 production in the present study could not be attributed to it. Animal studies are warranted to validate the extent of reduction in CH4 production and the key processes involved by supplementation with Kappaphycus alvarezii and Sargassum wightii at the recommended levels.},
}
@article {pmid39858847,
year = {2025},
author = {Zeng, X and Wang, Q and Song, Q and Liang, Q and Sun, Y and Song, F},
title = {Effects of Different Nitrogen Fertilizer Application Rates on Soil Microbial Structure in Paddy Soil When Combined with Rice Straw Return.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858847},
issn = {2076-2607},
support = {CZKYF2023-1-B015//Heilongjiang Scientific Research Institutions/ ; },
abstract = {Metagenomic sequencing of the microbial soil community was used to assess the effect of various nitrogen fertilizer treatments in combination with constant rice straw return to the soil in the tiller layer of Northeast China's black paddy soil used for rice production. Here, we investigated changes in the composition, diversity, and structure of soil microbial communities in the soil treated with four amounts of nitrogen fertilizers (53, 93, 133, and 173 kg/ha) applied to the soil under a constant straw return of 7500 kg/ha, with a control not receiving N. The relationships between soil microbial community structure and soil physical and chemical properties were determined. The results showed that the available K content of the soil significantly (p < 0.05) increased in soil receiving the lowest N-fertilizer dose. When applied at high amounts, N-fertilizer changed the Chao1 and ACE indices of the soil microorganisms (p < 0.05), and the treatments resulted in significant differences in the β-diversity of the soil microorganisms. By NMDS analysis it was demonstrated that the treatment significantly affected the structure of the soil microbial communities. Redundancy analysis showed that the main physicochemical drivers behind these differences were total nitrogen, total potassium, ammonium nitrogen, total phosphorus, and available potassium. The soil microbial communities in the control treatment were negatively correlated with nitrate and ammonium nitrogen; the lowest N-fertilizer treatment produced positive correlations with total nitrogen, total potassium, and total phosphorus and negative correlations with ammonium nitrogen; the highest dose negatively correlated with total nitrogen, available potassium, available phosphorus, total phosphorus, and pH. This study showed that moderate N fertilizer application is an effective way to increase soil microbial diversity and improve soil quality. This experiment provides technical support for the application of the alternative fertilizer technology of straw return to the field and provides a theoretical basis for rational fertilization of paddy fields in a cold climate.},
}
@article {pmid39858794,
year = {2024},
author = {Zou, Y and Zou, Q and Yang, H and Han, C},
title = {Investigation of Intestinal Microbes of Five Zokor Species Based on 16S rRNA Sequences.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858794},
issn = {2076-2607},
support = {201929/WT_/Wellcome Trust/United Kingdom ; 2022ZD0117700//the National Science and Technology Major Project/ ; },
abstract = {Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax psilurus) using 16S amplicon technology combined with bioinformatics. Microbial composition analysis showed similar intestinal microbes but different proportions among five zokor species, and their dominant bacteria corresponded to those of herbivores. To visualize the relationships among samples, PCoA and PERMANOVA tests showed that the intestinal microbes of zokors are largely clustered by host species, but less so by genetics and geographical location. To find microbes that differ among species, LefSe analysis identified Lactobacillus, Muribaculaceae, Lachnospiraceae_NK4A136_group, unclassified_f_Christensenellaceae, and Desulfovibrio as biomarkers for E. cansus, E. rothschildi, E. smithi, M. aspalax, and M. psilurus, respectively. PICRUSt metagenome predictions revealed enriched microbial genes for carbohydrate and amino acid metabolism in E. cansus and E. smithi, and for cofactor and vitamin metabolism as well as glycan biosynthesis and metabolism in E. rothschildi, M. aspalax, and M. psilurus. Our results demonstrated differences in the microbial composition and functions among five zokor species, potentially related to host genetics, and host ecology including dietary habits and habitat environment. These works would provide new insight into understanding how subterranean zokors adapt to their habitats by regulating intestinal microbes.},
}
@article {pmid39858581,
year = {2024},
author = {Koreeda, T and Honda, H and Onami, JI},
title = {Snowflake Data Warehouse for Large-Scale and Diverse Biological Data Management and Analysis.},
journal = {Genes},
volume = {16},
number = {1},
pages = {},
pmid = {39858581},
issn = {2073-4425},
mesh = {*Computational Biology/methods ; Humans ; Cloud Computing ; Data Management/methods ; High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; },
abstract = {With the increasing speed of genomic, transcriptomic, and metagenomic data generation driven by the advancement and widespread adoption of next-generation sequencing technologies, the management and analysis of large-scale, diverse data in the fields of life science and biotechnology have become critical challenges. In this paper, we thoroughly discuss the use of cloud data warehouses to address these challenges. Specifically, we propose a data management and analysis framework using Snowflake, a SaaS-based data platform. We further demonstrate its convenience and effectiveness through concrete examples, such as disease variant analysis and in silico drug discovery. By introducing Snowflake, researchers can efficiently manage and analyze a wide array of biological data, enabling the discovery of new biological insights through integrated analysis. Through these specific methodologies and application examples, we aim to accelerate research progress in the field of bioinformatics.},
}
@article {pmid39858184,
year = {2025},
author = {Zhou, YH and Liu, XP and Gu, XM and Lv, HX and Yang, Y and Cai, ZX and Di, B and Wang, CK and Gao, YY and Jin, L},
title = {Effects of Dietary Nano-Composite of Copper and Carbon on Antioxidant Capacity, Immunity, and Cecal Microbiota of Weaned Ira White Rabbits.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {2},
pages = {},
pmid = {39858184},
issn = {2076-2615},
support = {2023YFD1600500//National Key Research and Development Program of China/ ; 2023N0008//Agricultural Guiding (Key) Project of Fujian Provincial Science and Technology Department/ ; 2022L3085//Science and Technology Development Projects Funded by Chinese Central and Local Governments/ ; KFB23099A//Science and Technology Innovation Special Fund Project of Fujian Agriculture and Forestry University/ ; 2022J01587//Project of Natural Science Foundation of Fujian Province/ ; K83139297, 2019-2022//Fujian Specialist Funds of Chicken Industrial System in China/ ; },
abstract = {This experiment investigated the effects of dietary supplementation with nano-composites of copper and carbon (NCCC) on antioxidants, immune functions, and the cecum microbiota of weaned Ira white rabbits. A total of 240 weaned 35-day-old Ira white rabbits were randomly allocated to five dietary treatments (n = 6 per treatment, each replicate consisted of eight rabbits) that included the control group (CON) with a basal diet, the SAL group with 60 mg/kg salinomycin (SAL) in addition to the basal diet, and the NCCC I, II, III groups, which were supplemented with 50, 100, and 200 mg/kg NCCC, respectively, in addition to the basal diet. The test lasted for 28 d. The results showed that dietary NCCC supplementation increased the liver Cu/Zn-SOD content and up-regulated the gene expression of Cu/Zn-SOD (p < 0.05), while also reducing the content of MDA in the liver and enhancing the antioxidant capacity of Ira white rabbits. Moreover, the NCCC diet supplementation reduced the content of IL-6 and down-regulated the relative expression of IL-6 and IL-1β genes in the jejunum of Ira white rabbits (p < 0.05). In addition, the metagenomic analysis of 16 S rRNA showed significant differences in the cecal microbial structure of weaned Ira white rabbits in the NCCC III group compared with the CON, NCCC I, and NCCC II groups (p < 0.05). Firmicutes and Bacteroidetes were the dominant phyla of cecal microorganisms in weaned Ira rabbits in the NCCC diet groups. The dominant genera included unidentified Eubacteriaceae, unclassified Lachnospiraceae, Christensenellaceae, and Ruminococcus. Furthermore, the relative abundance of Ruminococcus in the NCCC I and II groups was lower than that in the CON group in the cecum of Ira white rabbits (p < 0.05). In summary, our results showed that diet supplementation with NCCC could enhance the antioxidant capacity in the liver, alleviate intestinal inflammation, and regulate the structure of intestinal flora, improving the health of Ira white rabbits.},
}
@article {pmid39857726,
year = {2025},
author = {Chou, MJ and Cheng, CH and Wang, HC and Tsai, MJ and Sheu, CC and Chang, WA},
title = {Investigating the Pulmonary Host Response of Acinetobacter baumannii Infection-Associated Pneumonia by Metagenomic Next-Generation Sequencing.},
journal = {Biomedicines},
volume = {13},
number = {1},
pages = {},
pmid = {39857726},
issn = {2227-9059},
support = {KMUH111-1M06//Kaohsiung Medical University Chung-Ho Memorial Hospital/ ; },
abstract = {Background: For investigating the host response in Acinetobacter baumannii associated pneumonia, we analyzed the host genetic sequences obtained from metagenomic next-generation sequencing (mNGS). Methods: The samples for mNGS were bronchoalveolar lavage fluid (BALF) collected from the lungs of patients infected with A. baumannii and from patients without bacterial infections. BALF samples from patients with pneumonia were collected from the lungs of patients infected with A. baumannii with New Delhi metallo-β-lactamase (NDM, before treatment), A. baumannii with NDM (post-treatment), A. baumannii without resistant genes, and those without bacterial infection. Partek was used for investigating enriched functions and pathways related to the pulmonary host response to pneumonia caused by A. baumannii with NDM infection and A. baumannii without antimicrobial-resistant genes. The STRING was employed for identifying protein interaction pathways related to the pulmonary host response to pneumonia caused by A. baumannii without antimicrobial-resistant genes. Results: In pulmonary host response to pneumonia caused by A. baumannii with NDM, five immune system-related pathways and five pathways related to signal transduction were identified. No significant differences were observed in the immune system and signal transduction pathways in the pulmonary host response to pneumonia caused by A. baumannii without antimicrobial-resistant genes. However, significant differences were noted in the phagosome, ferroptosis, and regulation of the actin cytoskeleton in cellular processes. Conclusions: mNGS provides information not only on pathogen gene expression but also on host gene expression. In this study, we found that pneumonia with A. baumannii carrying the NDM resistance gene triggers stronger immune responses in the lung, while pneumonia with A. baumannii lacking antimicrobial resistance genes is more linked to iron-related pathways.},
}
@article {pmid39857615,
year = {2024},
author = {Giampani, A and Simitsopoulou, M and Sdougka, M and Paschaloudis, C and Roilides, E and Iosifidis, E},
title = {The Combinational Effect of Enhanced Infection Control Measures and Targeted Clinical Metagenomics Surveillance on the Burden of Endemic Carbapenem and Other β-Lactam Resistance Among Severely Ill Pediatric Patients.},
journal = {Biomedicines},
volume = {13},
number = {1},
pages = {},
pmid = {39857615},
issn = {2227-9059},
support = {xx//Procter &amp; Gamble and Gilead Sciences and by the Department of Biology of Aristotle University of Thessaloniki/ ; },
abstract = {Background: Antimicrobial resistance (AMR) is recognized as one of the most important global public health threats. There is an urgent need to reduce the spread of these multidrug-resistant bacteria (MDR-B), particularly in extremely vulnerable patients. The aim of this study was to investigate whether targeted gene amplification performed directly on clinical samples can be used simultaneously with a bundle of enhanced infection control measures in a Pediatric Intensive Care Unit (PICU) endemic to MDR-B. Methods: This study had three phases: (1) the baseline phase was performed prior to intervention when first screening and sample collection were performed; (2) the intervention phase was performed when various enhanced infection control measures (EICM) were applied; and (3) the maintenance phase occurred when EICMs were combined with the implementation of targeted molecular surveillance. The presence of four carbapenemase genes, blaKPC, blaOXA-48-like, blaVIM, and blaNDM, as well as the β-lactamase genes blaTEM and blaSHV, was evaluated by PCR after DNA isolation directly from stool samples. The results were compared to culture-based phenotypic analysis. Results and Conclusions: The implementation of EICM appeared to reduce the resistance burden in this sample endemic to an MDR-B clinical setting. The direct implementation of a targeted and customized rapid molecular detection assay to clinical samples seems to be an effective clinical tool for the evaluation of EICM measures.},
}
@article {pmid39857379,
year = {2025},
author = {Wu, H and Qin, B and Yang, G and Ji, P and Gao, Y and Zhang, L and Wang, B and Liu, G},
title = {The Protective Effects of Melatonin on Hainan Black Goats Under Heat Stress: Understanding Its Actions and Mechanisms.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39857379},
issn = {2076-3921},
support = {32302749//National Natural Science Foundation of China/ ; ZDYF2021XDNY174//Hainan Province key research and development plan/ ; },
abstract = {As the global climate changes, high temperatures will cause heat stress, which significantly affects the productive efficiency of livestock. Currently, there is a lack of efficient methods to use in targeting this issue. In this study, we report that melatonin supplementation may represent an alternative method to reduce the negative impact of heat stress on livestock, particularly in Hainan black goats. Our results show that melatonin treatment increased the average daily gain of Hainan black goats that were exposed to constantly high temperatures for two months compared to controls. Our mechanistic exploration revealed that melatonin treatment not only reduced the oxidative stress and inflammatory reaction caused by heat stress but also improved goats' metabolic capacity, promoting their growth and development. More importantly, for the first time, we observed that melatonin treatment modified the abundance of the intestinal microflora, altering the metabolism of the goats, which further improved their tolerance to constant heat stress.},
}
@article {pmid39857331,
year = {2025},
author = {Liu, Y and Zhang, Y and Yao, H and Zheng, Z and Zhao, W and Lin, G},
title = {Analysis on Bacterial Community of Noctiluca scintillans Algal Blooms Near Pingtan Island, China.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
pmid = {39857331},
issn = {2079-7737},
support = {No. 2022L3010//Fujian Normal University/ ; },
abstract = {Noctiluca scintillans, known as a global red tide species, is a common red tide species found in Pingtan Island. To examine the bacterial community structure in different environments during the red tide period of N. scintillans on Pingtan Island, samples were collected from the Algal Bloom Area (ABA), Transition Area (TA), and Non-Algal Bloom Area (NBA) on 6 April 2022, and the environmental physicochemical factors and bacterial community were determined. The outbreak of N. scintillans red tide significantly impacted the water quality and bacterial community structure in the affected sea area. The water quality in the ABA has deteriorated markedly, with the contents of COD, NH4[+]-N, and PO4[3-] in the ABA being significantly higher than those in the TA and NBA, while the pH is significantly lower than that in the TA and NBA. The richness, diversity, and evenness of the bacterial community in the ABA are all lower than those of the TA and NBA. For instance, the Shannon index values of the three sampling points are 4.41, 5.41, and 6.37, respectively. At the phylum level, the dominant bacterial phyla in the ABA are Proteobacteria, Firmicutes, and Cyanobacteria; in the TA, they are Proteobacteria, Bacteroidetes, and Firmicutes; and in the NBA, they are Proteobacteria, Bacteroidetes, and Cyanobacteria. At the genus level, the dominant bacterial genera in the ABA are Vibrio, Carnobacterium, Candidatus_Megaira, Planktomarina, and Pseudoalteromonas; in the TA, they are Vibrio, Planktomarina, Lentibacter, Glaciecola, and Jannaschia; and in the NBA, they are Planktomarina, Amylibacter, NS5_marine_group, Aurantivirga, and marine_metagenome. In the ABA, the combined proportion of Vibrio and Carnobacterium exceeds 50%, with Vibrio_splendidus accounting for 93% of the total Vibrio population. These research results can provide a scientific basis for clarifying the environmental characteristics and bacterial composition during the large-scale N. scintillans red tide in Pingtan Island.},
}
@article {pmid39857318,
year = {2025},
author = {Kashchenko, G and Taldaev, A and Adonin, L and Smutin, D},
title = {Investigating Aerobic Hive Microflora: Role of Surface Microbiome of Apis Mellifera.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
pmid = {39857318},
issn = {2079-7737},
support = {No 075-15-2022-305//Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers 'Digital Biodesign and Personalized Healthcare'./ ; },
abstract = {This study investigated the surface microbiome of the honeybee (Apis mellifera), focusing on the diversity and functional roles of its associated microbial communities. While the significance of the microbiome to insect health and behavior is increasingly recognized, research on invertebrate surface microbiota lags behind that of vertebrates. A combined metagenomic and cultivation-based approach was employed to characterize the bacterial communities inhabiting the honeybee exoskeleton. Our findings reveal a complex and diverse microbiota exhibiting significant spatial and environmental heterogeneity. The identification of antimicrobial compound producers, validated through both culture and metagenomic analyses, including potentially novel Actinobacteria species, underscores the potential impact of these microbial communities on honeybee health, behavior, and hive dynamics. This research contributes to a more profound ecological understanding of the honeybee microbiome, particularly in its winter configuration.},
}
@article {pmid39857299,
year = {2025},
author = {Ramos Lopez, D and Flores, FJ and Espindola, AS},
title = {MeStanG-Resource for High-Throughput Sequencing Standard Data Sets Generation for Bioinformatic Methods Evaluation and Validation.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
pmid = {39857299},
issn = {2079-7737},
support = {OKL03271//Oklahoma State University - Oklahoma Agricultural Experiment Station/ ; },
abstract = {Metagenomics analysis has enabled the measurement of the microbiome diversity in environmental samples without prior targeted enrichment. Functional and phylogenetic studies based on microbial diversity retrieved using HTS platforms have advanced from detecting known organisms and discovering unknown species to applications in disease diagnostics. Robust validation processes are essential for test reliability, requiring standard samples and databases deriving from real samples and in silico generated artificial controls. We propose a MeStanG as a resource for generating HTS Nanopore data sets to evaluate present and emerging bioinformatics pipelines. MeStanG allows samples to be designed with user-defined organism abundances expressed as number of reads, reference sequences, and predetermined or custom errors by sequencing profiles. The simulator pipeline was evaluated by analyzing its output mock metagenomic samples containing known read abundances using read mapping, genome assembly, and taxonomic classification on three scenarios: a bacterial community composed of nine different organisms, samples resembling pathogen-infected wheat plants, and a viral pathogen serial dilution sampling. The evaluation was able to report consistently the same organisms, and their read abundances as provided in the mock metagenomic sample design. Based on this performance and its novel capacity of generating exact number of reads, MeStanG can be used by scientists to develop mock metagenomic samples (artificial HTS data sets) to assess the diagnostic performance metrics of bioinformatic pipelines, allowing the user to choose predetermined or customized models for research and training.},
}
@article {pmid39857256,
year = {2025},
author = {Dai, W and Zhu, H and Chen, J and Chen, H and Dai, D and Wu, J},
title = {Metagenomic Insights into Pigeon Gut Microbiota Characteristics and Antibiotic-Resistant Genes.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
pmid = {39857256},
issn = {2079-7737},
support = {BK20210005//Natural Science Foundation of Jiangsu Province/ ; jit-b-202105//Research Foundation for Advanced Talents/ ; 202413573100Y//College Students' Innovation Training Program/ ; 21KJB310015//Natural Science Research of Jiangsu Higher Education Institutions of China/ ; },
abstract = {BACKGROUND: Antibiotics were extensively used in the pigeon breeding industry previously to promote growth and prevent disease, leading to the spread of antibiotic-resistant genes (ARGs) in gut microbes, which has become a major public health concern.<br><br>METHODS: A metagenomic analysis was performed to investigate the gut microbial communities and ARGs in young and older pigeons in Nanjing, Jiangsu Province, China.<br><br>RESULTS: There were obviously distinct gut microbiota and functional compositions between young and older pigeons. Both Pseudomonadota and Uroviricota were dominant in young and older pigeons. Although sharing 24 gut microbiota phyla between young and older pigeons, Bacillota and Pseudomonadota were the dominant microbial phyla in them, respectively. Besides the shared metabolic pathways and biosynthesis of secondary metabolites, biosynthesis of amino acids was the most abundant Kyoto Encyclopedia of Genes and Genomes (KEGG) function in young pigeons, while microbial metabolism in diverse environments was abundant in older pigeons. A total of 142 ARGs conferring multidrug resistance, tetracycline, and aminoglycoside resistance were identified; the most abundant gene in young pigeons was tetracycline-tetW, while in older pigeons, it was multidrug-acrB.<br><br>CONCLUSIONS: Our findings revealed significant differences in the gut microbial communities and ARGs between young and older pigeons. This study enhances our understanding of pigeon gut microbiota and antibiotic resistomes, contributing to knowledge-based sustainable pigeon meat production.},
}
@article {pmid39856911,
year = {2025},
author = {Li, S and Han, Y and Yan, M and Qiu, S and Lu, J},
title = {Machine Learning and Multi-Omics Integration to Reveal Biomarkers and Microbial Community Assembly Differences in Abnormal Stacking Fermentation of Sauce-Flavor Baijiu.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {39856911},
issn = {2304-8158},
support = {Guizhou Provincial Science and Technology Foundation (NATURAL SCIENCE) (Basic Research on Science and Technology Cooperation in Guizhou Province - ZK [2023] General 149)//Jun Lu/ ; Guizhou Provincial Science and Technology Foundation (NATURAL SCIENCE) (Basic Research on Science and Technology Cooperation in Guizhou Province - ZK [2023] General 150).//Jun Lu/ ; },
abstract = {Stacking fermentation is critical in sauce-flavor Baijiu production, but winter production often sees abnormal fermentations, like Waistline and Sub-Temp fermentation, affecting yield and quality. This study used three machine learning models (Logistic Regression, KNN, and Random Forest) combined with multi-omics (metagenomics and flavoromics) to develop a classification model for abnormal fermentation. SHAP analysis identified 13 Sub-Temp Fermentation and 9 Waistline microbial biomarkers, along with 9 Sub-Temp Fermentation and 12 Waistline flavor biomarkers. Komagataeibacter and Gluconacetobacter are key for normal fermentation, while Ligilactobacillus and Lactobacillus are critical in abnormal cases. Excessive acid and ester markers caused unbalanced aromas in abnormal fermentations. Additionally, ecological models reveal the bacterial community assembly in abnormal fermentations was influenced by stochastic factors, while the fungal community assembly was influenced by deterministic factors. RDA analysis shows that moisture significantly drove Sub-Temp fermentation. Differential gene analysis and KEGG pathway enrichment identify metabolic pathways for flavor markers. This study provides a theoretical basis for regulating stacking fermentation and ensuring Baijiu quality.},
}
@article {pmid39856901,
year = {2025},
author = {Bai, C and Fan, B and Hao, J and Yao, Y and Ran, S and Wang, H and Li, H and Wei, R},
title = {Changes in Microbial Community Diversity and the Formation Mechanism of Flavor Metabolites in Industrial-Scale Spontaneous Fermentation of Cabernet Sauvignon Wines.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {39856901},
issn = {2304-8158},
support = {2023BQ103//Science and Technology Innovation Fund of Shanxi Agricultural University/ ; LYNJ202110//Research and application of key technologies for sustainable development of wine industry/ ; 2023AB004-01//Xinjiang Corps financial science and technology plan project/ ; },
abstract = {The key flavor compound formation pathways resulting from indigenous microorganisms during the spontaneous fermentation of wine have not been thoroughly described. In this study, high-throughput metagenomic sequencing and untargeted metabolomics were utilized to investigate the evolution of microbial and metabolite profiles during spontaneous fermentation in industrial-scale wine production and to elucidate the formation mechanisms of key flavor compounds. Metabolome analysis showed that the total amount of esters, fatty acids, organic acids, aldehydes, terpenes, flavonoids, and non-flavonoids increased gradually during fermentation. Enrichment analysis indicated that metabolic pathways related to the synthesis, decomposition, transformation, and utilization of sugars, amino acids, and fatty acids were involved in the formation of key flavor compounds in wine. Metagenomic analysis revealed that Saccharomyces, Hanseniaspora, Zygosaccharomyces, Wickerhamiella, Lactobacillus, and Fructobacillus were the dominant taxa during spontaneous fermentation. They were significantly positively correlated with organic acids, fatty acids, esters, phenols, aldehydes, terpenes, and phenols. In conclusion, this research provides new insights into the metabolic pathways of key flavor compounds formed by indigenous microorganisms during wine fermentation.},
}
@article {pmid39856742,
year = {2025},
author = {Benitez, AJ and Tanes, C and Friedman, ES and Zackular, JP and Ford, E and Gerber, JS and DeRusso, PA and Kelly, A and Li, H and Elovitz, MA and Wu, GD and Zemel, B and Bittinger, K},
title = {Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {21},
pmid = {39856742},
issn = {2049-2618},
support = {UL1 TR001878/TR/NCATS NIH HHS/United States ; UL1TR001878//NIH National Center for Research Resources Clinical and Translational Science Program/ ; KL2 TR001879/TR/NCATS NIH HHS/United States ; unrestricted donation//American Beverage Foundation for a Healthy America/ ; R01DK107565/DK/NIDDK NIH HHS/United States ; R35GM138369/GM/NIGMS NIH HHS/United States ; KL2TR001879/TR/NCATS NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Infant ; *Feces/microbiology/chemistry ; Female ; *Bile Acids and Salts/metabolism ; Male ; Prospective Studies ; *Breast Feeding ; Longitudinal Studies ; Infant, Newborn ; Metagenomics ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Child, Preschool ; Black or African American ; Amoxicillin ; Bifidobacterium/drug effects/isolation &amp; purification/genetics ; White ; },
abstract = {BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.<br><br>RESULTS: Stool samples were collected at ages 4, 12, and 24&#xa0;months for antibiotic-exposed (n&#x2009;=&#x2009;170) and unexposed (n&#x2009;=&#x2009;153) participants. A short-term substudy (n&#x2009;=&#x2009;39) collected stool samples at first exposure, and over 3&#xa0;weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2&#xa0;weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.<br><br>CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.},
}
@article {pmid39856709,
year = {2025},
author = {Li, D and Chen, W and Luo, W and Zhang, H and Liu, Y and Shu, D and Wei, G},
title = {Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {23},
pmid = {39856709},
issn = {2049-2618},
support = {42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; },
mesh = {*Seeds/microbiology ; *Germination ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Cellulose/metabolism ; Astragalus Plant/microbiology ; Soil Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.<br><br>RESULTS: Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.<br><br>CONCLUSIONS: Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.},
}
@article {pmid39856417,
year = {2025},
author = {Mamawal, DRD and Rivera, WL},
title = {Combined application of metagenomics and FEAST to trace sources of microbial eukaryotic contamination in the Pasig-Marikina-San Juan (PAMARISAN) river system in Metro Manila, Philippines.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {196},
pmid = {39856417},
issn = {1573-2959},
support = {E-249//National Research Council of the Philippines/ ; E-249//National Research Council of the Philippines/ ; },
mesh = {*Rivers/microbiology/chemistry ; *Environmental Monitoring ; Philippines ; *Metagenomics ; Animals ; Eukaryota/genetics ; Feces/microbiology ; Water Microbiology ; },
abstract = {Microbial eukaryotes are vital to global microbial diversity, but there is limited information about their composition and sources in contaminated surface waters. This study examined the pathogens and potential sources of microbial eukaryotic communities in polluted sink environments using the 18S rDNA amplicon sequencing combined with the fast expectation-maximization for microbial source tracking (FEAST) program. Six sampling sites were selected along the Pasig-Marikina-San Juan (PAMARISAN) River System, representing different locations within the waterway and classified as sinks (n = 12), whereas animal fecal samples collected from various farms were classified as sources (n = 29). Taxonomic composition revealed Stramenopila, Alveolata, Rhizaria (SAR), Archaeplastida, and Excavata in the rivers, accounting for 85.1%, 13.2%, and 0.36% mean abundance of microbial sink communities, respectively. Clinically relevant human pathogens were also observed in sink environments. The correlation test demonstrated that dissolved oxygen, total suspended solids, pH, temperature, fecal coliform count, and phosphates were important environmental factors driving community variations. Moreover, FEAST results indicated that sewage (19.6%) was the primary source of microbial eukaryotes, followed by duck (0.644%) and cow (0.566%) feces. Spatio-seasonal variations showed higher contributions at downstream stations and during the wet season, highlighting the role of rainfall in enhancing microbial dispersal. Results from community-based microbial source tracking can be used to explore factors shaping microbial eukaryotes in freshwater environments, assess potential pathogen-related hazards, and inform river conservation and management strategies. Furthermore, this also serves as preliminary data for microbial eukaryotic source tracking in the Philippines, laying groundwork for future research.},
}
@article {pmid39856391,
year = {2025},
author = {Tisza, MJ and Lloyd, RE and Hoffman, K and Smith, DP and Rewers, M and Javornik Cregeen, SJ and Petrosino, JF},
title = {Longitudinal phage-bacteria dynamics in the early life gut microbiome.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {420-430},
pmid = {39856391},
issn = {2058-5276},
support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; U01 DK63865//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63821//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK124166/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK63829//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; U01 DK128847/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology/classification ; Infant ; *Bacteria/virology/genetics/classification/isolation &amp; purification ; Child, Preschool ; Longitudinal Studies ; Metagenome ; Diabetes Mellitus, Type 1/microbiology/virology ; Feces/microbiology ; Female ; Male ; Metagenomics ; Infant, Newborn ; },
abstract = {Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.},
}
@article {pmid39856104,
year = {2025},
author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY},
title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {987},
pmid = {39856104},
issn = {2041-1723},
support = {R01 NS115537/NS/NINDS NIH HHS/United States ; R01NS115537//U.S. Department of Health &amp; Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; },
mesh = {*Diet, Ketogenic ; Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration &amp; dosage ; *Seizures/diet therapy/metabolism ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Infant Formula ; Female ; },
abstract = {The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.},
}
@article {pmid39856097,
year = {2025},
author = {Pidgeon, R and Mitchell, S and Shamash, M and Suleiman, L and Dridi, L and Maurice, CF and Castagner, B},
title = {Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {999},
pmid = {39856097},
issn = {2041-1723},
support = {PJT-437944//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
mesh = {Humans ; *Coumarins/metabolism ; *Gastrointestinal Microbiome ; *Operon/genetics ; Feces/microbiology ; Diet ; Bacterial Proteins/metabolism/genetics ; Proteomics ; },
abstract = {Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota. Once absorbed, uroA can trigger mitophagy and aryl hydrocarbon receptor signaling pathways, altering host immune function, mitochondrial health, and intestinal barrier integrity. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. We show that the ucd operon encodes a predicted molybdopterin-dependent enzyme complex that dehydroxylates urolithins at a specific position (9-OH). By interrogating publicly available metagenomics datasets, we observed that uroC-metabolizing Enterocloster species and ucd operon genes are prevalent in human feces. In ex vivo experiments with human fecal samples, only samples actively transcribing ucd could produce uroA, possibly explaining differences in urolithin metabolism between individuals. Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.},
}
@article {pmid39856057,
year = {2025},
author = {Hu, H and Huang, Y and Yang, F and Ma, L and Zhang, J and Deng, X and Ma, N and Wang, K and Tao, Y and Lin, Q and Li, Y and Bai, X and Pan, H},
title = {Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {141},
pmid = {39856057},
issn = {2052-4463},
mesh = {Animals ; *Metagenome ; Swine/microbiology ; *Mouth/microbiology ; *Microbiota ; Genome, Microbial ; Metagenomics ; Tibet ; },
abstract = {Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium-high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.},
}
@article {pmid39855705,
year = {2025},
author = {Hao, M and Hu, L and Han, M and Li, C and Chang, H and Luo, J and Jiang, H},
title = {[Mining and characterization of new enzymes based on Phi29 DNA polymerase].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {1},
pages = {427-436},
doi = {10.13345/j.cjb.240222},
pmid = {39855705},
issn = {1872-2075},
mesh = {*DNA-Directed DNA Polymerase/metabolism/genetics ; Bacillus Phages/enzymology/genetics ; Metagenome ; Bacteriophages/enzymology/genetics ; Viral Proteins/genetics/metabolism ; },
abstract = {In recent years, the bacteriophage Φ29 (Phi29) DNA polymerase has garnered increasing attention due to its high-fidelity amplification capacity at constant temperatures. To advance the industrial application of this type of isothermal polymerases, this study mined and characterized new enzymes from the microbial metagenome based on the known Phi29 DNA polymerase sequence. The results revealed that a new enzyme, Php29 DNA polymerase, was identified in the microbial metagenome with plants as the hosts. This enzyme exhibited higher strand displacement activity, with a 59.5% similarity to bacteriophage Φ29. Experimental validation demonstrated that the enzyme had 3'→5' exonuclease activity, and its amplification products can serve as substrates for further catalytic reactions. The discovery and validation of Php29 DNA polymerase gives insights into the future industrial application of isothermal polymerases.},
}
@article {pmid39855427,
year = {2025},
author = {Coffman, KA},
title = {The roles of viruses in tephritid pest multitrophic interactions and an outlook for biological control.},
journal = {Current opinion in insect science},
volume = {68},
number = {},
pages = {101333},
doi = {10.1016/j.cois.2025.101333},
pmid = {39855427},
issn = {2214-5753},
abstract = {Tephritid fruit fly pests remain a considerable problem for agricultural fruit production around the world. New control methods that do not rely on synthetic insecticides are increasingly desirable to diversify tephritid pest management programs. Biological control through the release of parasitoid wasps has historically provided effective suppression of fruit fly pests, although molecular factors that influence the success of fruit fly parasitoids are understudied. Microbes have been demonstrated to facilitate myriad interactions between insects and their environment and have been the subject of recent investigation within tephritids. Specifically, the diversity and function of viruses found within fruit flies and associated parasitoids is an emerging field of research that has the potential to deepen our understanding of previously hidden factors that facilitate sustainable pest control. Most work to date has focused on identifying resident viral communities within fruit flies using metagenomic and metatranscriptomic sequencing approaches. Additionally, a growing body of evidence has revealed a multitude of functional dynamics that viruses have with fruit fly hosts, including vertically transmitted commensal viruses and parasitoid-vectored pathogens. Heritable viruses transmitted by fruit fly parasitoids, in particular, have been shown to play prominent roles in fruit fly multitrophic interactions, in which viral infection can shape the survival rate and host range of infected parasitoids. Furthermore, at least one parasitoid virus represents a lethal pathogen to a wide range of fruit fly pest species. Parasitoid viruses could therefore present novel opportunities to leverage natural antagonistic interactions for fruit fly pest control innovations.},
}
@article {pmid39855018,
year = {2025},
author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Zhu, X and Yin, H and Dang, Z and Niu, J},
title = {Metagenomic and enzymatic mechanisms underpinning efficient water treatment of 2-ethylhexyl diphenyl phosphate (EHDPP) by the microbial consortium 8-ZY.},
journal = {Water research},
volume = {275},
number = {},
pages = {123178},
doi = {10.1016/j.watres.2025.123178},
pmid = {39855018},
issn = {1879-2448},
abstract = {The ubiquitous presence, potential toxicity, and persistence of 2-ethylhexyl diphenyl phosphate (EHDPP) in the environment have raised significant concerns. In this study, we successfully isolate a novel microbial consortium, named 8-ZY, and we demonstrate its remarkable ability to degrade EHDPP using an extremely low concentration of the inoculate. A total of 11 degradation metabolites were identified, including hydrolysis, hydroxylated, methylated, glucuronide-conjugated, and previously unreported byproducts, enabling us to propose new transformation pathways. Further, we unveiled the active members of the microbial consortium 8-ZY during the degradation of EHDPP. We observed the presence of diverse active populations, which included Bradyrhizobium, Rhodopseudomonas, Sphingomonas, Hyphomicrobium, Chitinophaga, Aminobacter, and Ralstonia. A metagenomic analysis revealed the presence of genes that encode phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase enzymes, thus indicating their crucial role in EHDPP degradation. Furthermore, we successfully isolated Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 from the 8-ZY consortium, confirming their significance in EHDPP degradation and metabolite formation. These findings underscored the diversity of strains and functional genes responsible for the transformation of EHDPP within the consortium 8-ZY, highlighting the essential role of synergistic interactions during EHDPP biodegradation processes. Molecular docking and dynamics simulation suggested that alkaline phosphatase, cytochrome P450, and hydroxylase stably bonded to EHDPP within their respective active pockets, targeting distinct sites on the EHDPP molecule. These findings provide a comprehensive understanding of the transformation mechanisms of OPEs and contribute valuable insights into their fate in the environment.},
}
@article {pmid39854991,
year = {2025},
author = {Pei, Y and Lei, A and Wang, M and Sun, M and Yang, S and Liu, X and Liu, L and Chen, H},
title = {Novel tetracycline-degrading enzymes from the gut microbiota of black soldier fly: Discovery, performance, degradation pathways, mechanisms, and application potential.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137286},
doi = {10.1016/j.jhazmat.2025.137286},
pmid = {39854991},
issn = {1873-3336},
abstract = {The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Although enzymatic remediation is a promising strategy for mitigating TC contamination, the availability of effective TC-degrading enzymes remains limited, and their mechanisms and applications are not fully understood. This study developed a comprehensive TC-degrading enzyme library from the gut microbiome of the highly TC-resistant saprophagous insect, black soldier fly larvae (BSFL), using an integrated metagenomic and comparative metatranscriptomic approach, identifying 105 potential novel TC-degradation genes. Bioinformatics analysis of 10 selected genes underscored the novelty of the identified enzymes. Among these, Trg2 demonstrated strong binding affinity and significant degradation capacity for TC. Key functional amino acid residues, including Thr231, Ala64, Ala82, Gly68, Gly79, and Ser81, were identified as essential for the interaction between TC and Trg2. Six TC degradation pathways were proposed, involving the transformation of TC into 19 metabolites through de-grouping, ring opening, oxidation, reduction, and addition reactions, effectively reducing TC toxicity. Furthermore, Trg2 exhibited resilience under harsh conditions, maintaining the capacity to remove about 45 % of the total TC in mariculture wastewater across eight successive batches. This study advances the understanding of TC degradation mechanisms and highlights the potential application of novel enzymes for bioremediation purposes.},
}
@article {pmid39854777,
year = {2025},
author = {Mardalisa, and Wang, R and Sabar, MA and Matsuura, N and Hara-Yamamura, H and Honda, R},
title = {Different fates between extracellular and intracellular antimicrobial resistome in full-scale activated sludge and membrane bioreactor processes.},
journal = {Water research},
volume = {274},
number = {},
pages = {123155},
doi = {10.1016/j.watres.2025.123155},
pmid = {39854777},
issn = {1879-2448},
abstract = {Treated effluent of wastewater treatment plants (WWTPs) are major sources of extracellular antimicrobial resistance genes (eARGs) into aquatic environments. This study aimed to clarify the fate and origins of eARGs from influent to treated effluent at a full-scale WWTP. The compositions of eARG and intracellular ARG (iARG) were acquired via shotgun metagenomic sequencing in influent wastewater, activated sludge, and treated effluent of the target WWTP, where identical wastewater was treated by conventional activated sludge (CAS) and membrane bioreactor (MBR) processes. The proportion of eARGs to iARGs increased from influent to effluent in both processes, reaching almost half of the total ARG. Most eARGs in influent were associated with clinically important antimicrobials, whereas eARGs in sludge and effluent were dominated by aminoglycoside resistance genes of aadA and APH variants. Although the eARGs composition in influent wastewater mirrored that of iARGs, a substantial shift occurred in activated sludge and effluent, highlighting the presence of distinct dissemination and reduction mechanisms between eARGs and iARGs. Notably, the origin of eARGs in treated effluent was mainly iARGs in the effluent rather than the carryover of eARG from activated sludge, which were substantially reduced in MBR, compared to CAS. Consequently, these differences in selective mechanisms led to different fates between eARG and iARG during wastewater treatment.},
}
@article {pmid39854281,
year = {2025},
author = {Gurbich, TA and Beracochea, M and De Silva, NH and Finn, RD},
title = {mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf037},
pmid = {39854281},
issn = {1367-4811},
abstract = {SUMMARY: In recent years there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. These assemblies often include novel species that are poorly represented in reference databases creating a need for a tool that can annotate both well-described and novel taxa, and can run at scale. Here, we present mettannotator-a comprehensive, scalable Nextflow pipeline for prokaryotic genome annotation that identifies coding and non-coding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarises the results of these tools in a GFF (General Feature Format) file that can be easily utilised in downstream analysis or visualised using common genome browsers. Here, we show how it works on 200 genomes from 29 prokaryotic phyla, including isolate genomes and known and novel metagenome-assembled genomes, and present metrics on its performance in comparison to other tools.<br><br>The pipeline is written in Nextflow and Python and published under an open source Apache 2.0 licence. Instructions and source code can be accessed at https://github.com/EBI-Metagenomics/mettannotator. The pipeline is also available on WorkflowHub: https://workflowhub.eu/workflows/1069.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid39853798,
year = {2025},
author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q},
title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.},
journal = {Statistics in medicine},
volume = {44},
number = {3-4},
pages = {e10291},
pmid = {39853798},
issn = {1097-0258},
support = {1R01DK131267-01/NH/NIH HHS/United States ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 2210912//National Science Foundation/ ; R01 GM141519/GM/NIGMS NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; 2113674//National Science Foundation/ ; R01 DK131267/DK/NIDDK NIH HHS/United States ; F32 DK128975/DK/NIDDK NIH HHS/United States ; },
mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.},
}
@article {pmid39853685,
year = {2025},
author = {Sun, Y and Gan, Z and Liu, S and Zhang, S and Zhong, W and Liu, J and Huang, X and He, W and Zhong, H and Cao, Q},
title = {Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early-Stage Nonsmoking Lung Adenocarcinoma Patients.},
journal = {Thoracic cancer},
volume = {16},
number = {2},
pages = {e15527},
pmid = {39853685},
issn = {1759-7714},
support = {220904094208//Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; 3320104100430//Exploration and Practice of a Tri-Party Personalized Oncology Strategy Based on Precision Medicine in Patient-Doctor-Research Collaboration/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/genetics/pathology ; *Adenocarcinoma of Lung/microbiology/genetics/pathology ; *Mycobiome ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; Gene Expression Profiling ; Aged ; Transcriptome ; Prognosis ; Tumor Microenvironment ; Case-Control Studies ; },
abstract = {BACKGROUND: The mycobiome in the tumor microenvironment of non-smokers with early-stage lung adenocarcinoma (ES-LUAD) has been minimally investigated.<br><br>METHODS: In this study, we conducted ultra-deep metagenomic and transcriptomic sequencing on 128 samples collected from 46 nonsmoking ES-LUAD patients and 41 healthy controls (HC), aiming to characterize the tumor-resident mycobiome and its interactions with the host.<br><br>RESULTS: The results revealed that ES-LUAD patients exhibited fungal dysbiosis characterized by reduced species diversity and significant imbalances in specific fungal abundances. Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. We observed correlations between Yarrowia lipolytica, Saccharomyces paradoxus, and tumor-infiltrating immune cells (TIICs), and identified a strong association (|rho|&#x2009;>&#x2009;0.7) between S. paradoxus and 14 transcription factors. A signature of three prognostic genes (GRIA1, CDO1, FHL1) closely associated with S. paradoxus was identified and they suggest that the interaction between the mycobiome and the host may contribute to prolonged overall survival (OS). Finally, a predictive model based on six fungi demonstrated decent classification performance in distinguishing ES-LUAD cases from HCs (AUC&#x2009;=&#x2009;0.724).<br><br>CONCLUSIONS: Our study demonstrates that the interactions between the mycobiome and transcriptome within tumors may help elucidate the pathogenic mechanisms of ES-LUAD. Fungi, as a potential predictive tool, can be used as an additional resource for accurately detecting and discriminating individuals with ES-LUAD.},
}
@article {pmid39853270,
year = {2025},
author = {Cardones, AR and Emiola, A and Hall, R and Sung, AD and Zhang, JY and Petty, AJ and Puza, C and Bohannon, LM and Bush, AT and Lew, MV and Fleming, E and Jin, YJ and Nichols, KR and Jain, V and Gregory, SG and Sullivan, KM and Chao, NJ and Oh, J},
title = {Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2021004792},
pmid = {39853270},
issn = {2473-9537},
abstract = {Gut dysbiosis is linked to mortality and the development of graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation (HSCT), but the impact of cutaneous dysbiosis remains unexplored. We performed a pilot observational study and obtained retroauricular and forearm skin swabs from 12 adult patients prior to conditioning chemotherapy/radiation, and at 1-week, 1-month and 3-months after allogeneic HSCT, and performed shotgun metagenomic sequencing. The cutaneous microbiome among HSCT patients was enriched for gram-negative bacteria such as E coli and Pseudomonas, fungi, and viruses. Enrichment with bacteriophages and Polyomavirus sp, was observed among patients who died within 1-year, while we observed longitudinal stability of the cutaneous microbiome at the 3-month time point among those who survived beyond 1 year post-HSCT, although these may simply be a reflection of the overall medical status of the patients. There was no association with fungal abundance and any of the outcomes observed. The cutaneous microbiome may be a reservoir of pathobionts among allogeneic HSCT patients. Our findings suggest that cutaneous dysbiosis exists post-HSCT, but the ultimate implication of this to patient outcomes remains to be seen. Larger studies are required.},
}
@article {pmid39853010,
year = {2024},
author = {Alexiev, A and Stretch, E and Kasschau, KD and Wilson, LB and Truong, L and Tanguay, RL and Sharpton, TJ},
title = {Clearing the Air on Pollutant Disruptions of the Gut-Brain Axis: Developmental Exposure to Benzo[a]pyrene Disturbs Zebrafish Behavior and the Gut Microbiome in Adults and Subsequent Generations.},
journal = {Toxics},
volume = {13},
number = {1},
pages = {},
pmid = {39853010},
issn = {2305-6304},
support = {1R01ES030226/ES/NIEHS NIH HHS/United States ; T32ES007060/ES/NIEHS NIH HHS/United States ; P30 ES030287/ES/NIEHS NIH HHS/United States ; R01 ES030226/ES/NIEHS NIH HHS/United States ; T32 ES007060/ES/NIEHS NIH HHS/United States ; },
abstract = {Developmental exposure to benzo[a]pyrene (BaP), a ubiquitous environmental pollutant, has been linked to various toxic effects, including multigenerational behavioral impairment. While the specific mechanisms driving BaP neurotoxicity are not fully understood, recent work highlights two important determinants of developmental BaP neurotoxicity: (1) the aryl hydrocarbon receptor (AHR), which induces host metabolism of BaP, and (2) the gut microbiome, which may interact with BaP to affect its metabolism, or be perturbed by BaP to disrupt the gut-brain axis. We utilized the zebrafish model to explore the role of AHR, the gut microbiome, and their interaction, on BaP-induced neurotoxicity. We tested (1) how developmental BaP exposure and AHR2 perturbation in zebrafish link to adult behavior, (2) how these variables associate with the structure and function of the adult zebrafish gut metagenome, and (3) whether these associations are multigenerational. Our findings reveal a reticulated axis of association between BaP exposure, developmental AHR2 expression, the zebrafish gut metagenome, and behavior. Results indicate that AHR2 is a key modulator of how BaP elicits neurotoxicity and microbiome dysbiosis. Additionally, this axis of association manifests generationally. These findings demonstrate the importance of studying pollutant-microbiome interactions and elucidate the role of specific host genes in neurotoxicity and dysbiosis.},
}
@article {pmid39852519,
year = {2024},
author = {Zhang, W and Li, Y and Chu, Y and Liu, H and Jing, H and Xia, Q},
title = {Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes.},
journal = {Marine drugs},
volume = {23},
number = {1},
pages = {},
pmid = {39852519},
issn = {1660-3397},
support = {KJRC2023C37//the innovational Found for the scientific and technological personnel of Hainan Province/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; 2022YFC2805400//the National Key R&amp;D Program of China/ ; 2022YFC2805505//the National Key R&amp;D Program of China/ ; },
mesh = {*Ecosystem ; *Drug Resistance, Microbial/genetics ; *Metagenomics/methods ; *Anti-Bacterial Agents/pharmacology ; Geologic Sediments/microbiology ; Seawater/microbiology ; Genes, Bacterial/genetics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; },
abstract = {The deep-sea ecosystem, a less-contaminated reservoir of antibiotic resistance genes (ARGs), has evolved antibiotic resistance for microbes to survive and utilize scarce resources. Research on the diversity and distribution of these genes in deep-sea environments is limited. Our metagenomics study employed short-read-based (SRB) and assembled-contig-based (ACB) methods to identify ARGs in deep-sea waters and sediments and assess their potential pathogenicity. SRB prediction was found to be more effective for studying the abundance and diversity of these genes, while combining both methods better illustrated the relationship of ARGs with the hosts. Deep-sea waters (DSW) and trenches had the highest diversity of ARGs, including β-lactams, multidrug resistance genes, and rifamycins. Mobile genetic elements, such as IncQ and RP4 plasmids, were also identified. The ratio of nonsynonymous to synonymous substitutions (pN/pS) values of these genes suggest different evolutionary strategies in response to deep-sea conditions and possible human impacts. These resistome profiles provide valuable insights into their natural origins as well as the ecological and evolutionary implications of antibiotic resistance in deep-sea ecosystems. The exploration of the global distribution of ARGs in diverse deep-sea environments is a novel approach that will assist in understanding their potential reservoirs and evolutionary mechanisms. Therefore, employing a comprehensive approach to studying ARGs is particularly necessary. Unique microbial life in deep-sea ecosystems, especially in deep-sea cold seeps sediments (DSCSS), deep-sea waters (DSW), and trench waters (TW), could be a valuable source of new antibiotics and resistance discovery.},
}
@article {pmid39852467,
year = {2025},
author = {Akkad, A and Nanda, N},
title = {New Diagnostics for Fungal Infections in Transplant Infectious Disease: A Systematic Review.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {39852467},
issn = {2309-608X},
abstract = {Fungal infections are common in highly immunosuppressed, solid organ transplant recipients. They can be quite difficult to diagnose in a timely manner; thus, we present a review of current studies focusing on broad categories of molecular diagnostics, i.e., metagenomic sequencing, magnetic resonance, and gas chromatography mass spectrometry. We further discuss their syndrome-specific utilization in the diagnosis of fungemia and disseminated disease, pneumonia, and central nervous system infections. We assess the level of evidence of their utility as fungal diagnostics particularly in solid organ transplant recipients using the STARD criteria. In addition, we provide future research directions to substantiate and appropriately utilize these platforms in clinical practice. Directed polymerase chain reaction testing and targeted metagenomic sequencing are being used clinically and show the most promise, though only in conjunction with conventional methods at this time. The majority of these platforms contain limited data, and thus further larger studies are needed in order to properly implement their use.},
}
@article {pmid39851614,
year = {2025},
author = {Srila, W and Sripilai, K and Binlateh, T and Thammanichanon, P and Tiskratok, W and Noisa, P and Jitprasertwong, P},
title = {Relationship Between the Salivary Microbiome and Oral Malodor Metabolites in Older Thai Individuals with Periodontitis and the Cytotoxic Effects of Malodor Compounds on Human Oral Squamous Carcinoma (HSC-4) Cells.},
journal = {Dentistry journal},
volume = {13},
number = {1},
pages = {},
pmid = {39851614},
issn = {2304-6767},
support = {NRIIS number 4285350//National Science, Research, and Innovation Fund (NSRF)/ ; //Thailand Science Research and Innovation/ ; //Suranaree University of Technology/ ; },
abstract = {Background/Objectives: Halitosis is primarily caused by the activity of oral microorganisms. In this study, we employed metagenomic sequencing and metabolomic approaches to investigate the differences in salivary microbiota and metabolite profiles between individuals with halitosis and periodontitis and healthy controls. Additionally, we expanded the study to examine how oral malodorous compounds interact with human oral squamous carcinoma (HSC-4) cells. Methods: Saliva samples were collected and analyzed using Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) to identify metabolites. We then assessed the correlations between the microbiota and metabolites. Furthermore, the impact of oral malodorous substances on HSC-4 cells was investigated by evaluating apoptosis, antioxidant activity, and inflammatory properties. Results: The microbiota and metabolite profiles showed significant differences between the halitosis with periodontitis group and the periodontally healthy group. The halitosis with periodontitis group exhibited significantly higher relative abundances of eight genera: Tannerella, Selenomonas, Bacteroides, Filifactor, Phocaeicola, Fretibacterium, Eubacterium saphenum, and Desulfobulbus. In contrast, the periodontally healthy group showed significantly higher relative abundances of Family XIII UCG-001, Haemophilus, and Streptobacillus. Two metabolites, 2,3-dihydro-1H-indole and 10,11-dihydro-12R-hydroxy-leukotriene E4, were significantly higher in individuals with halitosis and periodontitis. In the treatment of HSC-4 cells with metabolites, dimethyl sulfide (DMS) did not show significant effects while indole appeared to induce cell death in HSC-4 cells by triggering apoptotic pathways. Additionally, both indole and DMS affected the inflammatory and antioxidant properties of HSC-4 cells. Conclusions: This study provides insights into the mechanisms of halitosis by exploring the correlations between microbiota and metabolite profiles. Furthermore, oral metabolites were shown to impact the cellular response of HSC-4 cells.},
}
@article {pmid39851362,
year = {2025},
author = {Shabangu, KP and Chetty, M and Bakare, BF},
title = {Metagenomic Insights into Pollutants in Biorefinery and Dairy Wastewater: rDNA Dominance and Electricity Generation in Double Chamber Microbial Fuel Cells.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
pmid = {39851362},
issn = {2306-5354},
support = {1/CX/CSRD VA/United States ; 2//Durban University of Technology (DUT)/ ; 3//Cape Peninsula University of Technology (CPUT)/ ; },
abstract = {This study evaluates the potential of biorefinery and dairy wastewater as substrates for electricity generation in double chamber Microbial Fuel Cells (DCMFC), focusing on their microbial taxonomy and electrochemical viability. Taxonomic analysis using 16S/18S rDNA-targeted DGGE and high-throughput sequencing identified Proteobacteria as dominant in biorefinery biomass, followed by Firmicutes and Bacteriodota. In dairy biomass, Lactobacillus (77.36%) and Clostridium (15.70%) were most prevalent. Biorefinery wastewater exhibited the highest bioelectrochemical viability due to its superior electrical conductivity and salinity, achieving a voltage yield of 65 mV, compared to 75.2 mV from mixed substrates and 1.7 mV from dairy wastewater. Elevated phosphate levels in dairy wastewater inhibited bioelectrochemical processes. This study recommends Biorefinery wastewater as the most suitable purely organic substrate for efficient bioelectricity generation and scaling up of MFCs, emphasising the importance of substrate selection for optimal energy output for practical and commercial viability.},
}
@article {pmid39851307,
year = {2025},
author = {Tan, JJM and Keng, ZX and Chong, SH and Pan, GT and Singh, A and Supramaniam, C and Khoiroh, I},
title = {Efficient Degradation of Industrial Biowaste via In-Vessel Composting-Technical and Microbial Assessments.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
pmid = {39851307},
issn = {2306-5354},
support = {N/A//KPT Recycle Sdn. Bhd./ ; },
abstract = {In this study, a pilot-scale in-vessel composter was used to treat a mixture of industrial biowaste, with soybean curd residue and saw dust as the major substrates. The composter is capable of treating up to 350 tons/month of waste, producing up to 150 tons/month of high-quality compost within a retention time of 7-10 days. The final compost has an average nitrogen-phosphorus-potassium content of 6%, moisture content of 28%, pH of 6.1, organic matter of 68%, and carbon-nitrogen ratio of 19:1. It also has a good amount of humic acid and macronutrients. Composts from all stages of the composting process-pre-mix, directly after discharge, after one-month of curing, and right before packaging-were evaluated with metagenomic analysis to identify the microbes that may add value to the compost.},
}
@article {pmid39850835,
year = {2025},
author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y},
title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18835},
pmid = {39850835},
issn = {2167-8359},
mesh = {Humans ; *Biofilms/drug effects/growth &amp; development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; },
abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.<br><br>MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.<br><br>RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.<br><br>CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.},
}
@article {pmid39850616,
year = {2025},
author = {Du, B and Shama, A and Zhang, Y and Chen, B and Bu, Y and Chen, PA and Lin, C and Liu, J and Zheng, J and Li, Z and Chen, Q and Sun, Y and Fu, X},
title = {Gut microbiota and plasma metabolites in pregnant mothers and infant atopic dermatitis: A multi-omics study.},
journal = {The World Allergy Organization journal},
volume = {18},
number = {1},
pages = {101017},
pmid = {39850616},
issn = {1939-4551},
abstract = {BACKGROUND: Many studies reported the influence of infants' gut microbiota on atopic dermatitis (AD) postnatally, yet the role of maternal gut microbiota and plasma metabolites in infants' AD remains largely unexplored.<br><br>METHODS: Sixty-three pregnant mother-infants were enrolled and followed after childbirth in Guangzhou, China. Demographic information, maternal stool and plasma samples, and records for infants' AD were collected. Maternal gut microbiota/metabolome and plasma metabolome were profiled using shotgun metagenomics and non-targeted metabolomics. Logistic regression and multi-omics analysis were used to explore characteristic maternal gut microbiota in the AD and health groups.<br><br>RESULTS: The &#x3b1;-diversity of maternal gut microbiota in health group was significantly higher than AD group (Shannon diversity P&#xa0;=&#xa0;0.02, Simpson diversity P&#xa0;=&#xa0;0.04). Short-chain fatty acids (SCFAs) producing microorganisms, including Faecalibacterium, Roseburia, Butyricicoccus, and Ruminococcus, as well as the abundance of phenylalanine, tyrosine, and tryptophan biosynthesis pathway, were enriched in health group (LDA>2 and P&#xa0;<&#xa0;0.05). Virulent factors (VFs) involved in immune modulation were enriched in the health group, while VFs involving in adhesin were enriched in the AD group (P&#xa0;<&#xa0;0.05). Metabolomic analysis showed that a polyunsaturated fatty acid/linoleic acid, 13S-hydroxyoctadecadienoic, were negatively associated with AD in both the gut and plasma samples (FDR<0.05). Several other linoleic acids and flavonoids were negatively associated with AD (FDR<0.05). Neural network analysis revealed that microorganisms enriched in health group may produce these protective fatty acids.<br><br>CONCLUSIONS: Our findings show that maternal gut microorganisms/metabolites and plasma metabolites during pregnancy impact subsequent pathogenesis of infants AD. This illuminates new strategies against early AD in offspring.},
}
@article {pmid39850588,
year = {2024},
author = {Ji, L and Zhao, R and Pei, Y and Sun, Y and Sun, X and Ji, L and Wang, X and Liu, Y and Shen, Q and Yang, S and Wang, Y and Zhang, W},
title = {Identification and characterization of multiple novel viruses in fecal samples of cormorants.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1528233},
pmid = {39850588},
issn = {2297-1769},
abstract = {INTRODUCTION: Cormorants, as protected wild animals by the State Forestry Administration of China, have a broad distribution across China. Previous studies have shown that they can be infected with multiple viruses in the Flaviviridae, Orthomyxoviridae, Paramyxoviridae, and Polyomaviridae families. There is limited knowledge about the other viruses that cormorants may carry and infect.<br><br>METHODS: In this study, we employed viral metagenomics to identify novel viruses in the fecal samples collected from cormorants in Xiamen City, Fujian Province, China.<br><br>RESULTS: Two novel viruses were identified, including one novel picornavirus named Cormhepa01 and one novel avain hepevirus named CormhepaE. The genome of Cormhepa01 is 7,463&#x202f;bp in length, which encodes a 2,260 aa polyprotien. Similar to other known picornaviruses, the conserved NTPase, proteinase, and polymerase motifs are presented in the 2C, 3C, and 3D proteins separately. Based on the phylogenetic analysis and amino acid sequence alignment, the CormhepaE may be assigned to a new picornavirus genus. The partial genome of CormhepaE is 6,546&#x202f;bp in length. Compared with other avian hepatitis E virus strains, CormhepaE has multiple variable sites, which are distributed in motifs of the methyltransferase, helicase, and RdRp domains, separately. Based on the phylogenetic analysis, CormhepaE, together with another strain MG737712 isolated from sparrow, formed a new species of the Avihepevirus genus in the Hepeviridae family.<br><br>CONCLUSION: We identified and characterized two novel cormorant viruses in this study. The findings of this study increase our understanding of the diversity of viruses in cormorants and provide practical viral genome information for the prevention and treatment of potential viral diseases affecting this species.},
}
@article {pmid39850127,
year = {2024},
author = {Fakhraldeen, SA and Madhusoodhanan, R and Habibi, N and Al-Haddad, S and Alagarsamy, S and Habeebullah, SFK and Al-Zakri, WM and Thuslim, F and Fernandes, L and Al-Yamani, F and Al-Said, T},
title = {Shotgun metagenomics reveals the interplay between microbiome diversity and environmental gradients in the first marine protected area in the northern Arabian Gulf.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479542},
pmid = {39850127},
issn = {1664-302X},
abstract = {INTRODUCTION: The northwest Arabian Gulf encounters significant anthropogenic pressures, including nutrient enrichment from coastal development and effluent discharge.<br><br>METHODS: This study presents the first shotgun metagenomics-based characterization of microbial communities in Kuwaiti waters of the northwest Arabian Gulf, focusing on Kuwait's first Marine Protected Area (MPA) in Sulaibikhat Bay, a vital nursery ground for commercially important fish.<br><br>RESULTS: Analysis revealed significantly higher microbial diversity within the MPA compared to adjacent waters, with Rhodobacteraceae (27.8%) and Flavobacteriaceae (15.3%) being dominant. Elevated inorganic phosphorus, nitrogen, and salinity were key factors driving this diversity. Multivariate analysis highlighted phosphate as a critical component affecting the MPA microbial community structure, particularly for the families Microbacteriaceae, Flavobacteriaceae, and Rhodobacteraceae.<br><br>DISCUSSION: This study underscores the ecological importance of MPAs and highlights the impact of nutrient enrichment and other environmental stressors on microbial diversity, emphasizing the need to reduce nutrient influx to mitigate eutrophication and enhance marine ecosystem resilience in stressed environments.},
}
@article {pmid39849759,
year = {2025},
author = {Peng, Q and Huang, J and Li, S and Chen, Z and Zhu, Q and Yuan, H and Li, J and Massou, BB and Xie, G},
title = {Dynamics of microbial communities and metabolites during the fermentation of Ningxia goji berry wine: An integrated metagenomics and metabolomics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {201},
number = {},
pages = {115609},
doi = {10.1016/j.foodres.2024.115609},
pmid = {39849759},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Metabolomics ; *Metagenomics ; *Microbiota ; Volatile Organic Compounds/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; Fruit ; Taste ; Food Microbiology ; },
abstract = {Ningxia Goji Berry Wine (NGBW), a traditional Chinese fermented beverage, exhibits complex flavor quality changes during fermentation, the mechanisms of which remain insufficiently elucidated. This study aimed to elucidate the dynamic shifts in physicochemical properties, metabolites, and microbial communities throughout the controlled fermentation process of NGBW. Metabolomic analysis identified 8 key differential volatile metabolites (VOCs) and 406 differential non-volatile metabolites. The enrichment analysis of KEGG metabolic pathways revealed that, during the fermentation of NGBW, ten critical metabolic pathways-Purine metabolism, Glycine, Serine, and Threonine metabolism, Galactose metabolism, and the Citric Acid (TCA) Cycle-play essential roles. Amplicon sequencing indicated that 25 bacterial genera dominated the microbial ecosystem (relative abundance ≥ 0.1 %). Spearman correlation analysis revealed significant associations between 5 core microorganism and flavor compounds, and 25 core microbes with non-volatile metabolites, suggesting their pivotal roles in flavor formation. This study provides a theoretical basis for optimizing the fermentation process and enhancing the flavor quality of NGBW.},
}
@article {pmid39849638,
year = {2025},
author = {Peña-López, Y and Tareen, NG and Zhang, B and Raman, I and Arana, CA and Zhu, C and Liu, Y and Selvakumar, P and van Oers, NSC and Morris, S and Hooper, LV and Copley, LAB and Raj, P},
title = {Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis.},
journal = {Pediatric rheumatology online journal},
volume = {23},
number = {1},
pages = {9},
pmid = {39849638},
issn = {1546-0096},
support = {Biomedical award 2020//Hartwell Foundation/ ; },
mesh = {Humans ; *Arthritis, Infectious/diagnosis/immunology ; Child ; Female ; Male ; Child, Preschool ; *Synovial Fluid/immunology/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Proteomics/methods ; Prospective Studies ; Metagenomics/methods ; Adolescent ; Arthritis, Juvenile/diagnosis/immunology ; Infant ; Osteomyelitis/diagnosis/immunology ; Diagnosis, Differential ; Knee Joint ; Multiomics ; },
abstract = {BACKGROUND: An accurate diagnosis of septic versus reactive or autoimmune arthritis remains clinically challenging. A multi-omics strategy comprising metagenomic and proteomic technologies were undertaken for children diagnosed with presumed septic arthritis to advance clinical diagnoses and care for affected individuals.<br><br>METHODS: Twelve children with suspected septic arthritis were prospectively enrolled to compare standard of care tests with a rapid multi-omics approach. The multi-omics combined bacterial 16S rRNA metagenomics, single cell transcriptomics, and proteomics on knee joint fluid specimens. The diagnostic value of the multi-omics was ascertained relative to standard of care culture and PCR-negative results.<br><br>RESULTS: Ten children with suspected primary septic arthritis and two with acute hematogenous osteomyelitis (AHO) diagnoses were assessed. Joint fluid bacterial cultures were positive for 6/12 (50%) patients, consistent with elevated inflammatory markers (IL-4, IL-6, IL-17A, TNF-a, etc.). Metagenomic bacterial sequencing results were 100% concordant with the culture results. Six patients were culture- and PCR-negative. Multiomics analyses of the 6 culture negative patients established that 2/6 culture-negative children had inflammatory arthritis with potential Juvenile idiopathic arthritis (JIA) and 1 had post-Streptococcal Reactive Arthritis. The children without any bacteremia had autoantibodies (IgGs) in the joint-fluid targeting several nuclear antigens (i.e., dsDNA, histones, Jo-1, scl-70, Ro/SS-A, SmDs, CENP-A along with non-nuclear antigens i.e. Albumin, Collagens, Myosin, Laminin, etc. Single cell transcriptomics confirmed an abundance of CD4[+]&#xa0;follicular helper T (Tfh), CD8&#x2009;+&#x2009;T cells and B cells in the autoantibody positive subjects. The combination of 16S DNA sequencing (p&#x2009;=&#x2009;0.006), cytokine assays (p&#x2009;=&#x2009;0.009) and autoantibody profiling (p&#x2009;=&#x2009;0.02) were significantly distinct between those children with and without infections. This improved the diagnostic confidence for 9 of 12 (75%) children, key for treatment decisions.<br><br>CONCLUSIONS: The multiomics approach rapidly identified children with bacterial or autoimmune inflammatory conditions, improving diagnostic and treatment strategies for those with presumptive septic arthritis.},
}
@article {pmid39849445,
year = {2025},
author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z},
title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.},
journal = {BMC endocrine disorders},
volume = {25},
number = {1},
pages = {18},
pmid = {39849445},
issn = {1472-6823},
support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology&#xff0c;Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology&#xff0c;Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology&#xff0c;Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; },
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.<br><br>METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.<br><br>RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.<br><br>CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.<br><br>TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).},
}
@article {pmid39849165,
year = {2025},
author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit, and Sharma, V and Rai, N and Chand, P},
title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {3},
pmid = {39849165},
issn = {1432-0983},
mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation &amp; purification ; Streptococcus/genetics/isolation &amp; purification/classification ; },
abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.},
}
@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; Metagenome ; Seawater/microbiology ; Ecosystem ; Oceans and Seas ; Gammaproteobacteria/genetics/classification ; Alphaproteobacteria/genetics ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}
@article {pmid39848523,
year = {2025},
author = {Yu, MF and Chen, L and Liu, G and Liu, W and Yang, Y and Ma, L},
title = {Metagenomic deciphers the mobility and bacterial hosts of antibiotic resistance genes under antibiotics and heavy metals co-selection pressures in constructed wetlands.},
journal = {Environmental research},
volume = {269},
number = {},
pages = {120921},
doi = {10.1016/j.envres.2025.120921},
pmid = {39848523},
issn = {1096-0953},
abstract = {Both antibiotics and heavy metals exert significant selection pressures on antibiotic-resistance genes (ARGs). This study aimed to investigate the co-selection effects of doxycycline (DC) and cadmium (Cd) on ARGs in constructed wetlands (CWs). The results demonstrated that under antibiotic and heavy metal co-selection pressures, single high concentration DC/Cd or double high, relative abundances of metagenomics assembled genomes all reached 55.1%; meanwhile, the average ratio of ARG-containing contigs located on chromosomes was 61.8% (ranging from 50.4% to 70.6%) suggesting a more stable inheritance of ARGs. Antibiotic and heavy metal co-selection in single high concentration DC/Cd or double high groups stimulate the enrichment of ARG host bacteria, which exhibited complex multiple-resistant patterns accompanied by a host-specific pattern. Additionally, the potential transfer abilities of ARGs mediated by plasmids and integrative and conjugative elements (ICEs) were enhanced under single high-concentration DC/Cd or double high stresses. Together, antibiotic and heavy metal co-selection pressures increased occurrence frequencies of ARGs, MGEs, and their combinations and altered structural communities of ARG host bacteria, increasing the risk of the spread of ARGs. This study was helpful in understanding the dissemination of ARGs and simultaneously preventing the spread of heavy metal-resistant bacteria and ARGs under antibiotic and heavy metal co-selection in small- and micro-wetlands.},
}
@article {pmid39848515,
year = {2025},
author = {Zhang, M and Bai, L and Yao, Z and Li, W and Yang, W},
title = {Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats.},
journal = {Environmental research},
volume = {269},
number = {},
pages = {120907},
doi = {10.1016/j.envres.2025.120907},
pmid = {39848515},
issn = {1096-0953},
abstract = {The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.},
}
@article {pmid39848447,
year = {2025},
author = {Zhang, L and Fan, R and Li, W and Li, G and Luo, W and Xu, Z},
title = {Unravelling biotic and abiotic mechanisms of mature compost to alleviate gaseous emissions in kitchen waste composting by metagenomic analysis.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132102},
doi = {10.1016/j.biortech.2025.132102},
pmid = {39848447},
issn = {1873-2976},
mesh = {*Composting/methods ; *Metagenomics/methods ; *Methane/metabolism ; Gases ; Soil Microbiology ; Ammonia/metabolism ; Soil/chemistry ; Refuse Disposal/methods ; Carbon Dioxide/metabolism ; Hydrogen-Ion Concentration ; Nitrous Oxide/metabolism ; },
abstract = {Mature compost can reduce gaseous emissions in composting, but its regulation mechanisms via biotic and abiotic functions are largely unknown. This study used fresh and inactivated mature compost as additives in kitchen waste composting to unveil the relevant mechanisms using metagenomic analysis. Results showed that mature compost reduce gaseous emission by improving physiochemical properties and inoculating functional microbes. The abiotic function of mature compost alleviated methane and nitrous oxide emission by 20 % via enhancing air diffusion and pH to limit the activity of mcr, mtr, norB/C, and narG/H hosts. Compared to inactivated mature compost, the microbes in fresh counterpart promoted organic mineralization to slightly enhance ammonia release by 9 %, but alleviated 13 % of carbon dioxide emission through microbial humification to impel carbon sequestration. Therefore, another specialistic strategy (e.g. Calcium magnesium phosphate addition to form struvite Crystallization) should be integrated with mature compost to synergistically reduce gaseous emissions.},
}
@article {pmid39848182,
year = {2025},
author = {Wang, X and Liu, TC and Wang, XW and Dang, CC and Tan, X and Lu, Y and Liu, BF and Xing, DF and Ren, NQ and Xie, GJ},
title = {Microbial manganese redox cycling drives co-removal of nitrate and ammonium.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124095},
doi = {10.1016/j.jenvman.2025.124095},
pmid = {39848182},
issn = {1095-8630},
mesh = {*Manganese/metabolism ; *Oxidation-Reduction ; *Nitrates/metabolism ; *Ammonium Compounds/metabolism ; Nitrogen/metabolism ; Sewage/microbiology ; },
abstract = {Manganese (Mn), abundant in the Earth's crust, can act as an oxidant or a reductant for diverse nitrogen biotransformation processes. However, the functional microorganisms and their metabolic pathways, as well as interactions, remain largely elusive. Here, a microbial consortium was enriched from a mixture of freshwater sediments and activated sludge by feeding ammonium, nitrate and Mn(II), which established manganese-driven co-removal of nitrate and ammonium with removal rates of 5.83 and 2.30 mg N L[-1] d[-1], respectively. The batch tests and metagenomic analyses revealed a nitrate-dependent anaerobic manganese oxidation (NDMO) process mediated by Anaerolineales and Phycisphaerales and a manganese reduction coupled to anaerobic ammonium oxidation (Mnammox) process mediated by Chthonomonadales. Based on identified key genes involved in the nitrogen and manganese metabolic pathways, nitrate was likely reduced to nitrite and nitrogen gas in the NDMO process while ammonium was oxidized to nitrite in the Mnammox process, which in turn fuelled the Anammox process carried out by Candidatus Brocadia. This revealed the microbial interactions of NDMO, Mnammox, and Anammox processes responsible for manganese-driven co-removal of ammonium and nitrate. These findings provide a potential solution for biological nitrogen removal and expand our understanding of the nitrogen and manganese biogeochemical cycles.},
}
@article {pmid39847964,
year = {2025},
author = {Liang, Y and Wang, W},
title = {A Balamuthia amoebic encephalitis survivor in China, and literature review.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {3},
pages = {116698},
doi = {10.1016/j.diagmicrobio.2025.116698},
pmid = {39847964},
issn = {1879-0070},
abstract = {Balamuthia amoebic encephalitis (BAE) is a rare, fatal parasitic infection of the central nervous system, with a current mortality rate above 95%. The high fatality rate is largely attributed to atypical clinicopathological features, delayed diagnosis, and the absence of effective treatment methods, so quick recognition of this disease is vital. In this paper, we present a survivor of BAE, who was confirmed through histologic examination and metagenomic next-generation sequencing (mNGS) of brain lesions. This case, unlike most previous reports, was a successful survival case. It highlights the critical need for differential diagnosis in patients with central nervous system infectious diseases, particularly those with a history of skin lesions and patients presenting multifocal brain lesions. Moreover, mNGS could serve as a useful tool in rapid identification of causative rare pathogens. The application of decompressive craniectomy may offer treatment opportunities and improve the survival rate of BAE. The case description was followed by a review of the literatures, in order to improve clinicians' understanding of this disease.},
}
@article {pmid39847933,
year = {2025},
author = {Malla, MA and Nomalihle, M and Featherston, J and Kumar, A and Amoah, ID and Ismail, A and Bux, F and Kumari, S},
title = {Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137180},
doi = {10.1016/j.jhazmat.2025.137180},
pmid = {39847933},
issn = {1873-3336},
abstract = {The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources. Pseudomonas were the most abundant genus, followed by Flavobacterium, Acinetobacter, Acidovorax, and Limnohabitans. However, their relative abundance varied significantly both across the sampling sites and habitats i.e. SW and PS (p < 0.05). Additionally, various ARGs were detected in SW and PS, with PS (372) having significantly more potential ARGs than SW (293). The results further showed significant variations in the relative abundance of potential pathogenic bacteria across the sampling sites and habitats (p < 0.05). Further moreover, significant differences were observed in antibiotic resistome risk scores, ARGs and MGEs across different habitats. Over all, this study suggests that pollution source and water quality parameters had a significant impact on microbiome composition and antibiotic resistome in SW and PS.},
}
@article {pmid39847904,
year = {2025},
author = {Feng, C and Zhang, X and Gao, G and Ren, K and Li, Z and Xu, Z and Wei, D and Zhang, J},
title = {A new insight on simultaneous water purification and greenhouse gas reduction by constructing sulfur-siderite driven autotrophic denitrification pathways in constructed wetlands.},
journal = {Water research},
volume = {274},
number = {},
pages = {123130},
doi = {10.1016/j.watres.2025.123130},
pmid = {39847904},
issn = {1879-2448},
abstract = {Sulfur-siderite driven autotrophic denitrification (SSAD) has received increasing attention for nutrient removal in constructed wetlands (CWs). Nevertheless, its effectiveness in simultaneous water purification and greenhouse gases (GHGs) reduction remains obscure. In this study, three vertical flow constructed wetlands (VFCWs), filled with quartz sand (CCW), sulfur (S-CW), and sulfur-siderite mixed substrates (SS-CW), were constructed to investigate the underlying mechanisms of SSAD on water purification enhancement and GHGs reduction. Results indicated that SSAD optimized the carbon, nitrogen, phosphorus, and sulfur transformation processes and enhanced the electron transfer system activity (ETSA) in CWs. Meanwhile, it resulted in the highest total nitrogen (TN) removal efficiency (91.6 ± 2.2 %) and the lowest methane (CH4) and nitrous oxide (N2O) emissions from SS-CW. Compared with CCW, the reduction efficiencies of CH4 and N2O were 76.7 ± 6.7 % and 93.4 ± 2.2 %, respectively. This was mainly ascribed to constructing ammonia oxidation coupled with iron reduction (Feammox), SSAD and multi-electron driven anaerobic oxidation of methane (AOM) pathway in SS-CW which could achieve co-emission reduction of CH4 and N2O. Analysis of the functional genes and microbial community structure revealed that higher abundance of genes associated with GHGs mitigation, more denitrifying bacteria and methanotrophic bacteria were enriched in SS-CW. Further analysis of metagenomic results showed that both the electron transfer pathway and the GHGs mitigation pathway were significantly enhanced in SS-CW. The results of this study provide a new insight into using SSAD as a method to improve the nutrient removal efficiency of CWs while reducing GHGs.},
}
@article {pmid39847397,
year = {2024},
author = {Deng, Z and Lan, Z and Zhu, H and Ren, H and Jin, Z and Jiang, J and Lan, T and Zhou, J and Wang, J and Wan, P and Guo, Y and Xu, B and Zhu, H and Wen, Z},
title = {Metagenomic next-generation sequencing for the detection of bacterial translocation in the blood of patients following liver, biliary tract or pancreatic surgery.},
journal = {The British journal of surgery},
volume = {112},
number = {1},
pages = {},
pmid = {39847397},
issn = {1365-2168},
support = {82160128//National Natural Science Foundation of China/ ; ZA20220492//Self-Raised Project of Guangxi Health Committee/ ; },
}
@article {pmid39847144,
year = {2025},
author = {Niemelä, LRK and Pásztor, A and Frey, AD},
title = {Generation of ribosomal protein S1 mutants for improving of expression of difficult to translate mRNAs.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {20},
pmid = {39847144},
issn = {1432-0614},
support = {562/31/2014//Tekes/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; *Ribosomal Proteins/genetics ; *RNA, Messenger/genetics ; *Mutation ; 5' Untranslated Regions/genetics ; Protein Biosynthesis ; Operon ; Escherichia coli Proteins/genetics/metabolism ; Gene Library ; },
abstract = {Metagenomes present a source for novel enzymes, but under 1% of environmental microbes are cultivatable. Because of its useful properties, Escherichia coli has been used as a host organism in functional genomic screens. However, due to differing expression machineries in the expression host compared to the source organism of the DNA sequences, screening outcomes can be biased. Here, we focused on one of the limiting processes-translation initiation. To that end, we created an operon-like screening system in E. coli to select mutants of the ribosomal protein S1 with more relaxed sequence requirements for 5'-untranslated regions of mRNAs. We created two mutation libraries of the ribosomal protein S1, one covering domains 3 and 4 (D3-D4) and the second covering domains 3 to 5 (D3-D5). Most mutants from library D3-D4 proofed to be specific for a particular UTR sequence and improved only expression from a single construct. Only mutant 3 from library D3-D4 led to increased expression of four different reporters improving fluorescence levels by up to 21%. Mutants isolated from D3-D5 library led up to 90% higher expression compared to the control, though the mutants with highest improvements exhibited a specialist phenotype. The most promising mutant, mutant 4, exhibited a generalist phenotype and showed increased expression in all six reporter strains compared to the control. This could indicate the potential for a more promiscuous translation initiation of metagenomic sequences in E. coli although at the price of smaller increases compared to specialist mutants. KEY POINTS: • An operon-like selection system allowed to isolate generalist and specialist S1 mutants. • S1 mutants improved translation of mRNAs with 5'-UTRs from metagenomic sequences. • Use of S1 mutants could increase coverage from metagenomic libraries in functional screens.},
}
@article {pmid39846163,
year = {2025},
author = {Jena, PK and Arditi, M and Noval Rivas, M},
title = {Gut Microbiota Alterations in Patients With Kawasaki Disease.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.124.321201},
pmid = {39846163},
issn = {1524-4636},
support = {R01 HL139766/HL/NHLBI NIH HHS/United States ; R01 HL159297/HL/NHLBI NIH HHS/United States ; R01 HL149972/HL/NHLBI NIH HHS/United States ; R01 AI157274/AI/NIAID NIH HHS/United States ; R01 HL170580/HL/NHLBI NIH HHS/United States ; },
abstract = {The intestinal microbiota influences many host biological processes, including metabolism, intestinal barrier functions, and immune responses in the gut and distant organs. Alterations in its composition have been associated with the development of inflammatory disorders and cardiovascular diseases, including Kawasaki disease (KD). KD is an acute pediatric vasculitis of unknown etiology and the leading cause of acquired heart disease in children in the United States. The presence of gastrointestinal symptoms in the acute phase of KD has been associated with an increased risk of treatment resistance and the development of coronary artery aneurysms. Studies report alterations in fecal bacterial communities of patients with KD, characterized by the blooming of pathogenic bacteria and decreased relative abundance of short-chain fatty acid-producing bacteria. However, causality and functionality cannot be established from these observational patient cohorts of KD. This highlights the need for more advanced and rigorous studies to establish causality and functionality in both experimental models of KD vasculitis and patient cohorts. Here, we review the evidence linking an altered gut microbiota composition to the development of KD, assess the potential mechanisms involved in this process, and discuss the potential therapeutic value of these observations.},
}
@article {pmid39846015,
year = {2025},
author = {Cousson, A and Pablo, AL and Cournac, L and Piton, G and Dezette, D and Robin, A and Taschen, E and Bernard, L},
title = {Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103134},
pmid = {39846015},
issn = {2215-0161},
abstract = {Soil microbes are among the most abundant and diverse organisms on Earth but remain poorly characterized. New technologies have made possible to sequence the DNA of uncultivated microorganisms in soil and other complex ecosystems. Genome assembly is crucial for understanding their functional potential. Nanopore sequencing technologies allow to sequence long DNA fragments, optimizing production of metagenome-assembled genomes compared to short-read technology. Extracting DNA with a very high purity and high molecular weight is key to get the most out of this long read technologies. Here we present two extraction protocols to get DNA with high purity. First protocol is optimized to reach DNA quality suiting Nanopore shotgun metagenomics. It uses a non-toxic centrifugation gradient to separate bacterial cells from soil to extract DNA directly on cells. The median length of the acquired DNA sequences (N50) was 3 to 7 times greater than previously published in the literature, achieving an N50 of ∼14 kb. The other, a modification of a commercially available MP Biomedical DNA extraction kit, yielded high-purity DNA for full-length 16S Oxford Nanopore metabarcoding, with an N50 of ∼8 kb. The MP-based protocol achieves higher yields of ultra-pure DNA compared to the Nycodenz protocol, at the expense of shorter fragment lengths.},
}
@article {pmid39845824,
year = {2024},
author = {Fang, J and Fang, H and Guo, P and Peng, Y and Chen, P},
title = {Strongyloides stercoralis combined with concurrent multiple pathogens infections in an immunosuppressed patient: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1519065},
pmid = {39845824},
issn = {2296-858X},
abstract = {BACKGROUND: Strongyloides stercoralis is an opportunistic pathogenic parasite. Most individuals with normal immune function may not exhibit significant symptoms, and the signs are atypical, which can easily lead to missed diagnoses and delayed treatment. People with underlying diseases and weakened immunity are prone to develop severe conditions after infection with Strongyloides stercoralis.<br><br>CASE PRESENTATION: We report an immunocompromised patient in whom the pathogen was initially not detectable using traditional parasitic detection techniques. However, Strongyloides stercoralis was identified in both the alveolar lavage fluid and blood through metagenomic next-generation sequencing. Subsequently, Strongyloides stercoralis was detected in the alveolar lavage fluid after multiple rounds of testing using traditional microscopic examination techniques. Based on the mNGS results and other examination findings, the patient was diagnosed with Strongyloides stercoralis in combination with concurrent multiple pathogens infections. After the combined drug therapy of Meropenem, Vancomycin, and Albendazole, the patient's condition was gradually brought under control.<br><br>CONCLUSION: This case demonstrates the advantage of integrating traditional detection methods with metagenomics next-generation sequencing technology in the etiological diagnosis of immunocompromised individuals. It is conducive to clarifying the etiological diagnosis of patients and thereby facilitating the timely initiation of corresponding treatments.},
}
@article {pmid39845819,
year = {2024},
author = {Feng, Q and Yuan, H and Ma, J and Guo, Z and Xia, X and Zhao, G},
title = {Invasive Klebsiella pneumoniae liver abscess syndrome complicated by carbapenem-resistant Acinetobacter baumannii infection: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1511734},
pmid = {39845819},
issn = {2296-858X},
abstract = {BACKGROUND: A liver abscess caused by hypervirulent Klebsiella pneumoniae can lead to multiple invasive extrahepatic infections, including lung abscesses, endophthalmitis, brain abscesses, and necrotizing fasciitis. This condition, known as Klebsiella pneumoniae liver abscess invasion syndrome, progresses rapidly and is associated with severe illness, high disability rates, and significant mortality. However, bloodstream infections with co-infection involving carbapenem-resistant Acinetobacter baumannii are exceedingly rare.<br><br>CASE PRESENTATION: The Emergency Medicine Department of the First People's Hospital of Kunshan successfully treated a male patient diagnosed with liver, lung, and prostate abscesses. The patient underwent puncture and drainage, with analysis of the drainage fluid, sputum culture, and metagenomic next-generation sequencing (m-NGS) revealing a co-infection with blood-borne Klebsiella pneumoniae and Acinetobacter baumannii. Guided by drug sensitivity test results, the patient received treatment with polymyxin and cefoperazone sodium-sulbactam sodium for infection control and liver protection. The treatment was successful, and the patient fully recovered and was discharged.<br><br>CONCLUSION: By reporting this rare case and highlighting the drug resistance of the bacteria, we propose a new diagnosis and treatment plan for managing Klebsiella pneumoniae combined with carbapenem-resistant Acinetobacter baumannii infection, along with a literature review.},
}
@article {pmid39845816,
year = {2024},
author = {Shao, S and Liu, J and Wu, Z and Wu, S},
title = {Chlamydophila psittaci pneumonia followed by lower gastrointestinal ischemic necrosis: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1394897},
pmid = {39845816},
issn = {2296-858X},
abstract = {BACKGROUND: Psittacosis, also known as parrot fever, is an uncommon infectious disease caused by Chlamydophila psittaci (C. psittaci). While C. psittaci infections are usually not life-threatening, the pathogenesis and associated complications are not yet fully understood.<br><br>CASE DESCRIPTION: A 54-year-old male was hospitalized due to a cough, accompanied by expectoration and dyspnea. After admission, the patient's breathing rapidly deteriorated, and despite the use of a ventilator, it was challenging to maintain respiratory function. While initiating extracorporeal membrane oxygenation (ECMO) and empirical anti-infection treatments, the alveolar lavage fluid was collected and examined by metagenomics next generation sequencing (mNGS). The mNGS result indicated C. psittaci. Subsequently, the anti-infection regimen was immediately adjusted. The respiratory function improved on the 13th day after admission, and ECMO was withdrawn. However, the patient developed abdominal distension and intestinal edema. After intravenous infusion therapy, intestinal ischemia and necrosis occurred and surgical resection was performed. The patient's condition improved after the operation and he was transferred to a local hospital for rehabilitation.<br><br>CONCLUSION: This case report demonstrates the development of intestinal ischemic necrosis following severe C. psittaci pneumonia. This unique association has not been reported previously and highlights the importance of potential gastrointestinal complications in severe C. psittaci pneumonia, which are often underestimated. Timely diagnoses and treatments of such infections and complications are necessary to achieve favorable clinical outcomes.},
}
@article {pmid39845646,
year = {2024},
author = {Hadrich, I and Turki, M and Chaari, I and Abdelmoula, B and Gargouri, R and Khemakhem, N and Elatoui, D and Abid, F and Kammoun, S and Rekik, M and Aloulou, S and Sehli, M and Mrad, AB and Neji, S and Feiguin, FM and Aloulou, J and Abdelmoula, NB and Sellami, H},
title = {Gut mycobiome and neuropsychiatric disorders: insights and therapeutic potential.},
journal = {Frontiers in cellular neuroscience},
volume = {18},
number = {},
pages = {1495224},
pmid = {39845646},
issn = {1662-5102},
abstract = {BACKGROUND: The human gut mycobiome, a minor but integral component of the gut microbiome, has emerged as a significant player in host homeostasis and disease development. While bacteria have traditionally been the focus of gut microbiome studies, recent evidence suggests that fungal communities (mycobiota) may also play a crucial role in modulating health, particularly in neuropsychiatric disorders.<br><br>OBJECTIVE: This review aims to provide a comprehensive overview of current knowledge on the relationship between the gut mycobiome and neuropsychiatric disorders, exploring the potential of targeting fungal communities as a novel therapeutic strategy.<br><br>METHODS: We summarized recent findings from metagenomic analyses that characterize the diversity and composition of gut mycobiota and discuss how these communities interact with the host and other microorganisms via the gut-brain axis. Key methodologies for studying mycobiota, such as high-throughout sequencing and bioinformatics approaches, were also reviewed to highlight advances in the field.<br><br>RESULTS: Emerging research links gut mycobiota dysbiosis to conditions such as schizophrenia, Alzheimer's disease, autism spectrum disorders, bipolar disorder, and depression. Studies indicate that specific fungal populations, such as Candida and Saccharomyces, may influence neuroinflammation, gut permeability and immune responses, thereby affecting mental health outcomes.<br><br>CONCLUSION: Understanding the gut mycobiome's role in neuropsychiatric disorders opens new avenues for therapeutic interventions, including antifungal treatments, probiotics, and dietary modifications. Future research should integrate multi-omics approaches to unravel the complex interkingdom interactions within the gut ecosystem, paving the way for personalized medicine in mental health care.},
}
@article {pmid39845316,
year = {2024},
author = {Yang, HS and Zhang, J and Feng, HX and Qi, F and Kong, FJ and Zhu, WJ and Liang, CY and Zhang, ZR},
title = {Characterizing microbial communities and their correlation with genetic mutations in early-stage lung adenocarcinoma: implications for disease progression and therapeutic targets.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1498524},
pmid = {39845316},
issn = {2234-943X},
abstract = {BACKGROUND: Lung adenocarcinoma (LUAD), the most prevalent form of lung cancer. The transition from adenocarcinoma in situ (AIS), and minimally invasive adenocarcinoma (MIA) to invasive adenocarcinoma (IAC) is not fully understood. Intratumoral microbiota may play a role in LUAD progression, but comprehensive stage-wise analysis is lacking.<br><br>METHODS: Tumor and bronchoalveolar lavage fluid (BALF) samples from patients with AIS/MIA or IAC were collected for next-generation sequencing to characterize microbial diversity and composition. DNA extraction involved lysing samples with nuclease and protease, followed by homogenization and elution. Sequencing libraries were prepared and sequenced on the Illumina platform. Whole exome sequencing was performed to identify somatic mutations and genetic variants. Bioinformatics analysis, including taxonomic annotation with Kraken2 and de novo assembly with MEGAHIT, was conducted to process metagenomic data. Correlation analysis was performed to link microbial species with mutated genes using custom R scripts.<br><br>RESULTS: Metagenomic analysis revealed a distinct microbial profile in IAC compared to AIS/MIA, with increased abundance of Bacteroidetes and Firmicutes in the IAC group. Bosea sp. and Microbacterium paludicola, were less abundant in IAC, suggesting a potential protective role in early-stage disease. Conversely, Mycolicibacterium species were more prevalent in IAC, indicating a possible contribution to disease progression. Genetic sequencing identified PTPRZ1 strongly correlating with microbial composition, suggesting a mechanistic link between microbiota and genetic alterations in LUAD.<br><br>CONCLUSION: This study characterizes microbial communities in various stages of LUAD, revealing links between microbiota and genetic mutations. The unique microbiota suggests its role in LUAD progression and as a therapeutic target.},
}
@article {pmid39845046,
year = {2024},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1504487},
pmid = {39845046},
issn = {1664-302X},
abstract = {Metagenomic sequencing is increasingly being employed to understand the assemblage and dynamics of the oyster microbiome. Specimen collection and processing steps can impact the resultant microbiome composition and introduce bias. To investigate this systematically, a total of 54 farmed oysters were collected from Chesapeake Bay between May and September 2019. Six different specimen types and processing methods were evaluated for microbial community composition using shotgun metagenomics, namely fresh oyster homogenate (FOH), oyster homogenate after simulated temperature abuse (AOH), Luria broth-enriched oyster homogenate (EOH), dissected stomach homogenate (DSH), hemolymph (HLM), and stomach-gut content (SGC). In general, DSH, EOH, and FOH yielded the highest DNA concentration, while EOH had the highest microbial reads, followed by DSH, HLM, and FOH. HLM produced the highest bacterial species alpha diversity, followed by AOH, EOH, and SGC. Although alpha diversities did not differ significantly, beta-diversity measurements showed significant dissimilarity among methods (p < 0.05) indicating that the specimen types and processing steps do play an important role in representing the composition of the bacterial community. Bacterial species that had the highest log mean abundance included Cyanobium sp. PCC 7001 in FOH, Vibrio vulnificus in AOH, EOH, and DSH, and lastly Synechococcus sp. CB0205 in the DSH, HML, and SGC samples. EOH displayed higher bacterial hits, distinct microbial composition, and higher values of bacterial, phages, and antimicrobial resistance gene reads. Therefore, if studying the overall oyster microbial community, prioritizing optimum specimen collection and processing methods that align with the overall goal of the study is recommended.},
}
@article {pmid39844919,
year = {2025},
author = {Naim, W and Manetsberger, J and Lavilla Lerma, L and Benomar, N and Caballero Gómez, N and Cuesta-Bertomeu, IS and Gata Díaz, J&#xc1; and Abriouel, H},
title = {Impact of disinfection methods used in the slaughterhouse environment on microbiome diversity throughout the meat production chain.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100336},
pmid = {39844919},
issn = {2666-5174},
abstract = {Slaughterhouse environments are prone to microbial contamination, influenced by factors like set-up, size and area as well as disinfection practices. Thus, effective control measures are crucial to prevent the spread of pathogens and their contaminant genes (antimicrobial resistance genes and virulence factors) throughout the food chain. In the present study, we assessed the microbial contamination in environmental surfaces of three slaughterhouses located in the Jaén province (Spain). We also evaluated the impact of different disinfection strategies on microbial loads and diversity by means of culture dependent and independent methods. The results revealed a statistically significant inter- and intra-specific differences in microbial loads including the most important pathogens such as pseudomonads, staphylococci, Escherichia coli, Salmonella sp. and Campylobacter jejuni. Disinfection strategies using routine disinfectant (used by the slaughterhouse), HLE disinfectant, UV, or combinations thereof showed varying effectiveness. The newly developed sustainable HLE disinfectant was most effective, while UV had the lowest disinfection strength, and routine disinfectants failed to eradicate all pathogens. Metagenomic analysis identified Pseudomonadota as the dominant phylum, followed by Actinomycetota and Bacteroidota. Results furthermore indicated shifts from sacrifice to cold rooms, with an increase in Gammaproteobacteria, particularly Moraxellaceae (represented by Psychrobacter cryohalolentis) over Acinetobacter sp. In conclusion, this study highlights the potential of HLE disinfectant (alone or in combination with the routine disinfectant) as a more effective disinfection measure on environmental surfaces, particularly for combating multi-drug resistant pathogens compared to other disinfection methods currently used.},
}
@article {pmid39844843,
year = {2024},
author = {Shi, T and Lin, Y and Zheng, X and Ruan, H and Zhang, R and Liu, Y and Xu, S and Wang, H},
title = {Metagenomic next-generation sequencing for the clinical identification of spinal infection-associated pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1437665},
pmid = {39844843},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; Young Adult ; Aged, 80 and over ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: This study aimed to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) technology for identifying pathogens associated with spinal infection (SI).<br><br>METHODS: A retrospective analysis was conducted on clinical data from 193 patients with suspected SI between August 2020 and September 2024. Based on histopathological results, the patients were divided into the SI group (n=162) and the non-SI group (n=31). The diagnostic performance of mNGS technology was compared with that of laboratory examination, imaging examination, and microbial culture.<br><br>RESULTS: Among SI group, mNGS detected 135 pathogens in 77.78% (126/162) of the cases, including nine cases of multiple infections. One or more pathogens were detected using mNGS in 86 patients with SI and negative microbial cultures. Staphylococcus aureus (22.22%, n=30) and Mycobacterium tuberculosis (22.22%, n=30) were the major pathogens, while various rare pathogens such as anaerobes, Brucella, and Coxiella burnetii were also detected. For the 40 cases with positive results for both culture- and mNGS-based identification, high consistency (77.50%) was observed. Antibiotic use did not significantly affect the mNGS detection rate (P = 0.45). There was no significant difference in the positivity rate of mNGS between CT-guided needle biopsy (80.00%) and surgical sampling (77.17%) (P = 0.72). The sensitivity of mNGS (77.78%) was significantly higher than that of traditional microbial culture (27.16%), and the specificity was similar (90.32% vs. 96.77%). Although the sensitivities of erythrocyte sedimentation rate-based assay (91.36%), magnetic resonance imaging (88.27%), and C-reactive protein-based assay (87.65%) were better than those of mNGS, their specificities were generally low (20%-40%).<br><br>CONCLUSION: The pathogens responsible for SI are complex and diverse. As a novel diagnostic method, mNGS exhibits a high sensitivity and extensive pathogen coverage for SI diagnosis. When combined with imaging and laboratory indicators, mNGS can significantly improve the accuracy of SI diagnosis and provide strong support for clinical treatment.},
}
@article {pmid39844841,
year = {2024},
author = {Chen, X and Liang, Y and Yang, W and He, W and Xing, Z and Li, S and Cai, S and Fu, J and Peng, X and Chen, M and Wu, J},
title = {Application of metagenomic next-generation sequencing in the diagnosis of post-stroke infections: a case series study using multiple sample types.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1386377},
pmid = {39844841},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Female ; Retrospective Studies ; Aged ; Middle Aged ; *Stroke ; Sensitivity and Specificity ; Bacteria/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; },
abstract = {BACKGROUND: Metagenomic high-throughput sequencing (mNGS) represents a powerful tool for detecting nucleic acids from various pathogens, such as bacteria, fungi, viruses and parasites, in clinical samples. Despite its extensively employed in the pathogen diagnosis for various infectious diseases, its application in diagnosing stroke-related infection, and its potential impact on clinical decision-making, anti-infection treatment, clinical intervention, and patient prognosis remain insufficiently explored. Additionally, while mNGS offers promising potential, it facts limitations related to sensitivity, specificity, cost, and standardization, which could influence its integration into routine clinical practice.<br><br>METHODS: We retrospectively analyzed 18 stroke patients admitted to the First Affiliated Hospital of Medical College of Shantou University from January to February 2023, comparing culture-based methods with mNGS detection, and assessing its significance in etiological diagnosis. Additionally, we evaluated the performance differences among various sequencing platforms.<br><br>RESULTS: Among the 18 stroke patients enrolled, pulmonary infections were identified in 7 cases, urinary tract infections in 1 case, central nervous system infections in 10 cases, and combined pulmonary and central nervous system infections in 2 cases, with 2 cases yielding negative results. mNGS detected pathogens in 13 cases, aligning with clinical diagnoses (75% concordance), whereas culture-based methods yielded positive results in only 6 cases (22% concordance). Importantly, for 9 of the 18 patients, adjustments to anti-infective treatment regimens based on mNGS results led to improved symptomatic relief and infection control. This suggests that mNGS can contribute to more timely and precise treatment modifications, particularly for infections with low pathogen loads, potentially enhancing clinical outcomes.<br><br>CONCLUSION: Our findings highlights the utility of mNGS in diagnosing stroke-associated infections by providing a more comprehensive etiological diagnosis compared to traditional method. While mNGS shows promise in enhancing diagnostic accuracy and guiding clinical treatment, it high cost and technical challenges need addressing before widespread clinical adoption. Future research should focus on optimizing mNGS protocols, integration it with convertional diagnostic tools, and evaluating its cost-effectiveness and clinical impact through larger, multicentric studies.},
}
@article {pmid39844833,
year = {2024},
author = {Wang, M and Jin, Y and Zhang, W and Ye, L and Shao, H},
title = {Identifying subgroup of severe community-acquired pneumonia based on clinical metagenomics, a multicenter retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1516620},
pmid = {39844833},
issn = {2235-2988},
mesh = {Humans ; *Community-Acquired Infections/microbiology/mortality ; Male ; Retrospective Studies ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; *C-Reactive Protein/analysis ; Procalcitonin/blood ; Pneumonia/microbiology/mortality/drug therapy ; Biomarkers/blood ; Adrenal Cortex Hormones/therapeutic use ; Respiration, Artificial ; Intensive Care Units ; },
abstract = {OBJECTIVE: Severe community-acquired pneumonia (sCAP) is one of the major diseases within the ICU. We hypothesize that subtyping sCAP based on simple inflammatory markers, organ dysfunction, and clinical metagenomics results is feasible.<br><br>METHOD: In this study, we retrospectively enrolled immunocompetent sCAP patients requiring invasive mechanical ventilation, who underwent clinical metagenomics from 17 medical centers. We collected data on potentially pathogenic species reported by clinical metagenomics and clinical information for all patients. Latent class analysis (LCA) was applied to routine clinical parameters such as gender, age, white blood cell (WBC), lymphocytes, C-reactive protein (CRP), and Procalcitonin (PCT), identifying two optimally fitting models.<br><br>RESULTS: A total of 569 patients were enrolled. Compared to class B, class A was characterized by a younger age, higher CRP and PCT levels, and a higher incidence of coagulation dysfunction, liver failure, circulatory failure, and renal failure. However, the mortality rates were similar between the two groups. In class A, more cases of Streptococcus spp. and fewer cases of HSV-1 and Candida spp. were detected. Among the patients in the two phenotypes, 48.7% and 57.5% received corticosteroid treatment, respectively. In the class A, corticosteroid treatment was not associated with patient mortality (unadjusted hazard ratio (HR)=0.988; 95% confidence interval (CI), 0.634-1.541; p=0.959). In contrast, in the class B group, the use of corticosteroids was associated with a reduced mortality rate (adjusted HR=0.719; 95% CI, 0.525-0.986; p=0.04). Additional analysis showed that in class B, methylprednisolone was associated with reduced mortality (adjusted HR=0.61; 95% CI, 0.44-0.86; p=0.005), while dexamethasone was not associated with mortality (adjusted HR=1.4; 95% CI, 0.89-2.22; p=0.148). In addition, after dose conversion, the results showed that higher doses of corticosteroids in class B were associated with increased mortality (adjusted HR=1.01; 95% CI, 1.00-1.01; p=0.005).<br><br>CONCLUSION: We identified two classes based on clinical metagenomics and clinical features. Class B exhibited a better response to corticosteroid compared to class A. The rapid identification of these phenotypes could facilitate the screening of sCAP patients responsive to corticosteroid in future prospective clinical trials.},
}
@article {pmid39844349,
year = {2025},
author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC},
title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {2},
pages = {},
pmid = {39844349},
issn = {1574-6941},
support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; },
mesh = {*Glycine max/microbiology/growth &amp; development ; *Soil Microbiology ; *Bacillus thuringiensis/genetics/growth &amp; development ; *Soil/chemistry ; Rhizobium/genetics ; Quorum Sensing ; Microbiota ; Phosphorus/metabolism ; Biodiversity ; },
abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.},
}
@article {pmid39844180,
year = {2025},
author = {Chen, J and Pan, Q and Lu, L and Huang, X and Wang, S and Liu, X and Lun, J and Xu, X and Su, H and Guo, F and Yang, L and You, L and Xiao, H and Luo, W and Liu, HF and Pan, Q},
title = {Atg5 deficiency in basophils improves metabolism in lupus mice by regulating gut microbiota dysbiosis.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {40},
pmid = {39844180},
issn = {1478-811X},
support = {No. 82070757, 82270770//National Natural Science Foundation of China/ ; No. 82070757, 82270770//National Natural Science Foundation of China/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2021A05067//Science and Technology Planning Project of Zhanjiang City/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/metabolism ; *Basophils/metabolism ; *Dysbiosis ; Mice ; *Autophagy-Related Protein 5/genetics/metabolism ; Mice, Inbred MRL lpr ; Mice, Knockout ; Female ; Autophagy ; Mice, Inbred C57BL ; },
abstract = {Autophagic activation in immune cells, gut microbiota dysbiosis, and metabolic abnormalities have been reported separately as characteristics of systemic lupus erythematosus (SLE). Elucidating the crosstalk among the immune system, commensal microbiota, and metabolites is crucial to understanding the pathogenesis of autoimmune diseases. Emerging evidence shows that basophil activation plays a critical role in the pathogenesis of SLE; however, the underlying mechanisms remain largely unknown. Here, we investigated the effects of autophagic inhibition on the pathogenesis of basophils in SLE using Autophagy-related gene 5 (Atg5) knockout (Atg5[-/-]) as an autophagic inhibitor. Specifically, we knocked out basophilic Atg5 in vivo to investigate its impact on lupus metabolism. Furthermore, Atg5[-/-] basophils were transferred to basophil-depleted MRL/MpJ-Fas[lpr] (MRL/lpr) mice to study their effect on disease metabolism. Metagenomic and targeted metabolomic sequencing results indicated considerable reduction in the levels of plasma autoantibodies and inflammatory cytokines in the Atg5[-/-] basophil transfer group compared with that in the control group. Transplanting Atg5[-/-] basophils improved the gut microbiota balance in MRL/lpr mice, increasing the abundance of beneficial bacteria, such as Ligilactobacillus murinus and Faecalitalea rodentium, and reducing that of potentially pathogenic bacteria such as Phocaeicola salanitronis. The transplantation of Atg5-deficient basophils improved lupus symptoms by modulating lipid and amino acid metabolism. This improvement was linked to changes in the gut microbiota, particularly an increase in Ligilactobacillus murinus and Faecalitalea rodentium populations. These microbial shifts are believed to promote the production of beneficial metabolites, such as γ-linolenic acid and oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine, while reducing the levels of harmful metabolites such as arginine. These alterations in the metabolic profile contribute to the alleviation of lupus symptoms. Collectively, these findings reveal a novel role of basophil autophagy in SLE, highlighting its potential as a therapeutic target.},
}
@article {pmid39843539,
year = {2025},
author = {Laczkó, L and Nagy, NA and Nagy, &#xc1; and Maroda, &#xc1; and Sály, P},
title = {An updated reference genome of Barbatula barbatula (Linnaeus, 1758).},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {137},
pmid = {39843539},
issn = {2052-4463},
support = {OTKA PD142602//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; },
mesh = {Animals ; *Genome ; *Microsatellite Repeats ; Cypriniformes/genetics ; },
abstract = {The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.},
}
@article {pmid39843522,
year = {2025},
author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA},
title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {940},
pmid = {39843522},
issn = {2041-1723},
support = {AI166642//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21 AI166642/AI/NIAID NIH HHS/United States ; T32 AI007151/AI/NIAID NIH HHS/United States ; T32 AI007401/AI/NIAID NIH HHS/United States ; AI178595//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI173244/AI/NIAID NIH HHS/United States ; T32 GM127261/GM/NIGMS NIH HHS/United States ; R21 AI178595/AI/NIAID NIH HHS/United States ; AI173244//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21 AI132925/AI/NIAID NIH HHS/United States ; },
mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; },
abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.},
}
@article {pmid39843444,
year = {2025},
author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ},
title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {944},
pmid = {39843444},
issn = {2041-1723},
support = {DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; P30 CA046934/CA/NCI NIH HHS/United States ; DESC0023297//U.S. Department of Energy (DOE)/ ; EAR-2029686//National Science Foundation (NSF)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DEB-1754756//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; },
mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; },
abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.},
}
@article {pmid39843376,
year = {2025},
author = {Pichon, M and Burucoa, C and , },
title = {Diagnostic performance of the DISQVER metagenomic sequencing tool for the identification of pathogens in febrile neutropenic patients: the ADNEMIA trial.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e087773},
pmid = {39843376},
issn = {2044-6055},
mesh = {Humans ; *Metagenomics/methods ; Prospective Studies ; High-Throughput Nucleotide Sequencing ; Chemotherapy-Induced Febrile Neutropenia/diagnosis ; Febrile Neutropenia/diagnosis/microbiology ; Multicenter Studies as Topic ; Proof of Concept Study ; Anti-Bacterial Agents/therapeutic use ; Hematologic Neoplasms/complications ; },
abstract = {INTRODUCTION: While intensive protocols in onco-haematology have improved survival rates for patients with haematological malignancies, they have also resulted in an increased incidence of infection associated with therapy-induced immunosuppression (including chemotherapy-induced febrile neutropenia; FN). The occurrence of FN, associated with high morbidity and mortality, necessitates broad-spectrum antibiotic therapy, occasioning delayed chemotherapy and resulting in a loss of opportunity for the patient. Considering that without an identified pathogen, a 10% mortality rate can ensue, documentation is essential to the optimisation of antibiotic therapy. However, blood culture (the reference test) is limited for several reasons: such as fastidious culture, antibiotic treatment prior to sampling or insufficient sample volume. Sequencing technologies have led to the development of diagnostic approaches based on the detection of circulating DNA in blood. This study will aim to assess the clinical utility of metagenomic next-generation sequencing (mNGS)-DISQVER technology in detecting pathogenic microorganisms from blood samples of patients undergoing high-risk FN treatment.<br><br>METHODS AND ANALYSIS: This nationwide, prospective, multicentre, interventional, proof-of-concept clinical trial will enrol 200 patients. Will include patients&#x2265;18 years old, treated for malignancy, at high risk of FN (Multinational Association for Supportive Care in Cancer score&#x2264;21) with an expected duration of neutropenia&#x2265;7&#x2009;days. Patients who received antibiotic treatment within 24 hours prior to enrolment, have previously participated and/or have enhanced protection will be excluded. The primary outcome will be determined by considering the microorganisms responsible for this FN, weighted by the assessment of an adjudication committee. Secondary outcomes will evaluate patient management depending on the arm. The second secondary outcome will be determined by the duration of conventional assessment, frequency of microorganisms detected during routine care and percentage distribution of theoretical adjustments made to anti-infective treatment based on microorganisms diagnosed using the mNGS-DISQVER tool as compared with conventional practices. Identifying the pathogens responsible for high-risk FN from a blood sample, using an unbiased technique, can provide microbiological documentation and may even reveal unexpected microorganisms in these profoundly immunocompromised patients.<br><br>ETHICS AND DISSEMINATION: The protocol received approval from the Comit&#xe9; de Protection des Personnes Sud-M&#xe9;diterran&#xe9;e II. All participants will provide informed consent before participation. The trial has been registered on ClinicalTrials.gov (identifier NCT06075888). The results of the main trial and each of the secondary endpoints will be submitted for publication in a peer-reviewed journal.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov NCT06075888.},
}
@article {pmid39842557,
year = {2025},
author = {Loman, BR},
title = {Communities, mysteries, and pathophysiologies - Are gut microbes key to a healthy mind?.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.01.012},
pmid = {39842557},
issn = {1090-2139},
}
@article {pmid39842302,
year = {2025},
author = {Li, H and Zhang, X and Zhaxi, Y and Pan, C and Zhang, Z and Pan, J and Shahzad, K and Sun, F and Zhen, Y and Jinmei, J and Zhao, W and Song, T},
title = {Integrative multi-omics analysis reveals liver-gut axis adaptation in high-altitude goats.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {54},
number = {},
pages = {101422},
doi = {10.1016/j.cbd.2025.101422},
pmid = {39842302},
issn = {1878-0407},
abstract = {The liver-gut axis is an important regulatory axis for the host's metabolic functions. The study of liver gene expression, changes in metabolic products and the regulation of gut microbial communities in plateau animals under harsh environments can reveal the mechanisms by which Tibetan goats adapt to the plateau environment. This study employs transcriptome, metabolome and metagenomic analyses to reveal the differences in genes, metabolism, and gut microbiota between Jianzhou big-eared goats (JBG) and Xizang cashmere goats (TCG), which is of significant importance for improving survival models of high-altitude ruminants. The results showed that there were 553 DEGs in the liver of JBG and TCG. Hepatic metabolomic analysis revealed significant differences in metabolic activity between the JBG and TCG groups, with notable increases in glycerophospholipid and retinol metabolic pathways. The gut microbiota, including Andreesenia, Dielma, Oscillibacter, Agrobacterium, Hyella and Thermosinus, interact with liver metabolites and can regulate the high-altitude adaptability of goats. This study reveals that TCG enhance immune regulation and energy utilization efficiency by regulating liver gene expression, modulating metabolic pathways, and improving gut microbiota, thereby helping TCG maintain healthy survival capabilities in hypoxic and high-radiation environments.},
}
@article {pmid39841201,
year = {2025},
author = {Geng, P and Zhao, N and Zhou, Y and Harris, RS and Ge, Y},
title = {Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2455503},
doi = {10.1080/19490976.2025.2455503},
pmid = {39841201},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Mice ; *Carbohydrate Metabolism ; *Faecalibacterium prausnitzii/metabolism/genetics ; *Phylogeny ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Probiotics/administration &amp; dosage ; Male ; Metagenome ; },
abstract = {The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.},
}
@article {pmid39840975,
year = {2025},
author = {Ge, B and McDonald, RC and Yang, Q and Domesle, KJ and Sarria, S and Li, X and Hsu, C-H and Jarvis, KG and Tadesse, DA},
title = {Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0223024},
doi = {10.1128/aem.02230-24},
pmid = {39840975},
issn = {1098-5336},
abstract = {As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood &amp; Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing in silico filtering at removing chloroplast and mitochondrial sequences. There was a good agreement between 16S rRNA gene amplicon sequencing and shotgun metagenomics on community profiles in animal feed data sets; however, they differed in taxonomic resolution, with the latter superior at resolving at the species level. Although the overall prevalence of AMR genes was low, resistome analysis of animal feed data sets by shotgun metagenomics revealed 10 AMR gene/protein families, including beta-lactamases, erythromycin/lincomycin/pristinamycin/tylosin, fosfomycin, phenicol, and quinolone. Future expansion of microbiome and resistome profiling in animal food will help better understand the bacterial and AMR gene diversity in these commodities and help guide pathogen control and AMR prevention efforts.IMPORTANCEWith the growing interest and application of metagenomics in understanding the structure/composition and function of diverse microbial communities along the One Health continuum, this study represents one of the first attempts to employ these advanced sequencing technologies to characterize the microbiota and AMR genes in animal food. We unraveled the effects of DNA extraction kits on sample analysis by 16S rRNA gene amplicon sequencing and showed similar efficacies of two strategies at removing chloroplast and mitochondrial reads. The in-depth analysis using shotgun metagenomics shed light on the community compositions and the presence of an array of AMR genes in animal food. This exploration of microbiomes and resistomes in representative animal food samples by both sequencing approaches laid important groundwork for future metagenomic investigations to gain a better understanding of the baseline/core microbiomes and associated AMR functions in these diverse commodities and help guide pathogen control and AMR prevention efforts.},
}
@article {pmid39840973,
year = {2025},
author = {Wu, DG and Harris, CR and Kalis, KM and Bowen, M and Biddle, JF and Farag, IF},
title = {Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0222924},
doi = {10.1128/aem.02229-24},
pmid = {39840973},
issn = {1098-5336},
abstract = {UNLABELLED: Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate-degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.<br><br>IMPORTANCE: The benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their host's diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but there is a lack of a comprehensive understanding of the genome-based metabolic capabilities of specific microbes and how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. We found evidence that fish gut microbial communities share several core functions despite differences in microbial taxonomy. Herbivorous fish harbored a functionally diverse microbial community with plant matter degraders, while the piscivorous and invertivorous fish had microbiomes more specialized in protein degradation.},
}
@article {pmid39840396,
year = {2025},
author = {Qin, L and Liang, M and Song, J and Chen, P and Zhang, S and Zhou, Y and Li, H and Tang, J and Ma, Y and Yang, B and Xu, J and Zhang, J},
title = {Utilizing Targeted Next-Generation Sequencing for Rapid, Accurate, and Cost-Effective Pathogen Detection in Lower Respiratory Tract Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {329-340},
pmid = {39840396},
issn = {1178-6973},
abstract = {OBJECTIVE: To evaluate the diagnostic performance and clinical impact of targeted next-generation sequencing (tNGS) in patients with suspected lower respiratory tract infections.<br><br>METHODS: Following propensity score matching, we compared the diagnostic performances of tNGS and metagenomic next-generation sequencing (mNGS). Furthermore, the diagnostic performance of tNGS was compared with that of culture, and its clinical impact was assessed.<br><br>RESULTS: After propensity score matching, the coincidence rate of tNGS was comparable to that of mNGS (82.9% vs 73.9%, P=0.079). The detection rates for bacterial, viral, fungal, and mixed infections were not significantly different (P>0.05). Bacterial-viral co-infection (16.7%) was the most common mixed infection detected by tNGS. tNGS showed a higher detection rate than culture (75.2% vs 19.0%, P<0.01). The positive detection rate by tNGS was not significantly different between immunocompromised and immunocompetent patients (88.6% vs 80.5%, P=0.202), but was significantly higher than that by culture (P<0.001). Moreover, 65 patients (44.5%) had their medications modified based on the tNGS results, and the majority exhibited notable improvement regardless of treatment adjustment.<br><br>CONCLUSION: tNGS performs comparably to mNGS and surpasses culture in detecting lower respiratory tract infections. Nevertheless, tNGS is faster and more cost-effective than mNGS, making it highly significant for guiding rational treatment.},
}
@article {pmid39840283,
year = {2024},
author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S},
title = {Recent advances in deep learning and language models for studying the microbiome.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1494474},
pmid = {39840283},
issn = {1664-8021},
support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; U24 OD035523/OD/NIH HHS/United States ; },
abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.},
}
@article {pmid39839678,
year = {2025},
author = {Modha, S and Hughes, J and Orton, RJ and Lytras, S},
title = {Expanding the genomic diversity of human anelloviruses.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf002},
pmid = {39839678},
issn = {2057-1577},
abstract = {Anelloviruses are a group of small, circular, single-stranded DNA viruses that are found ubiquitously across mammalian hosts. Here, we explored a large number of publicly available human microbiome datasets and retrieved a total of 829 anellovirus genomes, substantially expanding the known diversity of these viruses. The majority of new genomes fall within the three major human anellovirus genera: Alphatorquevirus, Betatorquevirus, and Gammatorquevirus, while we also present new genomes of the under-sampled Hetorquevirus, Memtorquevirus, and Samektorquevirus genera. We performed recombination analysis and show evidence of extensive recombination across all human anelloviruses. Interestingly, more than 95% of the detected events are between members of the same genus and only 15 inter-genus recombination events were detected. The breakpoints of recombination cluster in hotspots at the ends and outside of the ORF1 gene, while a recombination coldspot was detected within the gene. Our analysis suggests that anellovirus evolution is governed by homologous recombination; however, events between distant viruses or ones producing chimaeric ORF1s likely lead to nonviable recombinants. The large number of genomes further allowed us to examine how essential genomic features vary across anelloviruses. These include functional domains in the ORF1 protein and the nucleotide motif of the replication loop region, required for the viruses' rolling-circle replication. A subset of the genomes assembled in both this and previous studies are completely lacking these essential elements, opening up the possibility that anellovirus intracellular populations contain nonstandard viral genomes. However, low-read depth of the metagenomically assembled contigs may partly explain the lack of some features. Overall, our study highlights key features of anellovirus genomics and evolution, a largely understudied group of viruses whose potential in virus-based therapeutics is recently being explored.},
}
@article {pmid39839264,
year = {2024},
author = {Wu, H and Cao, H and Gao, X and Shi, C and Wang, L and Gao, B},
title = {The role of metagenomic next-generation sequencing in diagnosing and managing post-kidney transplantation infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1473068},
pmid = {39839264},
issn = {2235-2988},
mesh = {*Kidney Transplantation/adverse effects ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Bacteria/genetics/isolation &amp; purification/classification ; Postoperative Complications/diagnosis ; },
abstract = {Kidney transplantation (KT) is a life-saving treatment for patients with end-stage renal disease, but post-transplant infections remain one of the most significant challenges. These infections, caused by a variety of pathogens, can lead to prolonged hospitalization, graft dysfunction, and even mortality, particularly in immunocompromised patients. Traditional diagnostic methods often fail to identify the causative organisms in a timely manner, leading to delays in treatment and poorer patient outcomes. This review explores the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of post-KT infections. mNGS allows for the rapid, comprehensive detection of a wide range of pathogens, including bacteria, viruses, fungi, and parasites, without the need for culture-based techniques. We discuss the advantages of mNGS in early and accurate pathogen identification, its role in improving patient management, and the potential challenges in its clinical implementation. Additionally, we consider the future prospects of mNGS in overcoming current diagnostic limitations and its potential for guiding targeted therapies, particularly in detecting antimicrobial resistance and emerging pathogens. This review emphasizes the promise of mNGS as an essential tool in improving the diagnosis and treatment of infections in KT recipients.},
}
@article {pmid39839123,
year = {2024},
author = {Monteiro, AFM and da Silva, FS and Cruz, ACR and da Silva, SP and Queiroz, ALN and Casseb, LMN and Martins, LC and Medeiros, DBA},
title = {Viral diversity in wild rodents in the regions of Canaã de Carajás and Curionopólis, State of Pará, Brazil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1502462},
pmid = {39839123},
issn = {1664-302X},
abstract = {Wild rodents serve as crucial reservoirs for zoonotic viruses. Anthropogenic and environmental disruptions, particularly those induced by mining activities, can destabilize rodent populations and facilitate the emergence of viral agents. In the Canaã dos Carajás and Curionópolis regions of Brazil, significant environmental changes have occurred due to mining expansion, potentially creating conditions conducive to the emergence of rodent-associated viral diseases. This study aimed to investigate the viral diversity in wild rodents captured in Canaã dos Carajás and Curionópolis, Pará, between 2017 and 2019. A total of 102 rodent samples were taxonomically identified through karyotyping and screened for anti-Orthohantavirus antibodies using the ELISA method. Subsequently, nucleotide sequencing and bioinformatics analyses were conducted on 14 selected samples to characterize the virome. This selection was based on the most commonly associated rodent genera as reservoirs of Orthohantavirus and Mammarenavirus. Of the 102 samples tested via ELISA, 100 were negative, and two showed optical density at the cutoff point. Sequencing of the 14 samples generated approximately 520 million reads, with 409 million retained after quality control. These reads were categorized into 53 viral families, including both DNA and RNA viruses, with Retroviridae, Baculoviridae, and Microviridae being the most abundant. Viral contigs were identified, including one fragment related to Arenaviridae and three to Filoviridae. Metagenomic analysis revealed high viral diversity in the sampled rodents, with the presence of viral families of public health concern, such as Arenaviridae and Filoviridae. The findings suggest that increased human activities associated with mining may contribute to the emergence of these viruses, underscoring the need for ongoing surveillance to prevent potential outbreaks.},
}
@article {pmid39839120,
year = {2024},
author = {Yu, J and Yang, S and Zhang, X and Liu, X and Tang, X and Wang, L and Chen, J and Luo, H and Liu, C and Song, C},
title = {Corrigendum: Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1545445},
doi = {10.3389/fmicb.2024.1545445},
pmid = {39839120},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1467864.].},
}
@article {pmid39839104,
year = {2024},
author = {Mendoza, JE and Tineo, D and Chuquibala-Checan, B and Atalaya-Marin, N and Taboada-Mitma, VH and Tafur-Culqui, J and Tarrillo, E and Gómez-Fernández, D and Goñas, M and Reyes-Reyes, MA},
title = {Global perspectives on the biodegradation of LDPE in agricultural systems.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1510817},
pmid = {39839104},
issn = {1664-302X},
abstract = {The increasing use of plastics globally has generated serious environmental and human health problems, particularly in the agricultural sector where low-density polyethylene (LDPE) and other plastics are widely used. Due to its low recycling rate and slow degradation process, LDPE is a major source of pollution. This paper addresses the problem of plastic accumulation in agriculture, focusing on LDPE biodegradation strategies. The studies reviewed include recent data and the methodologies used include state-of-the-art technologies and others that have been used for decades, to monitor and measure the degree of biodegradation that each treatment applied can have, including SEM, GCMS, HPLC, and microscopy. The countries investigating these biodegradation methodologies are identified, and while some countries have been developing them for some years, others have only begun to address this problem in recent years. The use of microorganisms such as bacteria, fungi, algae, and insect larvae that influence its decomposition is highlighted. A workflow is proposed to carry out this type of research. Despite the advances, challenges remain, such as optimizing environmental conditions to accelerate the process and the need for further research that delves into microbial interactions in various environmental contexts.},
}
@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}
@article {pmid39838455,
year = {2025},
author = {Liao, H and Li, J and Wang, YZ and Li, H and An, XL and Wang, T and Chang, RY and Zhu, YG and Su, JQ},
title = {Evolutionary diversification and succession of soil huge phages in glacier foreland.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {18},
pmid = {39838455},
issn = {2049-2618},
support = {4237070301//National Natural Science Foundation of China/ ; 42161134002//National Natural Science Foundation of China/ ; STEP, 2021QZKK0103//Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Soil Microbiology ; *Ice Cover/virology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Phylogeny ; *Genome, Viral ; Metagenomics ; Tibet ; Evolution, Molecular ; Soil ; },
abstract = {BACKGROUND: Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.<br><br>RESULTS: Here, we conduct a size-fractioned (<&#x2009;0.22 &#x3bc;m) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (&#x2264;&#x2009;41 years) and late stages (>&#x2009;41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.<br><br>CONCLUSIONS: Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. Video Abstract.},
}
@article {pmid39838431,
year = {2025},
author = {Sun, Q and Li, BR and Li, DH and Wang, XY and Wang, QY and Jiang, ZM and Ning, SB and Sun, T},
title = {WKB ameliorates DSS-induced colitis through inhibiting enteric glial cells activation and altering the intestinal microbiota.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {93},
pmid = {39838431},
issn = {1479-5876},
support = {No. 22YXQN034//Air Force Medical Center Youth Talent Program Project/ ; No. 2020-4-5123//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/pathology/microbiology/chemically induced/complications ; *Mice, Inbred C57BL ; Male ; *Neuroglia/metabolism/pathology ; Cytokines/metabolism ; Colon/pathology/microbiology ; Permeability ; Body Weight ; Inflammation/pathology ; Intestinal Mucosa/pathology/microbiology/metabolism ; Mice ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic condition influenced by diet, which affects gut microbiota and immune functions. The rising prevalence of IBD, linked to Western diets in developing countries, highlights the need for dietary interventions. This study aimed to assess the impact of white kidney beans (WKB) on gut inflammation and microbiota changes, focusing on their effects on enteric glial cells (EGCs) and immune activity in colitis.<br><br>METHODS: Male C57BL/6 mice were divided into four groups: normal diet (ND), ND with 2.5% dextran sulfate sodium (DSS) for colitis induction, ND with 20% WKB, and WKB with 2.5% DSS. The dietary intervention lasted 17 weeks, with DSS given in the final week. Colonic inflammation was assessed by body weight, disease activity index, and histopathology. Epithelial barrier integrity was evaluated using immunofluorescence, transmission electron microscopy, and permeability assays. EGCs activity was analyzed via immunofluorescence and quantitative real-time PCR. Immune responses were measured using flow cytometry and cytokine profiling, while gut microbiota changes were examined through metagenomic sequencing.<br><br>RESULTS: WKB supplementation significantly alleviated DSS-induced colitis in mice, evidenced by reduced weight loss, disease activity, and improved colonic histology. This effect was linked to enhanced mucosal barrier integrity, seen through increased tight junction protein and Muc2 expression, accompanied by favorable ultrastructural changes. WKB modulated EGCs activity via TNF-like cytokine 1&#xa0;A inhibition, resulting in reduced glial fibrillary acidic protein expression. Immunologically, it downregulated Th1 and Th17 pro-inflammatory cells, increased Treg cells, and altered cytokine profiles (reduced TNF-&#x3b1;, IFN-&#x3b3;, IL-17; increased IL-10). Metagenomic analysis showed that WKB restored gut microbiota balance, particularly enhancing beneficial bacteria like Akkermansia. KEGG pathway analysis further indicated that WKB supplementation improved key metabolic pathways, notably those related to phenylalanine, tyrosine, and tryptophan biosynthesis, thereby countering DSS-induced metabolic disruptions.<br><br>CONCLUSIONS: WKB shows promise for treating IBD by enhancing mucosal barriers, inhibiting EGCs activity, balancing Th1/Th17/Treg cells, and restoring gut microbiota and metabolic homeostasis, thereby alleviating colitis symptoms.},
}
@article {pmid39838419,
year = {2025},
author = {Liu, X and Ding, H and Zhang, X and Ta, N and Zhao, J and Zhang, Q and Liu, H and Sun, M and Zhang, X},
title = {Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {17},
pmid = {39838419},
issn = {2049-2618},
mesh = {Animals ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Altitude ; *Biomass ; Metagenome ; Animal Feed/microbiology ; Archaea/genetics/classification ; Gastrointestinal Tract/microbiology ; Plants/microbiology ; },
abstract = {BACKGROUND: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.<br><br>RESULTS: A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness&#x2009;>&#x2009;50% and contamination&#x2009;<&#x2009;10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness&#x2009;>&#x2009;80% and contamination&#x2009;<&#x2009;10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.<br><br>CONCLUSIONS: These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.},
}
@article {pmid39838369,
year = {2025},
author = {Fan, J and Zeng, F and Zhong, H and Cai, J and Shen, W and Cheng, C and He, C and Liu, Y and Zhou, Y and Chen, S and Zhu, Y and Liu, T and Zheng, JS and Wang, L and Chen, YM and Ma, W and Zhou, D},
title = {Potential roles of cigarette smoking on gut microbiota profile among Chinese men.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {25},
pmid = {39838369},
issn = {1741-7015},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Cigarette Smoking/adverse effects ; Middle Aged ; Adult ; China ; RNA, Ribosomal, 16S/genetics ; Asian People ; Actinomyces ; Aged ; East Asian People ; },
abstract = {BACKGROUND: Cigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.<br><br>METHODS: Here, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total&#x2009;=&#x2009;3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.<br><br>RESULTS: Actinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum &#x3b3;-glutamylcysteine (&#x3b3;-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.<br><br>CONCLUSIONS: We characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.},
}
@article {pmid39838275,
year = {2025},
author = {Nabisubi, P and Kanyerezi, S and Kebirungi, G and Sserwadda, I and Nsubuga, M and Kisitu, G and Nahirya, PN and Mulindwa, B and Akabwai, GP and Nantongo, S and Kekitiinwa, A and Kigozi, E and Luutu, NM and Katabazi, FA and Kalema, L and Katabalwa, A and Jjingo, D and Mboowa, G},
title = {Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with non-malarial febrile illness.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {96},
pmid = {39838275},
issn = {1471-2334},
support = {U2R TW010672/TW/FIC NIH HHS/United States ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; },
mesh = {Humans ; *Feces/microbiology/virology ; *Metagenomics ; Female ; *HIV Infections/complications/microbiology/virology ; Male ; Child, Preschool ; Child ; Fever/microbiology ; Uganda/epidemiology ; Infant ; Candida albicans/genetics/isolation &amp; purification/classification/pathogenicity ; Giardia/genetics/isolation &amp; purification/classification ; Bacteroides/genetics/isolation &amp; purification/classification ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management.<br><br>METHODS: In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children's Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline.<br><br>RESULTS: Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children.<br><br>CONCLUSION: Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.},
}
@article {pmid39838107,
year = {2025},
author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM},
title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {175},
pmid = {39838107},
issn = {1432-184X},
support = {PEJ2018-003019-A//Plan Estatal de Garant&#xed;a Juvenil (Fondo Social Europeo, Gobierno de Espa&#xf1;a/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andaluc&#xed;a 2014-2020/ ; },
mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; },
abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.},
}
@article {pmid39837861,
year = {2025},
author = {Kagaya, Y and Zhang, Z and Ibtehaz, N and Wang, X and Nakamura, T and Punuru, PD and Kihara, D},
title = {NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {881},
pmid = {39837861},
issn = {2041-1723},
support = {DMS2151678//NSF | Directorate for Mathematical &amp; Physical Sciences | Division of Mathematical Sciences (DMS)/ ; R01GM133840, R01GM123055//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM123055/GM/NIGMS NIH HHS/United States ; CMMI1825941//NSF | ENG/OAD | Division of Civil, Mechanical and Manufacturing Innovation (CMMI)/ ; IIS2211598//NSF | Directorate for Computer &amp; Information Science &amp; Engineering | Division of Information and Intelligent Systems (Information &amp; Intelligent Systems)/ ; R01 GM133840/GM/NIGMS NIH HHS/United States ; MCB1925643//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; DBI2003635, DBI2146026//NSF | BIO | Division of Biological Infrastructure (DBI)/ ; },
mesh = {*Nucleic Acid Conformation ; *RNA/chemistry/genetics ; Deep Learning ; Computational Biology/methods ; Neural Networks, Computer ; Sequence Alignment/methods ; Software ; },
abstract = {RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures. NuFold is a deep neural network trained end-to-end for the output structure from the input sequence. NuFold incorporates a nucleobase center representation, which enables flexible conformation of ribose rings. Benchmark study showed that NuFold clearly outperformed energy-based methods and demonstrated comparable results with existing state-of-the-art deep-learning-based methods. NuFold exhibited a particular advantage in building correct local geometries of RNA. Analyses of individual components in the NuFold pipeline indicated that the performance improved by utilizing metagenome sequences for multiple sequence alignment and increasing the number of recycling. NuFold is also capable of predicting multimer complex structures of RNA by linking the input sequences.},
}
@article {pmid39837860,
year = {2025},
author = {Alser, M and Eudine, J and Mutlu, O},
title = {Taming large-scale genomic analyses via sparsified genomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {876},
pmid = {39837860},
issn = {2041-1723},
mesh = {*Genomics/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Algorithms ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Databases, Genetic ; },
abstract = {Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences. Sparsified genomics provides benefits to many genomic analyses and has broad applicability. Sparsifying genomic sequences accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, respectively, while providing comparable memory footprint, 2x smaller index size, and more correctly detected variations compared to minimap2. Sparsifying genomic sequences makes containment search through very large genomes and large databases 72.7-75.88x (1.62-1.9x when indexing is preprocessed) faster and 723.3x more storage-efficient than searching through non-sparsified genomic sequences (with CMash and KMC3). Sparsifying genomic sequences enables robust microbiome discovery by providing 54.15-61.88x (1.58-1.71x when indexing is preprocessed) faster and 720x more storage-efficient taxonomic profiling of metagenomic samples over the state-of-the-art tool (Metalign).},
}
@article {pmid39837758,
year = {2025},
author = {Mizuno, Y and Yoshimura, T and Sawada, K and Tsuge, K and Nagano, Y and Yoshizaki, Y and Goto, M and Kobayashi, G},
title = {Crucial role of early addition of Wickerhamiella versatilis in enhancing aroma formation during soy sauce fermentation.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2024.12.010},
pmid = {39837758},
issn = {1347-4421},
abstract = {In modern Japanese soy sauce production, sealed outdoor fermentation tanks are used to ferment moromi with halotolerant starter cultures: the lactic acid bacterium Tetragenococcus halophilus and yeasts Wickerhamiella versatilis and Zygosaccharomyces rouxii. T. halophilus and W. versatilis are added in the early fermentation stage, while Z. rouxii is introduced about 1 month later to initiate alcoholic fermentation. Both W. versatilis and Z. rouxii contribute to the production of volatile organic compounds (VOC), with 4-ethylguaiacol (4-EG), uniquely produced by W. versatilis, being essential for the characteristic aroma of soy sauce. Prior metagenomic and metabolomic analyses indicated that 4-EG production occurs prior to Z. rouxii fermentation, though the increase in W. versatilis proportion follows it. Additional omics analysis of a production batch confirmed similar microbial and VOC dynamics, with no clear relationship between W. versatilis increase and 4-EG levels. To investigate this, a laboratory-scale experiment was conducted using filter-sterilized moromi supernatant as a medium, with staggered inoculations of the two yeasts. Viable cell density, 4-EG, and ethanol were measured as indicators of fermentation activity. Results showed that when W. versatilis was inoculated before Z. rouxii, 4-EG production commenced earlier, while W. versatilis cell density and ethanol production increased only after Z. rouxii fermentation began. Under these conditions, 4-EG and ethanol production were highest, suggesting that the presence rather than the increase of W. versatilis is crucial for 4-EG production. Consequently, the early addition of W. versatilis was considered an effective strategy to enhance 4-EG and VOC production in moromi.},
}
@article {pmid39837331,
year = {2025},
author = {Valdés-Mas, R and Leshem, A and Zheng, D and Cohen, Y and Kern, L and Zmora, N and He, Y and Katina, C and Eliyahu-Miller, S and Yosef-Hevroni, T and Richman, L and Raykhel, B and Allswang, S and Better, R and Shmueli, M and Saftien, A and Cullin, N and Slamovitz, F and Ciocan, D and Ouyang, KS and Mor, U and Dori-Bachash, M and Molina, S and Levin, Y and Atarashi, K and Jona, G and Puschhof, J and Harmelin, A and Stettner, N and Chen, M and Suez, J and Honda, K and Lieb, W and Bang, C and Kori, M and Maharshak, N and Merbl, Y and Shibolet, O and Halpern, Z and Shouval, DS and Shamir, R and Franke, A and Abdeen, SK and Shapiro, H and Savidor, A and Elinav, E},
title = {Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.12.016},
pmid = {39837331},
issn = {1097-4172},
abstract = {Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.},
}
@article {pmid39837034,
year = {2025},
author = {Liu, W and Chen, Z and Li, T and Wen, X},
title = {Geographical distribution and risk of antibiotic resistance genes in sludge anaerobic digestion process across China.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137290},
doi = {10.1016/j.jhazmat.2025.137290},
pmid = {39837034},
issn = {1873-3336},
abstract = {Anaerobic digestion (AD) is gaining increasing attention as the central reservoir of antibiotic resistance genes (ARGs), while the geographical distribution of ARGs in AD is neglected. Accordingly, a sampling scheme on full-scale AD plants across China was implemented, and the resistome therein was excavated. The abundance of ARGs in AD sludge ranged from 0.198 to 0.574 copies/cell. Some of the frequently reported and emergent ARGs were detected in our AD system. Both the abundance and composition of ARGs presented significant differences between the south and north regions of China, hinting the physical/economic factors may function in the formation of ARG profiles. The risk scores of AD samples were in middle of domestic and hospital wastewater. Risk scores were significantly higher in the north. Besides, the proportion of Rank I and Rank II ARGs was also higher in north, which explained the regional difference of ARG composition in a micro-perspective. This study provides a fundamental survey on the of ARG level and profile in AD process across China, reveals the biogeography of ARGs and inspires the control strategies of antibiotic resistance.},
}
@article {pmid39836258,
year = {2025},
author = {Mandal, M and Ghosh, B and Mandal, S},
title = {Comparison of the rhizospheric soil bacteriomes of Oryza sativa and Solanum melongena crop cultivars reveals key genes and pathways involved in biosynthesis of ectoine, lysine, and catechol meta-cleavage.},
journal = {Functional &amp; integrative genomics},
volume = {25},
number = {1},
pages = {20},
pmid = {39836258},
issn = {1438-7948},
mesh = {*Oryza/genetics/metabolism/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Lysine/biosynthesis/metabolism ; *Catechols/metabolism ; *Solanum melongena/genetics/microbiology/metabolism ; },
abstract = {Rice (Oryza sativa L.), Poaceae family, forms staple diet of half of world's population, and brinjal (Solanum melongena L.), an important solanaceous crop, are consumed worldwide. Rhizosphere research is gaining importance towards application of knowledge for improving productivity, sustainable agricultural practice, and rhizoremediation for nature restoration. While there are reports on rhizobacteriome of rice, studies comparing structural, functional and metabolomic traits of microbial communities in rhizospheres of rice and brinjal are not yet available. We demonstrated, in Oryza sativa (1144-Hybrid, Dhiren, Local Saran cultivars) and Solanum melongena (Jhiloria, Chandtara, Jotshna cultivars) rhizospheres from Malda, India, using integrated approach of 16 S ribosomal sequencing, shotgun metagenomics, and microbial metabolomics to decipher microbial diversity, association with soil physicochemical characteristics, key genes and pathways. Ectoine biosynthesis was significantly expressed in brinjal (Jhiloria), but not in rice rhizosphere. The dominant brinjal rhizobacteriome-specific bacteria comprised Thermus sp., Petrobacter succinatimandens, Thermoanaerobacter sp., and Diaphorobacter sp., that were involved in house-keeping functions including pentose phosphate pathway, biosynthesis of amino acids, lipopolysaccharide, and photosynthesis. The dominant bacteria unique to rice rhizobacteriome (Local Saran) consisted of Aeromonas sp., associated with catechol meta-cleavage, while Clostridium sp., Faecalibacterium prausnitzii, and Roseburia sp. were involved with lysine biosysnthesis in rice (1144-Hybrid). Our results imply novel information for improved breeding of brinjal specific cultivar with enhanced ectoine production associated with osmotic stress tolerance, rice specific cultivars with enhanced lysine production significant to human nutrition and catechol removal for the maintenance of environmental quality.},
}
@article {pmid39836086,
year = {2025},
author = {Xia, R and Yin, X and Balcazar, JL and Huang, D and Liao, J and Wang, D and Alvarez, PJJ and Yu, P},
title = {Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08265},
pmid = {39836086},
issn = {1520-5851},
abstract = {The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.},
}
@article {pmid39835966,
year = {2025},
author = {Levine, BH and Hoffman, JM},
title = {Microbiome transplants may not improve health and longevity in Drosophila melanogaster.},
journal = {Biology open},
volume = {14},
number = {1},
pages = {},
pmid = {39835966},
issn = {2046-6390},
support = {R00 AG059920/AG/NIA NIH HHS/United States ; //Augusta University; University of South Carolina/ ; R00AG059920/NH/NIH HHS/United States ; },
mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Longevity ; *Gastrointestinal Microbiome ; Female ; Male ; Microbiota ; },
abstract = {The gut microbiome, which is composed of bacteria, viruses, and fungi, and is involved in multiple essential physiological processes, changes measurably as a person ages, and can be associated with negative health outcomes. Microbiome transplants have been proposed as a method to improve gut function and reduce or reverse multiple disorders, including age-related diseases. Here, we take advantage of the laboratory model organism, Drosophila melanogaster, to test the effects of transplanting the microbiome of a young fly into middle-aged flies, across multiple genetic backgrounds and both sexes, to test whether age-related lifespan could be increased, and late-life physical health declines mitigated. Our results suggest that, overall, microbiome transplants do not improve longevity and may even be detrimental in flies, and the health effects of microbiome transplants were minor, but sex- and genotype-dependent. This discovery supports previous evidence that axenic flies, those with no gut microbiome, live healthier and longer lives than their non-axenic counterparts. The results of this study suggest that, at least for fruit flies, microbiome transplants may not be a viable intervention to improve health and longevity, though more research is still warranted.},
}
@article {pmid39835383,
year = {2025},
author = {Liu, J and Yang, B and Wu, Y and Yang, G and Zha, X and Jiang, W},
title = {Significance of Combining Bronchoalveolar Lavage Fluid With Targeted Next-Generation Sequencing in the Pathogen Detection-Based Diagnosis of Pulmonary Infections.},
journal = {The clinical respiratory journal},
volume = {19},
number = {1},
pages = {e70046},
pmid = {39835383},
issn = {1752-699X},
support = {8252//Tianjin Clinical Key Specialty Construction Project Funding (2024) - Respiratory Department/ ; },
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; Aged ; Adult ; Respiratory Tract Infections/diagnosis/microbiology ; Metagenomics/methods ; China/epidemiology ; },
abstract = {OBJECTIVE: In this study, we investigated the application value of bronchoalveolar lavage fluid (BALF) combined with targeted next-generation sequencing (tNGS) in the pathogen detection-based diagnosis of patients with lung infections.<br><br>METHOD: A retrospective analysis was conducted on patients who underwent tracheoscopy and conventional microbiological tests (CMTs) on BALF, coupled with metagenomic next-generation sequencing (mNGS) or tNGS. This investigation encompassed individuals with suspected lung infections at Tianjin First Central Hospital from March 2023 to July 2023. Diagnostic rates based on pathogens detected via tNGS were compared with CMTs within the tNGS group. Additionally, diagnostic rates obtained through tNGS were compared with mNGS between the two groups.<br><br>RESULTS: The data of a total of 169 patients (78 in the tNGS group and 91 in the mNGS group) were collected, and 145 patients (67 in the tNGS group and 78 in the mNGS group) were finally diagnosed with lung infections. The comprehensive positive pathogen detection-based diagnosis rate for tNGS was 86.6%, with a single-pathogen lung infection diagnosis rate of 85.7% and a mixed-pathogen pulmonary infection diagnosis rate of 88.0%. In contrast, the overall positive pathogen detection-based diagnosis rate for CMTs was 38.8%, comprising a single-pathogen pulmonary infection diagnosis rate of 28.6% and a mixed-pathogen pulmonary infection diagnosis rate of 20.0%. The difference in positive diagnosis rate was deemed statistically significant (p&#x2009;<&#x2009;0.05). In the mNGS group, the overall pathogen detection-based diagnosis rate was 89.7%, with a single-pathogen pulmonary infection diagnosis rate of 84.9%, and a 100% diagnosis rate for mixed-pathogen pulmonary infections. There was no statistically significant difference in the positive diagnosis rate when compared with the tNGS group (p&#x2009;>&#x2009;0.05).<br><br>CONCLUSION: In patients with pulmonary infections, the diagnosis rate based on BALF pathogen detection using tNGS exceeded that of CMTs, showing no statistically significant difference compared to mNGS.},
}
@article {pmid39834891,
year = {2025},
author = {Zhao, D and Zhang, L and Sun, Q and Cheng, J},
title = {A Case Report of Chlamydia psittaci Infective Endocarditis Complicated With Pneumonia.},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {7536462},
pmid = {39834891},
issn = {2090-6625},
abstract = {Psittacosis is a zoonotic disease caused by Chlamydia psittaci and is commonly found in birds and poultry. Human infection is uncommon, and most cases are sporadic. Infection of extrapulmonary organs by Chlamydia psittaci is extremely rare. A rare case of infective endocarditis complicated by pneumonia caused by Chlamydia psittaci was reported, which was diagnosed using metagenomic next-generation sequencing (mNGS). The patient recovered after receiving appropriate anti-infective treatment. Discussion on the pathogenesis, diagnosis, and treatment of this disease based on recent literature reports aimed to improve the prognosis of similar patients and enhance the understanding of clinicians.},
}
@article {pmid39834703,
year = {2024},
author = {Deng, Y and Wu, W and Huang, X and Yang, X and Yu, Y and Zhang, Z and Hu, Z and Zhou, X and Zhou, K and Liu, Y and Zhang, L},
title = {Characterization of rhizosphere bacterial communities in oilseed rape cultivars with different susceptibility to Plasmodiophora brassicae infection.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1496770},
pmid = {39834703},
issn = {1664-462X},
abstract = {Rhizosphere microbiomes are constantly mobilized during plant-pathogen interactions, and this, in turn, affects their interactions. However, few studies have examined the activities of rhizosphere microbiomes in plants with different susceptibilities to soil-borne pathogens, especially those that cause clubroot disease. In this study, we compared the rhizosphere bacterial community in response to infection of Plasmodiophora brassicae among the four different clubroot susceptibility cultivars of oilseed rape (Brassica napus). Our results revealed obvious differences in the responses of rhizosphere bacterial community to the P. brassicae infection between the four cultivars of oilseed rape. Several bacterial genera that are associated with the nitrogen cycle, including Limnobacter, Thiobacillus, Anaeromyxobacter, Nitrosomonas, Tumebacillus, and Halomonas, showed significantly different changes between susceptible and resistant cultivars in the presence of P. brassicae infection. Moreover, increased connectedness and robustness were exhibited in the rhizosphere bacterial community co-occurrence network in clubroot-susceptible cultivars that were infected with P. brassicae, while only slight changes were observed in clubroot-resistant cultivars. Metagenomic analysis of microbial metabolism also indicated differences in the rhizosphere bacterial community between susceptible and resistant cultivars that were infected with P. brassicae. Functional analysis of the nitrogen cycle showed that genes related to nitrification (nxrB) were upregulated in susceptible cultivars, while genes related to assimilatory nitrate reduction (nasA, narB, and nirA) were upregulated in resistant cultivars that were infected with P. brassicae. These findings indicate that the synthesis and assimilation process of NO3 [-] content were promoted in susceptible and resistant cultivars, respectively. Our study revealed differences in the characteristics of rhizosphere bacterial communities in response to P. brassicae infection between clubroot-susceptible and clubroot-resistant cultivars as well as the potential impact of these differences on the plant-P. brassicae interaction.},
}
@article {pmid39834589,
year = {2025},
author = {D'aes, J and Fraiture, MA and Bogaerts, B and Van Laere, Y and De Keersmaecker, SCJ and Roosens, NHC and Vanneste, K},
title = {Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products.},
journal = {Food chemistry. Molecular sciences},
volume = {10},
number = {},
pages = {100236},
pmid = {39834589},
issn = {2666-5662},
abstract = {Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermentation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final product is not authorized, contaminations occur frequently. Insight into the contamination source of a GMM is of crucial importance to allow the competent authorities to take appropriate action. The aim of this study was to explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and phylogenomic approaches. In most cases, analysis of 16 GMM-contaminated food enzyme products supported finding the same GM producer strains in different products, while often multiple GMM contaminations per product were detected. Presence of AMR genes in the samples was strongly associated with GMM contamination, emphasizing the potential public health risk. Additionally, a variety of other microbial contaminations were detected, identifying a group of samples with a conspicuously similar contamination profile, which suggested that these samples originated from the same production facility or batch. Together, these findings highlight the need for guidelines and quality control for traceability of these products to ensure the safety of consumers. This study demonstrates the added value of metagenomics to obtain insight in the microbial contamination profiles, as well as their underlying relationships, in commercial microbial fermentation products. The proposed approach may be applied to other types of microbial fermentation products and/or to other (genetically modified) producer strains.},
}
@article {pmid39834026,
year = {2025},
author = {Alleman, AB and Stolyar, S and Marx, CJ and Leducq, JB},
title = {Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf011},
pmid = {39834026},
issn = {1751-7370},
abstract = {Although the 16S (and 18S) rRNA gene has been an essential tool in classifying prokaryotes, using a single locus to revise bacteria taxonomy can introduce unwanted artifacts. There was a recent proposition to split the Methylobacterium genus, which contains diverse plant-associated strains and is important for agriculture and biotechnology, into two genera. Resting strongly on the phylogeny of 16S rRNA, 11 species of Methylobacterium were transferred to a newly proposed genus Methylorubrum. Numerous recent studies have independently questioned Methylorubrum as a valid genus, but the prior revision has left discrepancies amongst taxonomic databases. Here, we review phylogenomic and phenotypic evidence against Methylorubrum as a genus and call for its abandonment. Because Methylobacterium sensu lato forms a consistent and monophyletic genus, we argue for the restoration of the former and consensual Methylobacterium taxonomy. The large genomic, phenotypic, and ecological diversity within Methylobacterium however suggests complex evolutionary and adaptive processes and support the description of the most basal clade of Methylobacterium (group C) as a distinct genus in future work. Overall, this perspective demonstrates the danger of solely relying upon the 16S rRNA gene as a delimiter of genus level taxonomy and that further attempts must include more robust phenotypic and phylogenomic criteria.},
}
@article {pmid39833973,
year = {2025},
author = {Rampanelli, E and Romp, N and Troise, AD and Ananthasabesan, J and Wu, H and Gül, IS and De Pascale, S and Scaloni, A and Bäckhed, F and Fogliano, V and Nieuwdorp, M and Bui, TPN},
title = {Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {15},
pmid = {39833973},
issn = {2049-2618},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; Feces/microbiology ; Male ; Lysine/metabolism ; Female ; Fermentation ; Butyrates/metabolism ; Cohort Studies ; Clostridiales/metabolism/classification ; Fructose/metabolism ; Mice, Inbred C57BL ; Middle Aged ; Obesity/microbiology/metabolism ; Probiotics/administration &amp; dosage/metabolism ; Disease Models, Animal ; },
abstract = {BACKGROUND: The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a prevalent commensal bacterium with the unique ability to convert dietary fructoselysine to butyrate, a well-known signaling molecule with proven health benefits. Dietary fructoselysine is an abundant Amadori product formed in foods during thermal treatment and is part of foods rich in dietary advanced glycation end products which have been associated with cardiometabolic disease. It is therefore of interest to investigate the causal role of this bacterium and fructoselysine metabolism in metabolic disorders.<br><br>RESULTS: We assessed associations of I. butyriciproducens with metabolic risk biomarkers at both strain and functional levels using a human cohort characterized by fecal metagenomic analysis. We observed that the level of the bacterial strain as well as fructoselysine fermentation genes were negatively associated with BMI, triglycerides, HbA1c, and fasting insulin levels. We also investigated the fructoselysine degradation capacity within the Intestinimonas genus using a culture-dependent approach and found that I. butyriciproducens is a key player in the butyrogenic fructoselysine metabolism in the gut. To investigate the function of I. butyriciproducens in host metabolism, we used the diet-induced obesity mouse model to mimic the human metabolic syndrome. Oral supplementation with I. butyriciproducens counteracted body weight gain, hyperglycemia, and adiposity. In addition, within the inguinal white adipose tissue, bacterial administration reduced inflammation and promoted pathways involved in browning and insulin signaling. The observed effects may be partly attributable to the formation of the short-chain fatty acids butyrate from dietary fructoselysine, as butyrate plasma and cecal levels were significantly increased by the bacterial strain, thereby contributing to the systemic effects of the bacterial treatment.<br><br>CONCLUSIONS: I.&#xa0;butyriciproducens ameliorates host metabolism in the context of obesity and may therefore be a good candidate for new microbiota-therapeutic approaches to prevent or treat metabolic diseases. Video Abstract.},
}
@article {pmid39833926,
year = {2025},
author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S},
title = {Structure and metabolic function of spatiotemporal pit mud microbiome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {10},
pmid = {39833926},
issn = {2524-6372},
support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; },
abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.<br><br>RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in &#x3b1;- and &#x3b2;-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.<br><br>CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of &#x3b1;-diversity, &#x3b2;-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.},
}
@article {pmid39833778,
year = {2025},
author = {Yang, X and Liu, Z and Liu, X and Li, Q and Huang, H and Wei, Y and Sun, T},
title = {Severe pneumonia due to concurrent Legionella pneumophila and Acinetobacter baumannii infections: a case report.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {29},
pmid = {39833778},
issn = {1471-2466},
support = {2024KY589//Zhejiang Province Medical and Health Science and Technology Plan Project/ ; 2022RKX26//Lishui Municipal Science and Technology Bureau Project/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Acinetobacter baumannii/isolation &amp; purification ; *Legionella pneumophila/isolation &amp; purification ; *Anti-Bacterial Agents/therapeutic use ; *Legionnaires' Disease/diagnosis/drug therapy/complications/microbiology ; *Acinetobacter Infections/drug therapy/diagnosis ; *Tomography, X-Ray Computed ; Community-Acquired Infections/microbiology/drug therapy ; Pneumonia, Bacterial/microbiology/drug therapy/diagnosis/complications ; Coinfection ; Drug Resistance, Multiple, Bacterial ; },
abstract = {BACKGROUND: Legionella pneumophila is an uncommon pathogen causing community-acquired atypical pneumonia. Acinetobacter baumannii is a major pathogen responsible for hospital-acquired pneumonia, but it rarely causes serious infections in a community setting. Without prompt and appropriate treatments, infection from either of these two pathogens can cause a high mortality rate. Concurrent infection from both L. pneumophila and A. baumannii can cause serious outcomes, but it has rarely been reported previously.<br><br>CASE PRESENTATION: A 45-year-old male presented to our hospital with a productive cough and fever after staying in a local hotel. His chest computed tomography (CT) scan showed bilateral lower-lobe infiltration and left pleural effusion. Empirical antibiotics, including piperacillin-tazobactam, levofloxacin, meropenem, and doxycycline, were administered to him to treat community-acquired pneumonia. However, his condition deteriorated very rapidly, and he required endotracheal intubation and mechanical ventilation for respiratory support. Finally, metagenomic next-generation sequencing (mNGS) of his bronchoalveolar lavage fluid identified L. pneumophila and A. baumannii. The sputum culture demonstrated multidrug-resistant A. baumannii. He was diagnosed with pneumonia by concurrent infections from both L. pneumophila and A. baumannii. After careful consideration of the antibiotic susceptibility results and the antibacterial mechanism of each antibiotic, we switched the antibiotics to omadacycline and cefoperazone/sulbactam. His clinical symptoms gradually subsided. The repeat chest CT image showed no infiltration or pleural effusion.<br><br>CONCLUSIONS: Community-acquired pneumonia can be caused by concurrent infections of both L. pneumophila and A. baumannii. Close clinical monitoring, early pathogen detection and antibiotic susceptability tests, and appropriate antibiotic regimen adjustments should be applied to these patients who failed initial antibiotic treatments.},
}
@article {pmid39833544,
year = {2025},
author = {Yan, X and Liu, Y and Hu, T and Huang, Z and Li, C and Guo, L and Liu, Y and Li, N and Zhang, H and Sun, Y and Yi, L and Wu, J and Feng, J and Zhang, F and Jiang, T and Tu, C and He, B},
title = {A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {554-568},
pmid = {39833544},
issn = {2058-5276},
support = {32192423//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32022083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32192424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371562//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Chiroptera/virology ; Animals ; China ; *Metagenome ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; RNA, Viral/genetics ; Humans ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics/methods ; },
abstract = {Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.},
}
@article {pmid39833341,
year = {2025},
author = {Zhang, C and Yu, Y and Yue, L and Chen, Y and Chen, Y and Liu, Y and Guo, C and Su, Q and Xiang, Z},
title = {Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {95},
pmid = {39833341},
issn = {2399-3642},
support = {32171487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31870509//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32400413//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Diet ; Tibet ; RNA, Ribosomal, 16S/genetics ; Colobinae/microbiology ; Macaca mulatta ; Macaca/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.},
}
@article {pmid39833183,
year = {2025},
author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, DL and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Rynearson, T and Huntemann, M and LaButti, K and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Glavina Del Rio, T and Eloe-Fadrosh, EA},
title = {Author Correction: Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {113},
doi = {10.1038/s41597-025-04445-7},
pmid = {39833183},
issn = {2052-4463},
}
@article {pmid39832809,
year = {2025},
author = {Miebach, J and Green, D and Strittmatter, M and Mallinger, C and Le Garrec, L and Zhang, QY and Foucault, P and Kunz, C and Gachon, CMM},
title = {Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {2},
pages = {},
pmid = {39832809},
issn = {1574-6941},
support = {BB/P027806/1//UK Research and Innovation/ ; H2020-BG1-2016//Horizon Europe/ ; //MNHN/ ; },
mesh = {*Microbiota ; *Chlorophyta/microbiology/growth &amp; development ; *Bacteria/genetics/classification/growth &amp; development/isolation &amp; purification ; Ascomycota/genetics/growth &amp; development/physiology ; Metagenomics ; Biological Control Agents ; },
abstract = {Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.},
}
@article {pmid39831119,
year = {2024},
author = {Lenka, J and González-Tortuero, E and Kuba, S and Ferry, N},
title = {Bacterial community profiling and identification of bacteria with lignin-degrading potential in different gut segments of African palm weevil larvae (Rhynchophorus phoenicis).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1401965},
pmid = {39831119},
issn = {1664-302X},
abstract = {The microbiota within the guts of insects plays beneficial roles for their hosts, such as facilitating digestion and extracting energy from their diet. The African palm weevil (APW) lives within and feeds on the high lignin-containing trunk of palm trees; therefore, their guts could harbour a large community of lignin-degrading microbes. In this study, we aimed to explore the bacterial community within the gut of the APW larvae, specifically with respect to the potential for lignin degradation in various gut segments as a first step to determining the viability of mining bacterial lignin-degrading enzymes for the bioconversion of lignocellulosic biomass to biofuels and biomaterials. Bacterial metagenomic DNA was extracted from the foregut, midgut, and hindgut of larvae of the APW, and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. The generated data were analysed and taxonomically classified to identify the different bacterial phylotypes within the gut community cumulatively and per gut segment. We then determined the presence, diversity, and abundance of bacteria associated with lignin degradation within each larval gut compartment as a basis for suggesting the gut segment(s) where lignin degradation occurs the most. All sequences were classified and belonged to the bacterial kingdom. Firmicutes (54.3%) and Proteobacteria (42.5%) were the most dominant phyla within the gut, followed distantly by Bacteroidota (1.7%) and Actinobacteriota (1.4%). Enterococcus, Levilactobacillus, Lactococcus, Shimwellia, Megasphaera, Klebsiella, Pectinatus, Salmonella, Lelliotia, and Enterobacter constituted the most abundant genera found across all gut segments. The foregut and midgut had many similar genera, whilst the hindgut appeared unique. Overall, 29.5% of total gut bacteria comprising 21 genera were lignin degraders found predominantly in the Firmicutes and Proteobacteria phyla (56.8 and 39.5%, respectively), then moderately in Actinobacteriota (2.5%) and Bacteroidota (1.1%). The most abundant ligninolytic genera were Levilactobacillus (46.4%), Klebsiella (22.9%), Enterobacter (10.7%), Lactiplantibacillus (5.9%), Citrobacter (2.2%), Corynebacterium (1.8%), Paucilactobacillus (1.8%), Serratia (1.5%), Bacteroides (1.1%), and Leucobacter (1.0%) found in different amounts in different gut compartments. The foregut had the most diverse and highest abundance of lignin-degrading phylotypes, and we present reasons that point to the foregut as the main location for the depolymerization of lignin in the APW larval gut.},
}
@article {pmid39830903,
year = {2025},
author = {Cambray, GA and Kalinski, JJ},
title = {Microbial Characterization of a Zambian Honey Vinegar.},
journal = {Food science &amp; nutrition},
volume = {13},
number = {1},
pages = {e4549},
pmid = {39830903},
issn = {2048-7177},
abstract = {Forest Fruits Organic Honey Vinegar (FFOHV) is a spontaneously fermented (yeast) and acetified (Acetic Acid Bacteria-AAB) Miombo Woodland honey vinegar developed in Zambia. Live vinegars containing live microbial cultures are marketed for their probiotic health benefits. The correlation between a well-developed gut microbiome and human health is well studied and fermented products such as live vinegar containing AAB contribute to a healthy gut microbiome. This study details a metagenomic analysis of stable, bottled FFOHV (Zambia) alongside two commercially available live vinegar products: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV contained representatives of five bacterial and nine fungal genera, compared to BOACV with two bacterial and five fungal, and NSACV containing no bacterial and six fungal genera. FFOHV and BOACV showed a dominance of Komagataeibacter bacterial species. The dominant yeast was Vanrija humicola present in all three vinegar samples. FFOHV contained greater diversity of genera, with the notable species Monascus purpureus-a microbe that produces several health-enhancing compounds. The analysis showed that FFOHV is a microbially diverse product containing several potentially health-enhancing microbes. Graphical Abstract Text: This study presents a metagenomic analysis of Forest Fruits Organic Honey Vinegar (FFOHV) from Zambia, compared with two commercial live cider vinegars: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV exhibited a richer microbial diversity, containing five bacterial and nine fungal genera, including the health-promoting species Monascus purpureus. Both FFOHV and BOACV were dominated by Komagataeibacter species, with Vanrija humicola as the prevalent yeast across all samples. This confirmed FFOHV's unique potential probiotic benefits.},
}
@article {pmid39830168,
year = {2024},
author = {Zhao, Y and Zhao, M and Zhang, W},
title = {Identification of a novel papillomavirus in oral swabs from giant pandas (Ailuropoda melanoleuca).},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1457471},
pmid = {39830168},
issn = {2297-1769},
abstract = {To fully characterize papillomavirus diversity in giant pandas (Ailuropoda melanoleuca), we identified a novel papillomavirus (named AmPV5, GenBank accession number MZ357114) in oral swabs from giant pandas with the help of viral metagenomics technology in this study. The complete circular genome of AmPV5 is 7,935 bp in length, with a GC content of 39.1%. It encodes five early genes (E1, E2, E4, E6, and E7), two late genes (L1 and L2), and features conserved zinc-binding domains (CXXC- (X)28/29-CXXC) in E6 and E7 genes. E7 protein has an LxCxE domain (pRB binding) in its N-terminal region. The nucleotide sequence of AmPV5 L1 gene shares < 70% identity with other related sequences available in the GenBank database. Phylogenetic analysis indicated that AmPV5 fell within the Lambdapapillomavirus genus but formed a monophyletic branch away from other papillomaviruses found in Ailuropoda melanoleuca, Canis, Felis catus, Panthera uncia, Enhydra lutris, and Procyon lotor. According to the International Committee on Taxonomy of Viruses (ICTV) classification guidelines, AmPV5 is classified as a new species within the Lambdapapillomavirus genus. The discovery provides valuable insights into the viral diversity in giant pandas and highlights the need for continued surveillance of wildlife pathogens. Future studies should explore the potential role of AmPV5 in the health and disease ecology of this endangered species.},
}
@article {pmid39830096,
year = {2025},
author = {Fei, C and Booker, A and Klass, S and Vidyarathna, NK and Ahn, SH and Mohamed, AR and Arshad, M and Glibert, PM and Heil, CA and Martínez Martínez, J and Amin, SA},
title = {Friends and foes: symbiotic and algicidal bacterial influence on Karenia brevis blooms.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae164},
pmid = {39830096},
issn = {2730-6151},
abstract = {Harmful Algal Blooms (HABs) of the toxigenic dinoflagellate Karenia brevis (KB) are pivotal in structuring the ecosystem of the Gulf of Mexico (GoM), decimating coastal ecology, local economies, and human health. Bacterial communities associated with toxigenic phytoplankton species play an important role in influencing toxin production in the laboratory, supplying essential factors to phytoplankton and even killing blooming species. However, our knowledge of the prevalence of these mechanisms during HAB events is limited, especially for KB blooms. Here, we introduced native microbial communities from the GoM, collected during two phases of a Karenia bloom, into KB laboratory cultures. Using bacterial isolation, physiological experiments, and shotgun metagenomic sequencing, we identified both putative enhancers and mitigators of KB blooms. Metagenome-assembled genomes from the Roseobacter clade showed strong correlations with KB populations during HABs, akin to symbionts. A bacterial isolate from this group of metagenome-assembled genomes, Mameliella alba, alleviated vitamin limitations of KB by providing it with vitamins B1, B7 and B12. Conversely, bacterial isolates belonging to Bacteroidetes and Gammaproteobacteria, Croceibacter atlanticus, and Pseudoalteromonas spongiae, respectively, exhibited strong algicidal properties against KB. We identified a serine protease homolog in P. spongiae that putatively drives the algicidal activity in this isolate. While the algicidal mechanism in C. atlanticus is unknown, we demonstrated the efficiency of C. atlanticus to mitigate KB growth in blooms from the GoM. Our results highlight the importance of specific bacteria in influencing the dynamics of HABs and suggest strategies for future HAB management.},
}
@article {pmid39830095,
year = {2025},
author = {Junca, H and Steube, A and Mrowietz, S and Stallhofer, J and Vital, M and Dos Anjos Borges, LG and Pieper, DH and Stallmach, A},
title = {Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae167},
pmid = {39830095},
issn = {2730-6151},
abstract = {Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.},
}
@article {pmid39829898,
year = {2025},
author = {Ni, M and Fan, Y and Liu, Y and Li, Y and Qiao, W and Davey, LE and Zhang, XS and Ksiezarek, M and Mead, E and Touracheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39829898},
issn = {2692-8205},
support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; },
abstract = {The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and enable a single bacterial strain to exhibit variable phenotypic states. Genome-wide and site-specific ePV have been well characterized in human pathogens' antigenic variation and virulence factor production. However, the role of ePV in facilitating adaptation within the human microbiome remains poorly understood. Here, we comprehensively cataloged genome-wide and site-specific ePV in human infant and adult gut microbiomes. First, using long-read metagenomic sequencing, we detected genome-wide ePV mediated by complex structural variations of DNA methyltransferases, highlighting the ones associated with antibiotics or fecal microbiota transplantation. Second, we analyzed an extensive collection of public short-read metagenomic sequencing datasets, uncovering a greater prevalence of genome-wide ePV in the human gut microbiome. Third, we quantitatively detected site-specific ePVs using single-molecule methylation analysis to identify dynamic variations associated with antibiotic treatment or probiotic engraftment. Finally, we performed an in-depth assessment of an Akkermansia muciniphila isolate from an infant, highlighting that ePV can regulate gene expression and enhance the bacterial adaptive capacity by employing a bet-hedging strategy to increase tolerance to differing antibiotics. Our findings indicate that epigenetic modifications are a common and broad strategy used by bacteria in the human gut to adapt to their environment.},
}
@article {pmid39829854,
year = {2025},
author = {Ghazi, AR and Thompson, KN and Bhosle, A and Mei, Z and Yan, Y and Wang, F and Wang, K and Franzosa, EA and Huttenhower, C},
title = {Quantifying Metagenomic Strain Associations from Microbiomes with Anpan.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39829854},
issn = {2692-8205},
support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; },
abstract = {Genetic and genomic variation among microbial strains can dramatically influence their phenotypes and environmental impact, including on human health. However, inferential methods for quantifying these differences have been lacking. Strain-level metagenomic profiling data has several features that make traditional statistical methods challenging to use, including high dimensionality, extreme variation among samples, and complex phylogenetic relatedness. We present Anpan, a set of quantitative methods addressing three key challenges in microbiome strain epidemiology. First, adaptive filtering designed to interrogate microbial strain gene carriage is combined with linear models to identify strain-specific genetic elements associated with host health outcomes and other phenotypes. Second, phylogenetic generalized linear mixed models are used to characterize the association of sub-species lineages with such phenotypes. Finally, random effects models are used to identify pathways more likely to be retained or lost by outcome-associated strains. We validated our methods by simulation, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to alternative methodologies. We then applied our methods to a dataset of 1,262 colorectal cancer patients, identifying functionally adaptive genes and strong phylogenetic effects associated with CRC status, sometimes complementing and sometimes extending known species-level microbiome CRC biomarkers. Anpan's methods have been implemented as a publicly available R library to support microbial community strain and genetic epidemiology in a variety of contexts, environments, and phenotypes.},
}
@article {pmid39829744,
year = {2025},
author = {Tang, G and Carr, AV and Perez, C and Sarmiento, KR and Levy, L and Lampe, JW and Diener, C and Gibbons, SM},
title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39829744},
issn = {2692-8205},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 DK133468/DK/NIDDK NIH HHS/United States ; },
abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, qPCR, or spike-ins (i.e., adding cells or DNA from an organism not normally found in a sample), can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read ratios. We compare B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. We show how B:H ratios can be used to track antibiotic treatment response and recovery in both mice and humans, which showed 403-fold and 45-fold reductions in bacterial biomass during antibiotic treatment, respectively. Our results indicate that host and bacterial metagenomic DNA fractions in human stool fluctuate longitudinally around a stable mean in healthy individuals, and the average host read fraction varies across healthy individuals by < 8-9 fold. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning algorithms, enabling retrospective absolute biomass estimates from existing stool metagenomic data.},
}
@article {pmid39828685,
year = {2025},
author = {Chen, Y and Yi, ZT and Yu, HL and Wu, XY and Wang, JP and Nie, C and Li, H and Li, SH and Yan, QL and He, TW and Chen, MC and Yang, XY and Wen, JY and Lv, LJ},
title = {Does preeclampsia impact the gut microbiota of preterm offspring during early infancy?.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {84},
pmid = {39828685},
issn = {1479-5876},
support = {2019A1515110389//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Pre-Eclampsia/microbiology ; Pregnancy ; Infant, Newborn ; *Infant, Premature ; Adult ; Feces/microbiology ; Biodiversity ; },
abstract = {Preeclampsia (PE) is a pregnancy complication characterized by high blood pressure and organ damage. This study investigates the differences in the gut microbiota between preterm neonates born to mothers with PE and those born to mothers without PE (PR), aiming to understand how maternal health conditions like PE influence neonatal gut microbiota. The early gut microbiota plays a crucial role in neonatal health, and disturbances in its development can have long-term consequences. Fecal samples were collected from preterm neonates of PE and PR mothers at 2 and 6 weeks postpartum and analyzed using shotgun metagenomic sequencing. We found that PE significantly affected the gut microbial composition of preterm neonates, particularly at 2 weeks postpartum. The gut microbial diversity in the PE_2 group was notably lower compared to the PR_2 group, with no significant difference observed between the PR_6 and PE_6 groups. At the phylum level, Firmicutes and Proteobacteria were predominant, with significant differences observed, particularly a lower abundance of Actinobacteria in the PE_2 group. At the genus level, Escherichia, Enterococcus, and Klebsiella were more prevalent in the PE_2 group, whereas Bifidobacterium and Cutibacterium dominated the PR_2 group. The gut virome analysis showed no significant differences among the groups. Functional analysis revealed distinct metabolic pathway activities across the groups, suggesting that early disturbances due to PE impact the establishment of healthy gut microbiota. These findings underscore the substantial influence of maternal health on the early development of the neonatal gut microbiota and highlight the potential long-term health consequences. Additionally, the differences in metabolic pathways further emphasize the impact of preeclampsia on gut microbiota functionality.},
}
@article {pmid39828574,
year = {2025},
author = {Ma, XY and A, XR and Ma, JD and Zhou, JW and Cheng, P and Tang, Y},
title = {[Differential analysis of intestinal flora in patients with hepatic blastomycosis based on second-generation sequencing].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {1},
pages = {101-109},
doi = {10.3760/cma.j.cn112150-20240620-00487},
pmid = {39828574},
issn = {0253-9624},
support = {2022&#x2011;ZJ&#x2011;T01//Qinghai Province 2022 Innovation Platform Construction Special Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Echinococcosis, Hepatic/microbiology ; Metagenomics/methods ; },
abstract = {Exploring the variability of the intestinal flora of patients with hepatic blastocysticercosis and searching for members of the intestinal microflora that may play a role in the disease process by means of macro-genome sequencing technology. A case-control study was used to include fecal samples from patients with hepatic vesicular schistosomiasis admitted to Qinghai Provincial People's Hospital between October 2023 and January 2024 and individuals attending health checkups. The experimental group (AE group) consisted of 10 patients with liver vesicular schistosomiasis and the control group (NC group) consisted of 9 individuals attending health checkups. Macrogenomic sequencing was performed on these two groups of samples using the Illumina Novaseq 6000 sequencing platform, using fastp (v0.20.1) to remove junctions, and bbmap (v38.93-0) to remove the hosted sequences, followed by sequence splicing using MEGAHIT (v1.2.9), and then using prodigal (v2.6.3) to The spliced scaffold was subjected to ORF prediction and translated into amino acid sequences, followed by the construction of a non-redundant gene set using MMSeqs2 (v13.45111), and finally compared with the non-redundant gene set using salmon (v1.8.0). Species were annotated by the non-redundant database, species abundance was calculated in each sample, and the two sets were tested using Wilcoxon rank sum test. Finally, the differences in intestinal flora between the two groups were statistically analyzed using linear discriminant analysis, and the correlation between the differential intestinal flora and clinical indicators was analyzed using redundancy analysis (RDA). The results showed that the effective data volume of each sample was distributed from 10.41 to 12.46 G. The number of ORFs in the de-redundantly constructed gene catalogue (non-redundant gene set) was 4 951 408, and the annotation rate of the non-redundant genes was 97.97% when compared with the NR database. The ages of the study subjects in the two groups were (44.78±4.58) years in the NC group and (42.90±10.44) years in the AE group, and the difference was not statistically significant (t=0.530, P=0.476). The two groups were matched for body mass index (BMI) (t=2.368, P=0.142), gender (χ[2]=0.200, P=0.655), and dietary habits. There was no statistically significant difference in alpha diversity in the AE group (ACE index, t=0.942; chao1 index, t=0.947; shannon index, t=0.813, the simpson's index, t=0.613, P>0.05), while beta diversity analysis showed significant differences in the overall structure of the two communities (Stress=0.054 5). A total of 120 species were annotated at the phylum level, of which two differed. While 1 736 species were annotated at the genus level, 69 were different, and 309 were different at the species level. The AE group ranked the top 6 in terms of abundance of Anaplasma, Escherichiaceae, Clostridium, Alternaria, Ruminalia, and Treponema spp. at the genus level; whereas, Segatella, Prevotella, E. faecalis, Rossella, and beneficial rod-shaped bacteria were more abundant in the NC group. There were differences in the abundance and diversity of intestinal flora between the two groups, and the structure of community composition was significantly different. Statistical results by linear discriminant analysis (LDA) showed that LDA scores >2 in the NC group included beneficial bacillus spp. and E. faecalis spp. in young infants, etc. LDA scores >2 in the AE group at the mid-species level included Clostridium polterococcus, unknown microorganisms in the genus Clostridium intestinalis, Hathaway's Henkett's bacillus, and Clostridium oryzae in the genus Clostridium refractory to culture and small Clostridium spp. in the AE group. Clostridium intestinalis. The RDA results showed a negative correlation between beneficial rod genera and liver function indices, and a positive correlation between Clostridium intestinalis genera and liver function indices. In conclusion, patients with hepatic blastomycosis have altered intestinal flora abundance and diversity, with significant structural changes in community composition and differences in several genera, including Mycobacterium anisopliae and Clostridium intestinalis, and imbalances in the intestinal flora may affect hepatic function by influencing intestinal metabolites and may have an impact on the development of hepatic blastomycosis, a finding that warrants further in-depth study.},
}
@article {pmid39828197,
year = {2025},
author = {Lin, B and Zhang, Y and Hao, Y and Lu, M and Xiang, H and Ding, D and Niu, S and Li, K and Li, J and Huang, Z},
title = {Insights into nitrogen metabolism and humification process in aerobic composting facilitated by microbial inoculation.},
journal = {Environmental research},
volume = {269},
number = {},
pages = {120894},
doi = {10.1016/j.envres.2025.120894},
pmid = {39828197},
issn = {1096-0953},
abstract = {To enhance the retention of compost nutrients, specifically in nitrogen metabolism and humification, compound microbial agents were added during the aerobic composting of bagasse pith and buffalo manure. The introduction of the microbial agent successfully colonized the mixture, boosted the degradation capacity of organic matter, and facilitated the formation of nitrogenous substances and humic substances (HSs). The incorporation of a composite microbial inoculum led to a substantial rise in total Kjeldahl nitrogen (TKN) by 62.04%, nitrate nitrogen (NO- 3-N) by 291.65%, and amino acid (AA) by 78.77%. Furthermore, this intervention resulted in achieving a humic acid (HA) to fulvic acid (FA) ratio of 1.64. Metagenomic sequencing revealed enhanced synergistic interactions among microorganisms through inoculation, increasing the abundance of functional genes related to nitrification and nitrogen fixation compared to the uninoculated control. Spearman correlation analysis identified unclassified_c__Deltaproteobacteria, unclassified_f__Planctomycetaceae, Chryseosolibacter, unclassified_f__Hyphomicrobiaceae as the principal producers of HA. This research provides insights into the interactions between nitrogen metabolism and humification in composting, aiming to effectively retain compost nutrients and support the long-term sustainability of agriculture.},
}
@article {pmid39828044,
year = {2025},
author = {Carluccio, M and Sabatino, R and Borgomaneiro, G and Cesare, AD and Rizzo, L},
title = {Bacterial community dynamics in a biofilm-based process after electro-assisted Fenton pre-treatment of real olive mill wastewater.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132095},
doi = {10.1016/j.biortech.2025.132095},
pmid = {39828044},
issn = {1873-2976},
mesh = {*Biofilms ; *Olea ; *Wastewater/chemistry/microbiology ; *Bacteria ; Iron/pharmacology/chemistry ; Hydrogen Peroxide/pharmacology ; Bioreactors/microbiology ; Water Purification/methods ; Industrial Waste ; Biodegradation, Environmental ; },
abstract = {In this work, the effect of the electro-assisted Fenton (EAF) process on the bacterial community of a moving bed biofilm reactor (MBBR) for olive mill wastewater (OMW) co-treatment with urban wastewater (UWW) was investigated. According to metagenomic analysis, pre-treatment by EAF, while removing total phenols (TPHs) up to 84 % ± 3 % and improving biodegradability of OMW from 0.38 to 0.62, led to the emergence of bacterial genera in the MBBR (R2) that were not detected under conditions without pre-treatment (R1). Indeed, in that condition, Candidatus Competibacter replaced Amaricoccus as dominant denitrifying bacteria. In both cases, the bacterial community composition matched with high simultaneous nitrification-denitrification efficiency (up to 98 %). Finally, Chlorobium (2.5-4.1 %), sulphate-reducing bacteria and Geobacter (up to 1.6 ± 0.4 %), anaerobic bacteria that utilise iron oxides, were observed exclusively with EAF application, suggesting potential for the development of new integrated microbial electrochemical systems.},
}
@article {pmid39827989,
year = {2025},
author = {Cheng, CK and Ye, L and Wang, Y and Wang, YL and Xia, Y and Wong, SH and Chen, S and Huang, Y},
title = {Exercised gut microbiota improves vascular and metabolic abnormalities in sedentary diabetic mice through gut‒vascular connection.},
journal = {Journal of sport and health science},
volume = {},
number = {},
pages = {101026},
doi = {10.1016/j.jshs.2025.101026},
pmid = {39827989},
issn = {2213-2961},
abstract = {BACKGROUND: Exercise elicits cardiometabolic benefits, reducing the risks of cardiovascular diseases and type 2 diabetes. This study aimed to investigate the vascular and metabolic effects of gut microbiota from exercise-trained donors on sedentary mice with type 2 diabetes and the potential mechanism.<br><br>METHODS: Leptin receptor-deficient diabetic (db/db) and nondiabetic (db/m[+]) mice underwent running treadmill exercise for 8 wk, during which fecal microbiota transplantation (FMT) was parallelly performed from exercise-trained to sedentary diabetic (db/db) mice. Endothelial function, glucose homeostasis, physical performance, and vascular signaling of recipient mice were assessed. Vascular and intestinal stresses, including inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, were investigated. RNA sequencing analysis on mouse aortic and intestinal tissues was performed. Gut microbiota profiles of recipient mice were evaluated by metagenomic sequencing.<br><br>RESULTS: Chronic exercise improved vascular and metabolic abnormalities in donor mice. Likewise, FMT from exercised donors retarded body weight gain and slightly improved grip strength and rotarod performance in recipient mice. Exercise-associated FMT enhanced endothelial function in different arteries, suppressed vascular and intestinal stresses, and improved glucose homeostasis in recipient mice, with noted microRNA-181b upregulation in aortas and intestines. Altered gut microbiota profiles and gut-derived factors (e.g., short-chain fatty acids and glucagon-like peptide-1) as well as improved intestinal integrity shall contribute to the cardiometabolic benefits, implying a gut&#x2012;vascular connection.<br><br>CONCLUSION: This proof-of-concept study indicates that exercised microbiota confers cardiometabolic benefits on sedentary db/db mice, extending the beneficial mechanism of exercise through gut&#x2012;vascular communication. The findings open up new therapeutic opportunities for cardiometabolic diseases and shed light on the development of exercise mimetics by targeting the gut microbiota.},
}
@article {pmid39827799,
year = {2025},
author = {Kuroda, K and Yamamoto, K and Isshiki, R and Tokizawa, R and Shiiba, C and Hino, S and Yamano, N and Usui, E and Miyakawa, T and Miura, T and Kamino, K and Tamaki, H and Nakayama, A and Narihiro, T},
title = {Metagenomic and metatranscriptomic analyses reveal uncharted microbial constituents responsible for polyhydroxybutyrate biodegradation in coastal waters.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137202},
doi = {10.1016/j.jhazmat.2025.137202},
pmid = {39827799},
issn = {1873-3336},
abstract = {Polyhydroxybutyrate (PHB) has attracted attention as a representative polymer for biodegradable plastics produced by microorganisms. Since information regarding the fate of PHB released into the environment is limited, it is necessary to identify them based on metagenomic information. We estimated the PHB biodegradability in coastal water samples collected from 15 near shore sites around Japan using oxygen consumption as an indicator in laboratory-scale incubation experiments and conducted 16S rRNA gene-based microbial community profiling. The PHB-biodegradation-rate was significantly positively correlated with the diversity indices of the microbial community in seawater prior to incubation, indicating that seawater with higher diversity is more advantageous for biodegradation. We identified 41 operational taxonomic units exhibiting a significant positive correlation between their abundance and PHB-degradation-rates; these included several microorganisms with hitherto unreported PHB-degrading ability. Next, we analyzed gene expression patterns over incubation time using seawater samples employing metagenomic and metatranscriptomic approaches. Fifty-seven putative extracellular PHB/PHA depolymerase genes were found in 38 metagenomic bins and their expression changed with increasing biodegradation rates, indicating that PHB released into the marine environment is subject to degradation by phylogenetically diverse PHB-depolymerase-producing bacteria. These findings should contribute to expanding the knowledge on degradation of biodegradable plastics by complex marine microbial ecosystems.},
}
@article {pmid39827796,
year = {2025},
author = {He, LX and He, LY and Tang, YJ and Qiao, LK and Xu, MC and Zhou, ZY and Bai, H and Zhang, M and Ying, GG},
title = {Deciphering spread of quinolone resistance in mariculture ponds: Cross-species and cross-environment transmission of resistome.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137198},
doi = {10.1016/j.jhazmat.2025.137198},
pmid = {39827796},
issn = {1873-3336},
abstract = {Mariculture is known to harbor antibiotic resistance genes (ARGs), which can be released into marine ecosystems via oceanic farming ponds, posing a public health concern. In this study, metagenomic sequencing was used to decipher the profiles of quinolone-resistant microbiomes and the mechanisms of quinolone resistance in sediment, seawater, and fish gill samples from five mariculture ponds. Residues of both veterinary-specific (enrofloxacin and sarafloxacin) and prohibited quinolones (ofloxacin, ciprofloxacin, pefloxacin, norfloxacin, and lomefloxacin) were detected. We identified a total of 285 subtypes of ARGs across all samples. Pathogens played a crucial role in the prevalence and distribution of these ARGs. Out of the annotated 629 bacterial species, 42 were identified as pathogenic, predominantly belonging to the Proteobacteria phylum. Notably, the Acinetobacter genus was prevalent in the gills and exhibited correlations with various ARGs. The presence of the plasmid-mediated quinolone resistance (PMQR) genes in various bacterial species and the identification of sulfonamide resistance genes across different samples indicated the potential for cross-species and cross-environment transmission of ARGs. Metagenomic binning revealed that Exiguobacterium harbored five ARGs (vanA, vanB, fexA, msr(G), mefF), while Shewanella carried six ARGs (blaOXA-436, adeF, qacl, ANT (2'')-Ia, dfrA1, rsmA). Mutations in gyrA and parC contributed to quinolone resistance in these multidrug-resistant Exiguobacterium and Shewanella. Our findings suggest a potential for ARG transmission across various bacterial species and environments in mariculture. This study emphasized the risk of resistance spread within the mariculture ecosystem.},
}
@article {pmid39827519,
year = {2025},
author = {Lin, W and Zhao, K and Wu, Q and Xu, F and Cui, L and Lin, H and Ye, C and Yu, X},
title = {Biofilms on pipelines shape the microbiome and antibiotic resistome in drinking water.},
journal = {Water research},
volume = {274},
number = {},
pages = {123136},
doi = {10.1016/j.watres.2025.123136},
pmid = {39827519},
issn = {1879-2448},
abstract = {Biofilms in the drinking water distribution system (DWDS) provide shelter for pathogens and antibiotic resistance genes (ARGs). However, how biofilms alter the microbiome and antibiotic resistome in tap water, as well as the precise quantitative evaluation of their health risks, remains unclear. Herein, biofilm reactors supplied with municipal drinking water were operated for 120 days. Metagenomic sequencing identified significant differences in microbial compositions among the biofilms, influent, and effluents. A total of 69-305 ARGs were detected in this DWDS, and ARG abundances increased in the biofilms (0.246-1.576 cpc) and effluents (0.309-0.503 cpc) compared to the influent (0.131 cpc). Metagenomic assembly pinpointed potential pathogenic ARG hosts such as Acinetobacter, Pseudomonas, and Escherichia. The co-occurrence of ARGs and mobile genetic elements indicated potential mobility, which was further supported by transformation assays demonstrating gene transfers at a frequency of 10[-6]. Furthermore, source tracking revealed that biofilms contributed high proportions (19 %-34 %) to the ARG profiles of effluents. The ARG risk scores increased from the influent (20.39) to the effluents (39.85-55.50), with highest level (55.50) in the cast iron effluent. Overall, this study provides novel insights into the impacts of biofilm growth on the microbiome and antibiotic resistome in tap water, along with their potential health risks in the DWDS.},
}
@article {pmid39827261,
year = {2025},
author = {Guccione, C and Patel, L and Tomofuji, Y and McDonald, D and Gonzalez, A and Sepich-Poore, GD and Sonehara, K and Zakeri, M and Chen, Y and Dilmore, AH and Damle, N and Baranzini, SE and Hightower, G and Nakatsuji, T and Gallo, RL and Langmead, B and Okada, Y and Curtius, K and Knight, R},
title = {Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {825},
pmid = {39827261},
issn = {2041-1723},
support = {R01 CA241728/CA/NCI NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; R01 CA270235/CA/NCI NIH HHS/United States ; AGA Research Scholar Award AGA2022-13-05//AGA Research Foundation/ ; NIH/NIGMS T32GM007198//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R21 HG013433/HG/NHGRI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; CDC award 75D301-22-C-14717//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; NIH Pioneer DP1AT010885//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U19 AG063744/AG/NIA NIH HHS/United States ; NCI U24CA248454//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Metagenomics/methods ; *Genome, Human ; Female ; Male ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome/genetics ; Computational Biology/methods ; Skin/microbiology ; },
abstract = {As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.},
}
@article {pmid39827180,
year = {2025},
author = {Van Goethem, MW and Bezuidt, OKI and Pierneef, R and Vikram, S and Hopkins, DW and Aspray, T and Hall, G and Woodborne, S and Hogg, ID and Northen, TR and Kong, W and Daffonchio, D and Cowan, DA and Van de Peer, Y and Delgado-Baquerizo, M and Makhalanyane, TP},
title = {Novel adaptive immune systems in pristine Antarctic soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2368},
pmid = {39827180},
issn = {2045-2322},
support = {118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Phylogeny ; *CRISPR-Cas Systems ; Microbiota/genetics ; Metagenomics/methods ; Adaptive Immunity/genetics ; Genome, Bacterial ; Bacteria/genetics ; Prophages/genetics ; Metagenome ; },
abstract = {Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.},
}
@article {pmid39827174,
year = {2025},
author = {Peng, Q and Lin, L},
title = {Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {18},
number = {1},
pages = {9},
pmid = {39827174},
issn = {2731-3654},
support = {2023YFC3403500//National Key Research and Development Program of China/ ; 32370115//National Natural Science Foundation of China/ ; },
abstract = {Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This greatly hinders our understanding of the global carbon cycle and the "bottom-up" design of synthetic consortia to enhance lignin conversion. Here, we developed two groups of lignin degrading consortia, L6 and L18, through the 6- and 18-month in situ lignin enrichments in the coastal East China Sea, respectively. Lignin degradation by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. Further comparative metagenomic analysis, based on metagenomic assembly, revealed that L18 harbored abundant metagenome-assembled genomes (MAGs) that encoded diverse and unique lignin degradation gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched in L18, highlighting the role of anaerobic lignin degradation. Furthermore, the generalist taxa, which possess metabolic flexibility, increased during the extended enrichment period, indicating the advantage of generalists in adapting to heterogenous resources. This study advances our understanding of the metabolic strategies of coastal prokaryotic consortia and lays a foundation for the design of synthetic communities for sustainable lignocellulose biorefining.},
}
@article {pmid39827146,
year = {2025},
author = {Angel, NZ and Sullivan, MJ and Alsheikh-Hussain, A and Fang, L and MacDonald, S and Pribyl, A and Wills, B and Tyson, GW and Hugenholtz, P and Parks, DH and Griffin, P and Wood, DLA},
title = {Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {4},
pmid = {39827146},
issn = {1757-4749},
abstract = {BACKGROUND: Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections.<br><br>RESULTS: The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2-100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing.<br><br>CONCLUSIONS: The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions.},
}
@article {pmid39826761,
year = {2025},
author = {Zhou, Z and Liu, S and Saleem, M and Liu, F and Hu, R and Su, H and Dong, D and Luo, Z and Wu, Y and Zhang, Y and He, Z and Wang, C},
title = {Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132081},
doi = {10.1016/j.biortech.2025.132081},
pmid = {39826761},
issn = {1873-2976},
mesh = {*Composting/methods ; *Manure/virology ; Bacteria/genetics ; Metagenome ; Virome ; },
abstract = {The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.},
}
@article {pmid39826760,
year = {2025},
author = {Zhang, Z and Zhang, C and Yang, Y and Zhang, Z and Guo, K and Zhang, X and Qin, Z and Huang, J and Li, Y},
title = {Roles of nitrite in facilitating nitrogen and sulfur conversion in the hybrid bioreactor of Sulfate-reduced ammonium oxidation and anaerobic ammonium oxidation.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132085},
doi = {10.1016/j.biortech.2025.132085},
pmid = {39826760},
issn = {1873-2976},
mesh = {*Bioreactors ; *Sulfur/metabolism ; *Oxidation-Reduction ; *Nitrogen/metabolism ; *Sulfates/metabolism ; Anaerobiosis ; *Nitrites/metabolism ; *Ammonium Compounds/metabolism ; Sewage/microbiology ; },
abstract = {The hybrid bioreactor combining sulfate-reducing ammonium oxidation (Sulfammox) and Anammox offered potential for simultaneous nitrogen and sulfur removal, but the removal efficiency and microbial mechanism remain unclear. This study demonstrated that in the hybrid bioreactor, the ammonium utilization rate (AUR) of Sulfammox increased by 5.42 times. The promotion of NO2[-] on nitrogen and sulfur conversion in Sulfammox could be attributed to: 1) Increasing extracellular polymers substance (EPS) accelerated the stratification of granule sludge; 2) Increasing the relative abundance of Candidatus Brocadia by 29.55 times and Candidatus Anammoxoglobus by 3.17 times; 3) Upregulating the expression of nitrification (amo, hao and nxr) and sulfur metabolism (sat, aprAB dsr and sox) genes, associated with the pathways NH4[+]→NH2OH → NO2[-]→NO3[-] and SO4[2-]→S[2-]→SO4[2-]. Moreover, Candida Brocadia sapporoensis emerged as a potential specie of Sulfammox, mediating nitrification by hao and nxr, and sulfate reduction by sat and aprAB, thereby enabling electron transfer between nitrogen and sulfur.},
}
@article {pmid39826606,
year = {2025},
author = {Hidalgo, KJ and Cueva, LG and Giachini, AJ and Schneider, MR and Soriano, AU and Baessa, MP and Martins, LF and Oliveira, VM},
title = {Long-term microbial functional responses in soil contaminated with biofuel/fossil fuel blends triggered by different bioremediation treatments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {368},
number = {},
pages = {125685},
doi = {10.1016/j.envpol.2025.125685},
pmid = {39826606},
issn = {1873-6424},
abstract = {The use of biofuel blends with fossil fuels is widespread globally, raising concerns over novel contamination types in environments impacted by these mixtures. This study investigates the microbial functional in soils contaminated by biofuel and fossil fuel blends and subjected to various bioremediation treatments. Using metagenomic analysis, it was compared hydrocarbon degradation functional profiles across areas polluted with ethanol/gasoline and biodiesel/diesel blends. Results indicate that long-term natural attenuation areas exhibited distinct functional profiles compared to actively bioremediated areas. However, same hydrocarbon degradation genes were enriched across all areas, highlighting functional redundancy despite taxonomic variation in hydrocarbon-degrading microbes. Finally, several of the keystone species found were hydrocarbon degraders, such as members of the families Clostridiaceae and Comamonadaceae, representing potential targets for biostimulation in future remediation efforts. This long-term, field-scale study uniquely focuses on the functional profiles of microbial communities, offering new insights into the bioremediation of complex biofuel/fossil fuel contaminants in situ.},
}
@article {pmid39826254,
year = {2025},
author = {Oliveira de Farias, B and Saggioro, EM and Montenegro, KS and Magaldi, M and Oliveira Santos, HS and Pimenta, RL and Bianco, K and Clementino, MM},
title = {Degradation of plasmid-mediated resistance genes in poultry slaughterhouse wastewater employing a UV/H2O2 process: A metagenomic approach.},
journal = {Chemosphere},
volume = {372},
number = {},
pages = {144109},
doi = {10.1016/j.chemosphere.2025.144109},
pmid = {39826254},
issn = {1879-1298},
mesh = {Animals ; *Plasmids/genetics ; *Wastewater/microbiology ; *Hydrogen Peroxide ; *Poultry ; *Abattoirs ; *Ultraviolet Rays ; *Escherichia coli/genetics/drug effects ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; },
abstract = {Poultry slaughterhouse effluents are important hotspots for the spread of both antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs), contributing to the antimicrobial resistance (AMR). This study reports a novel investigation to assess the effects of UV/H2O2 treatment on the removal of metaplasmidome-mediated ARGs from poultry slaughterhouse effluents. The effluent samples were subjected at 0.005-0.15 mol L[-1] of H2O2 and pH conditions (3, 5, 7 and 9). Bacterial community (rrs 16S rRNA), Escherichia coli (uidA) antimicrobial resistance (sul1 and int1) and metagenomic plasmid DNA removal were assessed. The UV/H2O2 treatment employing H2O2 = 0.01 mol L[-1] at pH 3 resulted in decreased of several markers (uidA, sul1 and int1). A metaplasmidome indicated the persistence of Burkholderiales order. The UV/H2O2 process reduced plasmid-associated ARGs by 92.5% and 90.4% at pH 3 and 7, respectively. Persistent genes were mainly composed of genes associated with efflux pumps and resistance to beta-lactams and fluoroquinolones. These findings contribute to mitigate the spread of AMR in the agricultural sector, especially through the implementation of more efficient treatments, and reducing the use of antibiotics in livestock farming.},
}
@article {pmid39826029,
year = {2025},
author = {Reuben, RC and Torres, C},
title = {Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {2},
pages = {41},
pmid = {39826029},
issn = {1573-0972},
mesh = {*Milk/microbiology ; Animals ; *Microbiota ; Female ; *Metagenomics/methods ; *Mastitis/microbiology ; Mastitis, Bovine/microbiology ; Proteomics ; Humans ; Cattle ; Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis/microbiology ; },
abstract = {Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis. While single omics studies have undoubtedly contributed to our current understanding of milk microbiome and mastitis, they often provide limited information, targeting only a single biological viewpoint which is insufficient to provide system-wide information necessary for elucidating the biological footprints and molecular mechanisms driving mastitis and milk microbiome dysbiosis. Therefore, integrating a multi-omics approach in milk microbiome research could generate new knowledge, improve the current understanding of the functional and structural signatures of the milk ecosystem, and provide insights for sustainable mastitis control and microbiome management.},
}
@article {pmid39825576,
year = {2025},
author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA},
title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70022},
pmid = {39825576},
issn = {1462-2920},
mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; },
abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.},
}
@article {pmid39824927,
year = {2025},
author = {Prasad, BVV and Atmar, RL and Ramani, S and Palzkill, T and Song, Y and Crawford, SE and Estes, MK},
title = {Norovirus replication, host interactions and vaccine advances.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39824927},
issn = {1740-1534},
support = {P01 AI057788/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; },
abstract = {Human noroviruses (HuNoVs) are the leading cause of acute gastroenteritis worldwide in all age groups and cause significant disease and economic burden globally. To date, no approved vaccines or antiviral therapies are available to treat or prevent HuNoV illness. Several candidate vaccines are in clinical trials, although potential barriers to successful development must be overcome. Recently, significant advances have been made in understanding HuNoV biology owing to breakthroughs in virus cultivation using human intestinal tissue-derived organoid (or enteroid) cultures, advances in structural biology technology combined with epitope mapping and increased metagenomic sequencing. New and unexpected strain-specific differences in pandemic versus non-pandemic virus structures, replication properties and virus-host interactions, including host factors required for susceptibility to infection and pathogenesis, are discussed.},
}
@article {pmid39824780,
year = {2025},
author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S},
title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.},
journal = {Ecology letters},
volume = {28},
number = {1},
pages = {e70064},
doi = {10.1111/ele.70064},
pmid = {39824780},
issn = {1461-0248},
support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 &amp; 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Bacteria/metabolism/genetics ; *Genome, Bacterial ; *Genome Size ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; },
abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.},
}
@article {pmid39824489,
year = {2025},
author = {Yu, Z and Somasundaram, S and Yan, M},
title = {Rumen protozoa and viruses: New insights into their diversity and potential roles through omics lenses-A review.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25780},
pmid = {39824489},
issn = {1525-3198},
abstract = {The rumen microbiome is essential for breaking down indigestible plant material, supplying ruminants with most of their metabolizable energy and protein. While research has primarily focused on bacteria and archaea, protozoa and viruses (phages) have only gained attention in recent years. Protozoa contribute to feed digestion and fermentation, but as predators, they regulate microbial populations by lysing large quantities of microbial cells (the primary protein source for ruminants) and influence the amount of microbial protein reaching the small intestines, along with other mechanisms of interactions. While rumen viruses (or phages) are abundant and diverse, they remain the least understood component of the rumen ecosystem. They can profoundly affect the rumen microbiome by directly lysing their hosts and reprogramming host metabolism through multiple mechanisms, including gene transfer and alteration of central carbon metabolism. Recent advances in omics technologies have deepened our understanding of these viruses, revealing their complex roles in rumen function. This review integrates current knowledge and recent discoveries from omics studies, highlighting the transformative impact of omics-based approaches. It also identifies critical knowledge gaps and outlines future research directions, including selective inhibition of rumen protozoa, development of phages as potential intervention tools to manage specific undesirable rumen microbes, and the causal impacts of rumen viruses on microbial dynamics and animal productivity.},
}
@article {pmid39824262,
year = {2025},
author = {Özdemir, A and Sarzhanov, F and Doğruman-Al, F and Gündoğdu, A and Nalbantoğlu, U and Yozgat, A and Yıldız, BD and Büyüktuncer, Z},
title = {Exploring the complex interplay of Blastocystis, morbid obesity, and bariatric surgery on gut microbial dynamics.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107306},
doi = {10.1016/j.micpath.2025.107306},
pmid = {39824262},
issn = {1096-1208},
abstract = {This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p < 0.05. Postoperative colonization of Blastocystis was observed in previously negative individuals, revealing subtypes and shifts in microbial taxa. Blastocystis-positive participants post-bariatric surgery showed a significant increase in Lachnospira, alongside higher abundances of Bacteroides, Oscillospira, Barnesiellaceae, and Rikenellaceae, with reduced Lactobacillus levels compared to Blastocystis-negative individuals. Collective analysis highlighted higher Clostridiales and RF32 in Blastocystis-positive post-surgery individuals, coupled with decreased Enterobacteriaceae. The study challenges previous notions, suggesting a complex interplay between Blastocystis, morbid obesity, and bariatric surgery. Despite limitations, including small sample sizes and absent gut microbiome diversity comparisons, this pioneering research calls for further investigation into the intricate mechanisms and implications for metabolic health. This study is registered at clinicaltrials.gov (NCT05085769).},
}
@article {pmid39824110,
year = {2025},
author = {Gou, Y and Liu, Y and Hu, A and Mao, G and Dong, R and Li, S and Liu, P and Liu, Y and Ji, M},
title = {Dissemination of genes associated with antibiotic resistance and bacterial virulence during ecosystem succession in two Tibetan glacier forefields.},
journal = {The Science of the total environment},
volume = {963},
number = {},
pages = {178514},
doi = {10.1016/j.scitotenv.2025.178514},
pmid = {39824110},
issn = {1879-1026},
mesh = {*Ice Cover/microbiology ; Tibet ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Virulence/genetics ; Bacteria/genetics ; Virulence Factors/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {The release of pathogens and DNA from the cryosphere (glacier, permafrost, and, sea ice) has become a new threat to society and environment. Due to enhanced glacier retreat, the size of glacier forefields has greatly expanded. Herein, we used a combination of metagenomic and metatranscriptomic methods and adopted a sequence-based approach to investigate the distribution and changing patterns of virulence factor genes (VFGs) and antibiotic resistance genes (ARGs) in two glacier forefields. The forefields are separated by approximately 400 km located in the center and north of the Tibetan Plateau, which are used to demonstrate the gene dissemination capacity across short (10 m) and long (730 m) spatial transects. The results revealed a diverse range of actively transcribed VFGs and ARGs. The relative abundance of ARG reduced with ecosystem succession, while that of VFG was similar, suggesting that the ARG is under a stronger environmental selection pressure. VFGs and ARGs were dominated by those associated with adherence and vancomycin resistance, respectively. Notably, toxin production related genes were identified but a low abundance, indicating a low risk to health in glacier forefields. The dissemination risks were low for both VFGs and ARGs, which was strongly constrained by dispersal limitation. Additionally, the limited dissemination was mainly through vertical transmission, instead of horizontal transfer. In conclusion, the sequence-based approach revealed a low risk to health in recently deglaciated areas, with the risk of VFGs and ARGs being disseminated into downstream ecosystems remaining low.},
}
@article {pmid39824023,
year = {2025},
author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY},
title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.},
journal = {Water research},
volume = {274},
number = {},
pages = {123140},
doi = {10.1016/j.watres.2025.123140},
pmid = {39824023},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.},
}
@article {pmid39823425,
year = {2025},
author = {Wang, F and Wang, X and Duan, J and Yang, S and Wei, J and Yang, S and Zheng, Q},
title = {The impact of straw and its post-pyrolysis incorporation on functional microbes and mineralization of organic carbon in yellow paddy soil.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0314984},
pmid = {39823425},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Soil/chemistry ; *Charcoal/chemistry ; *Fertilizers ; Pyrolysis ; Oryza/growth &amp; development/metabolism ; Carbon Cycle ; China ; },
abstract = {The impact of straw and biochar on carbon mineralization and the function of carbon cycle genes in paddy soil is important for soil nutrient management and the transformation of carbon pools. This research is based on a five-year field experiment with four treatments: no fertilizer application (CK); chemical fertilizer only (NPK); straw combined with chemical fertilizer (NPKS); and biochar combined with chemical fertilizer (NPKB). By integrating indoor mineralization culture with metagenomic approaches, we analyzed the response of organic carbon mineralization and carbon cycle genes in typical paddy soil from Guizhou Province, China, to different fertilization treatments. The result shows that the various fertilization treatments significantly increased the levels of soil organic carbon, dissolved organic carbon, microbial biomass carbon, and readily oxidizable organic carbon. The NPKS treatment increased the rate of soil organic carbon mineralization, whereas the NPKB treatment decreased it. Overall, the NPK and NPKB treatments increased the relative abundance of carbon fixation genes. The NPKS treatment increased the relative abundance of carbon degradation genes. The NPKS treatment increased the abundance of Proteobacteria, whereas the NPKB treatment decreased the abundance of Actinobacteria. Biochar after straw pyrolysis can reduce carbon loss and enhance sequestration of soil carbon, whereas straw decreases soil organic carbon stability, accelerating the transformation of soil carbon pools. Future research should encompass long-term impact assessments to comprehensively understand the enduring effects of these fertilization treatments on soil carbon mineralization and the function of carbon cycle genes.},
}
@article {pmid39823339,
year = {2025},
author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O},
title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadr6070},
pmid = {39823339},
issn = {2375-2548},
mesh = {*Ulva/genetics ; *Salinity ; *Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Metagenomics/methods ; },
abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.},
}
@article {pmid39823337,
year = {2025},
author = {Wu, D and Seshadri, R and Kyrpides, NC and Ivanova, NN},
title = {A metagenomic perspective on the microbial prokaryotic genome census.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2166},
pmid = {39823337},
issn = {2375-2548},
mesh = {*Metagenomics/methods ; *Phylogeny ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Metagenome ; Humans ; Genome, Archaeal ; Genome, Bacterial ; Genome, Microbial ; },
abstract = {Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.},
}
@article {pmid39823335,
year = {2025},
author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS},
title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2583},
pmid = {39823335},
issn = {2375-2548},
mesh = {*Anthozoa/microbiology/metabolism/physiology ; Animals ; *Microbiota ; *Phenotype ; Symbiosis ; Metagenomics/methods ; Bacteria/metabolism/genetics ; },
abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.},
}
@article {pmid39823322,
year = {2025},
author = {Gebert, JT and Scribano, FJ and Engevik, KA and Huleatt, EM and Eledge, MR and Dorn, LE and Philip, AA and Kawagishi, T and Greenberg, HB and Patton, JT and Hyser, JM},
title = {Viroporin activity is necessary for intercellular calcium signals that contribute to viral pathogenesis.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq8115},
pmid = {39823322},
issn = {2375-2548},
support = {F31 DK132942/DK/NIDDK NIH HHS/United States ; S10 OD028480/OD/NIH HHS/United States ; F30 DK131828/DK/NIDDK NIH HHS/United States ; F32 DK130288/DK/NIDDK NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; R01 AI158683/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Rotavirus/pathogenicity ; Mice ; *Viral Nonstructural Proteins/metabolism/genetics ; *Calcium Signaling ; *Rotavirus Infections/virology/metabolism ; Calcium/metabolism ; Humans ; Viroporin Proteins/metabolism/genetics ; Glycoproteins/metabolism/genetics ; Toxins, Biological/metabolism ; Immunity, Innate ; Host-Pathogen Interactions ; Disease Models, Animal ; Cell Line ; },
abstract = {Viruses engage in a variety of processes to subvert host defenses and create an environment amenable to replication. Here, using rotavirus as a prototype, we show that calcium conductance out of the endoplasmic reticulum by the virus encoded ion channel, NSP4, induces intercellular calcium waves that extend beyond the infected cell and contribute to pathogenesis. Viruses that lack the ability to induce this signaling show diminished viral shedding and attenuated disease in a mouse model of rotavirus diarrhea. This implicates nonstructural protein 4 (NSP4) as a virulence factor and provides mechanistic insight into its mode of action. Critically, this signaling induces a transcriptional signature characteristic of interferon-independent innate immune activation, which is not observed in response to a mutant NSP4 that does not conduct calcium. This implicates calcium dysregulation as a means of pathogen recognition, a theme broadly applicable to calcium-altering pathogens beyond rotavirus.},
}
@article {pmid39822514,
year = {2024},
author = {Tan, L and Chen, B and Xu, Y and Wen, Z and Feng, B and Chen, D and Wang, X and Cui, X and Hu, D},
title = {Clinical value of metagenomic sequencing in system evaluation of potential donors and donor-derived infection in kidney transplantation.},
journal = {American journal of translational research},
volume = {16},
number = {12},
pages = {7707-7715},
pmid = {39822514},
issn = {1943-8141},
abstract = {OBJECTIVE: To explore the application and the clinical value of metagenomic sequencing in system evaluation of potential kidney donors, along with donor-derived infection in kidney transplantation.<br><br>METHODS: A prospective study was conducted on 40 voluntary renal donors in Ningbo Urology and Kidney Disease hospital from January 2021 to August 2023. The results of donor pathogen fed back by metagenomic sequencing were analyzed to understand the clinical significance of metagenomic sequencing in donor evaluation.<br><br>RESULTS: (1) Detection rate of pathogens. The probability of pathogens detected by traditional laboratories and metagenomic sequencing was 72.50% and 90.00%, respectively. Compared with traditional laboratory tests, metagenomic sequencing detected significantly more pathogens (P < 0.05). The percentage of co-infection of multiple pathogens detected by traditional laboratory tests (31.03%) in donors was significantly lower than that detected by metagenomic sequencing (88.89%) (P < 0.001). Traditional laboratory tests detected bacteria in 20 donors and fungi in 9 donors, but its performance on detecting viruses and mycoplasmas was limited. Metagenomic sequencing detected bacteria in 30 donors, fungi in 12 donors, viruses in 9 donors, and mycoplasmas in 9 donors. The positive rates of bacteria, viruses and mycoplasmas detected by metagenomic sequencing were significantly higher than those detected by traditional laboratory tests (P < 0.05). (2) Predictive value. The sensitivity, specificity, positive predictive value, and negative predictive value of metagenomic sequencing were 97.30%, 100.00%, 100% and 75.00%, respectively, while those of traditional laboratory tests were 78.39%, 100.00%, 100.00% and 27.27%, respectively. (3) The diagnostic efficiency of metagenomic sequencing was superior to that of traditional laboratory tests. (4) Time needed for result feedback. From specimen collection to the result feedback given to the clinician, the time required for traditional laboratory tests was longer than that for metagenomic sequencing, with significant differences (P < 0.001). In addition, the required time for traditional laboratory tests in detecting bacterial positivity was longer than that for metagenomic sequencing, with a statistically significant difference (P < 0.001).<br><br>CONCLUSION: This study probes into the application of metagenomic sequencing in the evaluation of donor pathogens, especially in negative samples detected by traditional laboratory tests. Our findings suggest that metagenomic sequencing can improve the sensitivity and specificity of diagnosis, increase the detection rate of pathogens, and minimize the turnover time.},
}
@article {pmid39822451,
year = {2024},
author = {Hazan, S and Bao, G and Vidal, A and Sfera, A},
title = {Gut Microbiome Alterations Following Oral Serum-Derived Bovine Immunoglobulin Administration in the Management of Dysbiosis.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e75884},
pmid = {39822451},
issn = {2168-8184},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are chronic disorders of the gastrointestinal tract associated with gut microbiota dysbiosis and inflammation. Serum-derived bovine immunoglobulin (SBI) is used to manage IBS and IBD and has shown prebiotic-like effects in ex vivo models. Re-establishing a healthy gut microbiome with novel treatments like SBI could help treat the underlying causes of these diseases leading to higher and sustained patient response. The objective of this study was to assess whether supplementation with SBI would improve dysbiosis in IBD and IBS patients.<br><br>METHODS: This cross-sectional, single-site study had each participant serving as their own control. Stool samples from 18 patients with either IBS or IBD were analyzed before and after SBI administration. The relative abundance of bacterial diversity was assessed using metagenomic next-generation sequencing-based profiling.<br><br>RESULTS: Species diversity statistically significantly increased for measures of richness (Shannon index) (p < 0.0082) and evenness (Gini-Simpson index) (p&#xa0;< 0.0017). Phylum-level changes showed a 2.7-fold increase in Actinobacteria (p = 0.0181), 0.66-fold decrease in Bacteroidetes (p = 0.0401), and 0.38-fold decrease in Proteobacteria (p = 0.0071) after treatment with SBI. At the genus level, the relative abundances showed decreased Alistipes (p = 0.0121) and decreased Bacteroides (p = 0.0108) as well as increased Bifidobacterium (p = 0.0204), compared to pre-treatment levels. At the genus level, a 1.8-fold increase of Bifidobacterium breve (p = 0.0225) occurred upon treatment with SBI.<br><br>CONCLUSION: These findings confirm the prebiotic effects of SBI and suggest an additional mechanism of action in managing IBD and IBS symptoms. SBI re-establishes homeostasis in patients with IBD and IBS by decreasing Proteobacteria and increasing Bifidobacteria and species diversity. These insights highlight the promise of new therapeutic strategies for managing IBS and IBD by targeting dysbiosis and underscore the potential of personalized treatments based on a patient's gut microbiome profile.},
}
@article {pmid39821458,
year = {2025},
author = {Mathew, DE and Soni, A and Dhimmar, A and Gajjar, A and Parab, AS and Phakatkar, SS and Sahastrabudhe, H and Manohar, CS and Shinde, PB and Mantri, VA},
title = {Characterization, Bio-Prospection, and Comparative Metagenomics of Bacterial Communities Revealing the Predictive Functionalities in Wild and Cultured Samples of Industrially Important Red Seaweed Gracilaria dura.},
journal = {Current microbiology},
volume = {82},
number = {2},
pages = {85},
pmid = {39821458},
issn = {1432-0991},
support = {HCP 024//Council for Scientific and Industrial Research, India/ ; },
mesh = {*Gracilaria/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Phylogeny ; Microbiota ; Seaweed/microbiology ; Metagenome ; Proteobacteria/genetics/isolation &amp; purification/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The present study explores the microbial community associated with the industrially important red seaweed Gracilaria dura to determine the diversity and biotechnological potential through culture and metagenomics approaches. In the first part of the investigation, we isolated and characterized 75 bacterial morphotypes, with varied colony characteristics and metabolic diversity from the wild seaweed. Phylogenetic analysis identified isolates in Proteobacteria, Firmicutes, and Actinobacteria, with Bacillus sp. being prevalent. B. licheniformis and Streptomyces sp. were notable in producing important enzymes like L-asparaginase, and polysaccharide lyases. Antimicrobial activity was significant in 21% of isolates, effective against seaweed pathogens such as Vibrio and Xanthomonas. Rhodococcus pyridinivorans showed strong pyridine degradation, suggesting bioremediation potential. Several isolates exhibited phosphate solubilization and nitrate indicating the roles of bacteria as algal growth promoters and biocontrol agents. Subsequent metagenome analysis of wild and cultured samples provides insights into bacterial communities associated with G. dura, revealing their distribution and functional roles. Proteobacteria (~ 95%) dominated the communities, further bacterial groups involved in algal growth, carpospore liberation, stress resistance, biogeochemical cycles, and biomedical applications were identified. A notable difference in bacteriomes was observed between the samples, with 25% remaining stable. The samples are cultured in the lab to generate seedlings for farming and serve as germplasm storage during the monsoon season. Microbiome surveys are crucial for understanding the association of pathogens and the overall health of the seedlings, supporting successful seaweed farming. Our findings provide valuable insights into G. dura-associated microbial communities and their role in algal growth, which has aquacultural implications.},
}
@article {pmid39821111,
year = {2025},
author = {Mohammed, MM and Sekar, P and Al Jamal, J and Abu Taha, L and Bachir, A and Al Kawas, S},
title = {Comparative analysis of salivary antimicrobial resistance genes in dental students: A PCR and questionnaire study.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0315450},
pmid = {39821111},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Saliva/microbiology ; Adult ; *Students, Dental ; Surveys and Questionnaires ; Young Adult ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is a major global healthcare challenge, with limited treatment options due to the decline in new antibiotics. The human oral cavity, home to diverse bacteria, is crucial for maintaining oral and systemic health. Recent studies suggest that saliva may serve as a reservoir for AMR genes. However, there is a lack of research on this topic in the UAE and most Middle Eastern countries. This study investigated the presence of AMR genes in saliva from forty 5th-year dental students and forty 1st-year dental students.<br><br>MATERIALS &amp; METHODS: Demographic and health information was collected via a 28-question structured questionnaire. Real-Time PCR was used to detect a panel of preselected AMR genes in bacterial DNA from saliva samples.<br><br>RESULTS: Participants' ages ranged from 20 to 31 years, with 41 females and 39 males. The prevalence of AMR genes varied: blaCTX-M grp 1 (29%), blaCTX-M grp 9 (85%), blaCTX-M grp 8 (39%), blaOXA-48 (69%), blaKPC-1 (6%), blaVIM (49%), DHA (53%), ACC (25%), MOX (59%), armA (83%), and rmtB (63%). There were no significant differences in AMR gene prevalence between 5th-year and 1st-year students or between male and female students.<br><br>CONCLUSION: The study revealed a high occurrence of AMR genes in the oral microbiome. Comprehensive metagenomic analysis is recommended to further evaluate the prevalence and relative abundance of these genes in the UAE population. Establishing a database for these ARGs could aid in effective future monitoring.},
}
@article {pmid39820425,
year = {2025},
author = {Huang, H and Cheng, Z and Wang, Y and Qiao, G and Wang, X and Yue, Y and Gao, Q and Peng, S},
title = {Multi-omics dataset of individual variations in growth performance of large yellow croaker.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {90},
pmid = {39820425},
issn = {2052-4463},
mesh = {Animals ; *Perciformes/genetics/growth &amp; development ; *Gastrointestinal Microbiome ; Metabolomics ; Transcriptome ; Metagenomics ; China ; Multiomics ; },
abstract = {Large yellow croaker (Larimichthys crocea) is a highly economically important marine fish species in China. However, substantial individual variations in growth performance have emerged as a limiting factor for the sustainable development of the large yellow croaker industry. Gut microbiota plays a crucial role in fish growth and development by regulating metabolic processes. To explore these dynamics, we employed metagenomics, transcriptomics, and untargeted metabolomics to comprehensively analyze the structure of the intestinal microbiome and its relationship with intestinal metabolism and host gene expression. We constructed association models for "gut microbiota-differentially expressed genes", "differentially expressed genes-metabolites," and "gut microbiota-metabolites." Sequencing data and LC-MS/MS raw data have been deposited in NCBI and MetaboLights databases for public access. Our findings offer critical insights into the molecular mechanisms underlying growth variations in L. crocea and provide valuable data for the selective breeding of improved strains.},
}
@article {pmid39819730,
year = {2025},
author = {Liu, X and Tang, Y and Chen, H and Liu, JX and Sun, HZ},
title = {Rumen DNA virome and its relationship with feed efficiency in dairy cows.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {14},
pmid = {39819730},
issn = {2049-2618},
support = {32322077//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/virology/microbiology ; Cattle ; *Virome ; *High-Throughput Nucleotide Sequencing ; *Animal Feed/virology ; Female ; DNA, Viral/genetics ; Metagenome ; Viruses/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.<br><br>RESULTS: Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P&#x2009;<&#x2009;0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.<br><br>CONCLUSIONS: This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.},
}
@article {pmid39819379,
year = {2025},
author = {Terzin, M and Robbins, SJ and Bell, SC and Lê Cao, KA and Gruber, RK and Frade, PR and Webster, NS and Yeoh, YK and Bourne, DG and Laffy, PW},
title = {Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {11},
pmid = {39819379},
issn = {2049-2618},
mesh = {*Seawater/microbiology ; *Coral Reefs ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics/methods ; *Microbiota/genetics ; Archaea/genetics/classification ; Salinity ; Seasons ; Synechococcus/genetics/classification ; },
abstract = {BACKGROUND: Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.<br><br>RESULTS: Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.<br><br>CONCLUSION: This study reveals that functional information in reef-associated seawater microbes more&#xa0;robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR. Video Abstract.},
}
@article {pmid39818083,
year = {2025},
author = {Pandey, B and Pandey, AK and Bhardwaj, L and Dubey, SK},
title = {Biodegradation of acetaminophen: Current knowledge and future directions with mechanistic insights from omics.},
journal = {Chemosphere},
volume = {372},
number = {},
pages = {144096},
doi = {10.1016/j.chemosphere.2025.144096},
pmid = {39818083},
issn = {1879-1298},
mesh = {*Acetaminophen/metabolism ; *Biodegradation, Environmental ; Humans ; Metabolomics ; Environmental Pollutants/metabolism ; Genomics ; Proteomics ; },
abstract = {Acetaminophen (APAP), one of the most frequently used antipyretic and analgesic medications, has recently grown into a persistent organic contaminant of emerging concern due to its over-the-counter and widespread use. The excessive accumulation of APAP and its derivatives in various environmental matrices is threatening human health and the ecosystem. The complexity of APAP and its intermediates augments the need for adequate innovative and sustainable strategies for the remediation of contaminated environments. Bioremediation serves as an efficient, eco-friendly, cost-effective, and sustainable approach to mitigate the toxic impacts of APAP. The present review provides comprehensive insights into the ecotoxicity of APAP, its complex biodegradation pathways, and the various factors influencing biodegradation. The omics approaches viz., genomics/metagenomics, transcriptomics/metatranscriptomics, proteomics, and metabolomics have emerged as powerful tools for understanding the diverse APAP-degraders, degradation-associated genes, enzymatic pathways, and metabolites. The outcomes revealed amidases, deaminases, oxygenases, and dioxygenases as the lead enzymes mediating degradation via 4-aminophenol, hydroquinone, hydroxyquinol, 3-hydroxy-cis, cis-muconate, etc. as the major intermediates. Overall, a holistic approach with the amalgamation of omics aspects would accelerate the bioaugmentation processes and play a significant role in formulating strategies for remediating and reducing the heavy loads of acetaminophen from the environmental matrices.},
}
@article {pmid39817161,
year = {2024},
author = {Aththanayaka, AMMTB and Dayananda, BSWMTB and Ranasinghe, HAK and Amarasinghe, LD},
title = {Evolution of dirofilariasis diagnostic techniques from traditional morphological analysis to molecular-based techniques: a comprehensive review.},
journal = {Frontiers in parasitology},
volume = {3},
number = {},
pages = {1427449},
pmid = {39817161},
issn = {2813-2424},
abstract = {Dirofilariasis, caused by the nematode Dirofilaria spp., poses significant challenges in diagnosis due to its diverse clinical manifestations and complex life cycle. This comprehensive literature review focuses on the evolution of diagnostic methodologies, spanning from traditional morphological analyses to modern emerging techniques in the context of dirofilariasis diagnosis. The review traces the historical progression of diagnostic modalities, encompassing traditional approaches such as microscopic examination, serological tests (including ELISA and IFA), radiographic imaging, ultrasonography, and necropsy, which laid the foundation for subsequent advancements. The integration of molecular diagnostics marks a significant turning point in dirofilariasis diagnosis with the adoption of polymerase chain reaction (PCR) assays and real-time PCR (qPCR) facilitating enhanced sensitivity and specificity. Furthermore, recent strides in next-generation sequencing (NGS) technologies, including whole-genome sequencing (WGS), targeted sequencing (TS), metagenomic sequencing (MS), and RNA sequencing (transcriptome sequencing), have revolutionized the landscape of dirofilariasis diagnostics. Emerging techniques such as loop-mediated isothermal amplification (LAMP), digital PCR (dPCR), and digital microfluidics are also explored for their potential to augment diagnostic accuracy. The review addresses challenges associated with standardizing molecular protocols, tackling false positives/negatives, and discusses the advantages and limitations of each technique. By providing a comprehensive overview of dirofilariasis diagnostic strategies, from traditional to cutting-edge methods, this review aims to enhance understanding of the disease's diagnostic landscape. The insights gained have implications for improved disease management and guide future research endeavors toward refining diagnostic protocols and advancing therapeutic interventions.},
}
@article {pmid39816454,
year = {2025},
author = {Samanta, A and Sarma, MS},
title = {"Post-Kasai Portoenterostomy Cholangitis: What Have We Learnt So Far?".},
journal = {Journal of clinical and experimental hepatology},
volume = {15},
number = {3},
pages = {102471},
pmid = {39816454},
issn = {0973-6883},
abstract = {Post-Kasai portoenterostomy (KPE) cholangitis is one of the most common complications that has a negative impact on liver function and native liver survival. Early diagnosis and judicious empiric antimicrobial management are, therefore, important to prevent further liver damage and decompensation. However, there is no consensus regarding the standard definition of post-KPE cholangitis, and established guidelines on evaluation and management are also lacking. Metagenomic next-generation sequencing, a new molecular diagnostic technique, has the potential for detecting broader spectrum of pathogens, especially in blood culture-negative patients. Antibiotic prophylaxis to prevent cholangitis has been widely used, but questions over the choice of antibiotics, route of administration, and optimal duration remain unsettled. The available evidence on the efficacy of antibiotic prophylaxis in preventing cholangitis has shown conflicting results. This review offers a summary of the current research on advances in diagnostic approaches, including molecular techniques, and therapeutic challenges in managing intractable cholangitis.},
}
@article {pmid39816362,
year = {2024},
author = {Gong, Z and Ye, G and Xu, S and He, X},
title = {The characteristics of intestinal flora of Tibetan sheep in different regions at high altitude were revealed based on metagenomic technique.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34380},
pmid = {39816362},
issn = {2405-8440},
abstract = {Tibetan sheep play a vital role in the livelihoods of herders and are an important part of the ecosystem of the Tibetan Plateau. In order to study the characteristics of the gut microorganisms of Tibetan sheep at high altitude, this study employed macrogenomic techniques to analyse the diversity and differences in the gut flora of Tibetan sheep in different regions of high altitude and high cold. The results demonstrated that at the phylum level, the dominant phylum in the ileo-cecum segment of Tibetan sheep in Qilian, Henan and Gonghe counties was identical, namely Euryarchaeota, Firmicutes and Ascomycota. At the level of the archaebacterial genus, the dominant bacteria of the ileocecal segment of Tibetan sheep in Qilian County, Henan County and Gonghe County were Methanobrevibacter. At the level of bacterial genus, the dominant bacteria of Tibetan sheep ileocecal in Qilian County and Henan County were Bacteroides, while in Gonghe County, the dominant bacteria were Bifidobacterium. At the level of fungal genus, there were notable differences in the abundance of Tibetan sheep ileocecal genus across different regions. However, the abundance of cecum genus exhibited a more consistent trend across regions. From the perspective of functional prediction, the metabolic pathways enriched in the intestinal segments of Tibetan sheep in different regions were found to be identical, with the relative abundance of each functional gene also being essentially uniform. This result will provide a foundation for further research on the mechanism of action of gut microbes in ruminants at high altitude and alpine regions.},
}
@article {pmid39816186,
year = {2025},
author = {Tian, J and Wang, C and Song, P and You, Z and Jia, X and Li, X and Pang, F},
title = {Predictive Application Value of Metagenomic Next-Generation Sequencing in the Resistance of Carbapenem-Resistant Enterobacteriaceae.},
journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2025},
number = {},
pages = {6619016},
pmid = {39816186},
issn = {1712-9532},
abstract = {Objective: Although metagenomic next-generation sequencing (mNGS) technology has achieved notable outcomes in pathogen detection, there remains a gap in the research regarding its application in predicting the antibiotic resistance of pathogenic bacteria. This study aims to analyze the clinical application value of mNGS in predicting the resistance of carbapenem-resistant Enterobacteriaceae (CRE), as well as the relevant influencing factors, thereby providing valuable insights for clinical antimicrobial therapy. Methods: Nonduplicate isolates of Enterobacterales bacteria collected from Liaocheng People's Hospital from April 2023 to June 2024 were selected, and CRE bacteria were screened. mNGS was used to detect resistance genes, and the results were compared with those of polymerase chain reaction (PCR) to evaluate the specificity and sensitivity of gene detection. Furthermore, the performance of mNGS in identifying pathogenic microorganisms and predicting antibiotic resistance was assessed by comparing the sequencing results with those of antimicrobial susceptibility testing (AST). Results: A total of 46 isolates were confirmed as CRE through traditional AST and were further identified using the Vitek MS and Vitek 2 systems. The results indicated 27 isolates of Klebsiella pneumoniae, 14 isolates of Escherichia coli, 2 isolates of Enterobacter hormaechei, 2 isolates of Enterobacter cloacae, and 1 isolate of Citrobacter freundii. These isolates were subjected to both mNGS and PCR for detection. The calculation of the area under the receiver operating characteristic (ROC) curve demonstrated the reliability of mNGS in detecting resistance genes. Conclusion: mNGS demonstrated high sensitivity in predicting the presence of carbapenemase resistance genes in CRE, showing potential in early indication of isolate resistance information, thereby facilitating timely guidance for clinical treatment strategies.},
}
@article {pmid39816160,
year = {2025},
author = {Kaur, A and Russell, I and Liu, R and Holland, A and Bhandari, R and Potnis, N},
title = {Navigating Host Immunity and Concurrent Ozone Stress: Strain-Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation in Xanthomonas on Pepper.},
journal = {Evolutionary applications},
volume = {18},
number = {1},
pages = {e70069},
pmid = {39816160},
issn = {1752-4571},
abstract = {The evolving threat of new pathogen variants in the face of global environmental changes poses a risk to a sustainable crop production. Predicting and responding to how climate change affects plant-pathosystems is challenging, as environment affects host-pathogen interactions from molecular to the community level, and with eco-evolutionary feedbacks at play. To address this knowledge gap, we studied short-term within-host eco-evolutionary changes in the pathogen, Xanthomonas perforans, on resistant and susceptible pepper in the open-top chambers (OTCs) under elevated Ozone (O3) conditions in a single growing season. We observed increased disease severity with greater variance on the resistant cultivar under elevated O3, yet no apparent change on the susceptible cultivar. Despite the dominance of a single pathogen genotype on the susceptible cultivar, the resistant cultivar supported a heterogeneous pathogen population. Altered O3 levels led to a strain turnover, with a relatively greater gene flux on the resistant cultivar. Both standing genetic variation and de novo parallel mutations contributed toward evolutionary modifications during adaptation onto the resistant cultivar. The presence of elevated O3, however, led to a relatively higher genetic polymorphism, with random and transient mutations. Population heterogeneity along with genetic variation, and the promotion of interdependency are mechanisms by which pathogen responds to stressors. While parallel mutations may provide clues to predicting long-term pathogen evolution and adaptive potential. And, a high proportion of transient mutations suggest less predictable pathogen evolution under climatic alterations. This knowledge is relevant as we study the risk of pathogen emergence and the mechanisms and constraints underlying long-term pathogen adaptation under climatic shifts.},
}
@article {pmid39814151,
year = {2025},
author = {Qiao, X and Zhang, L and Yuan, T and Wu, Y and Geng, Y and Li, Y and Li, B and Zhang, L and Zhuang, WQ and Yu, K},
title = {Mixotrophic anammox bacteria outcompete dissimilatory nitrate reduction and denitrifying bacteria in propionate-containing wastewater.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132077},
doi = {10.1016/j.biortech.2025.132077},
pmid = {39814151},
issn = {1873-2976},
mesh = {*Wastewater/microbiology ; *Denitrification ; *Propionates/metabolism ; *Nitrates/metabolism ; *Oxidation-Reduction ; Bacteria/metabolism ; Nitrogen/metabolism ; Ammonia/metabolism ; Anaerobiosis ; Ammonium Compounds/metabolism ; },
abstract = {Organic carbon can influence nitrogen removal during the anaerobic ammonia oxidation (anammox) process. Propionate, a common organic compound in pretreated wastewater, its impacts on mixotrophic anammox bacteria and the underlying mechanisms have not been fully elucidated. This study investigated the core metabolism and shift in behavior patterns of mixotrophic Candidatus Brocadia sapporoensis (AMXB) under long-term propionate exposure. Genome-resolved metagenomic analysis revealed that AMXB could convert nitrate generated by anammox bacteria to ammonium via the DNRA pathway, leveraging propionate as an electron donor. This recycled ammonium was then used to sustain the anammox process, thereby enhancing nitrogen removal efficiency. Notably, AMXB grew more efficiently than DNRA and denitrifying bacteria due to its more energy-efficient propionate metabolic pathway. This finding suggests that AMXB, as a mixotrophic anammox bacterium, has a competitive advantage in nitrogen metabolism in low C/N wastewater, contributing to efficient nitrogen removal.},
}
@article {pmid39814067,
year = {2024},
author = {Ji, J and Jung, S},
title = {PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {1},
pages = {},
pmid = {39814067},
issn = {1367-4811},
support = {//National Research Foundation of Korea/ ; 2022R1A2C1007345//Korea government/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; Humans ; Metabolomics/methods ; Metabolic Networks and Pathways ; Microbiota/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolome ; Stomach Neoplasms/metabolism/microbiology/genetics ; },
abstract = {MOTIVATION: Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.<br><br>RESULTS: We introduce Predicting Changes in Microbial metaBolites (PredCMB), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene-metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.<br><br>Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.},
}
@article {pmid39813953,
year = {2025},
author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL},
title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109260},
doi = {10.1016/j.envint.2025.109260},
pmid = {39813953},
issn = {1873-6750},
mesh = {*Wastewater/microbiology ; *Airports ; United Kingdom ; Drug Resistance, Bacterial/genetics ; Aircraft ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Metagenomics ; },
abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.},
}
@article {pmid39813930,
year = {2025},
author = {Urbelienė, N and Gasparavičiūtė, R and Vaitekūnas, J and Meškienė, R and Valantinaitė, U and Kruopis, P and Gudiukaitė, R and Meškys, R},
title = {A screening method for polyester films-degrading microorganisms and enzymes.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137177},
doi = {10.1016/j.jhazmat.2025.137177},
pmid = {39813930},
issn = {1873-3336},
abstract = {Enzymatic degradation of plastic pollution offers a promising environmentally friendly waste management strategy, however, suitable biocatalysts must be screened and developed. Traditional screening methods using soluble or solubilised polymers do not necessarily identify enzymes that are effective against solid or crystalline polymers. This study presents a simple, time-saving and cost-effective method for identifying microorganisms and enzymes capable of degrading polymeric films. The method was tested on polycaprolactone (PCL), polyethylene terephthalate (PET), polylactate (PLA) and polyhydroxybutyrate/polyhydroxyvalerate (PHB/PHV) films. It involves two steps: first, screening for PCL diol (PCLD)-degrading microorganisms on agar plates, and second, testing these microorganisms on polyester films. Using this screening method, over 100 PCLD-degrading microorganisms and 27 E. coli clones carrying genomic or metagenomic DNA fragments have been isolated. In addition, recombinant cutinases from Streptomyces scabiei and Thermobifida fusca have been tested. Approximately 66 % of the microorganisms forming halos on PCLD agar plates hydrolysed PCL and 6 % - the biaxially oriented PET film. In addition, five PLA- and four PHB/PHV-degrading esterases have been identified. The proposed method is effective for detecting both wild-type and recombinant microorganisms, as well as recombinant enzymes from in vitro transcription-translation reactions. Screening for thermostable and thermophilic enzymes, including those resistant to organic solvents or environmental inhibitors, is also easily implemented.},
}
@article {pmid39813926,
year = {2025},
author = {Qu, C and Tang, J and Liu, J and Wang, W and Song, F and Cheng, S and Tang, X and Tang, CJ},
title = {Quorum sensing-enhanced electron transfer in anammox consortia: A mechanism for improved resistance to variable-valence heavy metals.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137130},
doi = {10.1016/j.jhazmat.2025.137130},
pmid = {39813926},
issn = {1873-3336},
abstract = {Quorum sensing (QS) is recognized for enhancing bacterial resistance against heavy metals by regulating the production of extracellular substances that hinder metal penetration into the intracellular environment. However, it remains unclear whether QS contributes to resistance by regulating electron transfer, thereby transforming metals from more toxic to less toxic forms. This study investigated the regulatory mechanism of acyl-homoserine lactone (AHL)-mediated QS on electron transfer under As(III) and Cr(VI) stress. Metagenomic binning results revealed that Candidatus Brocadia sinica serves as a major contributor to AHL production for regulating heavy metal resistance, while other symbiotic bacteria offer complementary resistance pathways. In these bacteria, the AHL synthesis gene htdS plays a pivotal role in QS regulation of electron transfer and heavy metal resistance. Experimental findings demonstrated that AHL increased the electron transport system activity by 19.8 %, and upregulated electron transfer gene expression by 1.1- to 6.9-fold. The enhanced electron transfer facilitated a 28.7 % increase in the transformation of As(III) to less toxic As(V) and monomethylarsonic acid, ultimately achieving efficient nitrogen removal under As(III) stress. This study expands our understanding of how QS strengthens bacterial resistance to heavy metals, offering novel strategies for enhancing nitrogen removal of anammox in heavy metal-contaminated environments.},
}
@article {pmid39813892,
year = {2024},
author = {Su, R and Zhao, D and Zhang, X and Zhang, H and Cheng, J and Xu, L and Wu, QL and Zeng, J},
title = {Dissimilatory nitrate reduction pathways drive high nitrous oxide emissions and nitrogen retention under the flash drought in the largest freshwater lake in China.},
journal = {Water research},
volume = {274},
number = {},
pages = {123075},
doi = {10.1016/j.watres.2024.123075},
pmid = {39813892},
issn = {1879-2448},
abstract = {Flash drought (FD) events induced by climate change may disrupt the normal hydrological regimes of floodplain lakes and affect the plant-microbe mediated dissimilatory nitrate reduction (DNR), i.e., denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA), thus having important consequences for nitrous oxide (N2O) emissions and nitrogen (N) retention. However, the responses of the DNR pathways in the floodplain lake to the record-breaking FD in 2022 in Yangtze River of China, as well as the underlying microbial mechanisms and feedbacks to climate change remain poorly understood. Here, we collected exposed sediments and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during 2022 FD and the dry seasons prior to and after this event. The potential DNR rates and the synergistic metabolism of microbial guilds involved in DNR were investigated using [15]N isotope pairing technique, high-throughput and metagenomic sequencing. We found that the in situ N2O fluxes in the littoral wetlands were highest during the flash drought, especially in the exposed sediments. The potential DNRA rates were highest under flash drought conditions, and DNRA dominated the DNR for both exposed sediments (80.4 %) and Carex cinerascens-associated soils (57.5 %). Nutrients (i.e., N and P) and DNRA bacterial communities played a key role in producing the extremely high N2O fluxes from exposed sediments, which could be explained by the synergistic metabolism of DNRA bacteria and denitrifiers through the exchange of the key intermediates in DNR. Therefore, the climate change-induced flash drought promoted greater nitrous oxide emissions and N retention in the littoral wetlands of Poyang Lake, producing a greater flux of greenhouse gas emissions and elevating the risk of lake eutrophication. Hence, flash droughts reinforce a positive feedback between climate change and nitrous oxide emission from these aquatic ecosystems.},
}
@article {pmid39813691,
year = {2024},
author = {Sumboh, JG and Agyenkwa-Mawuli, K and Schwinger, E and Donkor, IO and Akorli, J and Dwomoh, D and Ashong, Y and Osabutey, D and Ababio, FO and Nusbaum, O and Humphries, D and Cappello, M and Koram, KA and Kwofie, SK and Wilson, MD},
title = {Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0384},
pmid = {39813691},
issn = {1476-1645},
abstract = {To identify potential sources of hookworm infections in a Ghanaian community of endemicity that could be targeted to interrupt transmission, we tracked the movements of infected and noninfected persons to their most frequented locations. Fifty-nine participants (29 hookworm positives and 30 negatives) wore GPS trackers for 10 consecutive days. Their movement data were captured in real time and overlaid on a community grid map. Soil samples were collected and divided into two parts: one for determining the physical and chemical properties and the other for culture of helminth larvae. Soil parameters were determined using standard methods, and the number of larvae recovered from Baermann cultures (expressed as larvae per gram of soil) was recorded. We found no significant difference in the larval counts between sites of infected and noninfected participants (P = 0.59). Sandy-loam soil, pH, and effective cation exchange capacity were associated with high larval recovery counts (P <0.001), whereas nitrogen and clay content were associated with low counts (P <0.001). Genomic DNA was extracted from helminth larvae, and species were identified using metagenomic analysis of DNA sequences. The dominant helminth species identified were Panagrolaimus superbus, Parastrongyloides trichosuri, Trichuris trichiura (human whipworm), and Ancylostoma caninum (dog hookworm). Despite Necator americanus being the predominant species in the community, no larvae of this species were identified. This study, however, demonstrates the feasibility of applying molecular tools for identifying environmental factors and places associated with exposure to human and zoonotic helminths, including areas that may be targeted to break transmission in communities where infection is endemic.},
}
@article {pmid39813598,
year = {2025},
author = {Ren, M and Xia, Y and Pan, H and Zhou, X and Yu, M and Ji, F},
title = {Duodenal-jejunal bypass ameliorates MASLD in rats by regulating gut microbiota and bile acid metabolism through FXR pathways.},
journal = {Hepatology communications},
volume = {9},
number = {2},
pages = {},
pmid = {39813598},
issn = {2471-254X},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Rats ; *Bile Acids and Salts/metabolism ; *Duodenum/surgery/metabolism/microbiology ; Male ; *Fecal Microbiota Transplantation ; Jejunum/surgery/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Fatty Liver/metabolism ; Anti-Bacterial Agents/pharmacology ; Diet, High-Fat ; Gastric Bypass ; Insulin Resistance ; },
abstract = {BACKGROUND: Although bariatric and metabolic surgical methods, including duodenal-jejunal bypass (DJB), were shown to improve metabolic dysfunction-associated steatotic liver disease (MASLD) in clinical trials and experimental rodent models, their underlying mechanisms remain unclear. The present study therefore evaluated the therapeutic effects and mechanisms of action of DJB in rats with MASLD.<br><br>METHODS: Rats with MASLD were randomly assigned to undergo DJB or sham surgery. Rats were orally administered a broad-spectrum antibiotic cocktail (Abx) or underwent fecal microbiota transplantation to assess the role of gut microbiota in DJB-induced improvement of MASLD. Gut microbiota were profiled by 16S rRNA gene sequencing and metagenomic sequencing, and bile acids (BAs) were analyzed by BA-targeted metabolomics.<br><br>RESULTS: DJB alleviated hepatic steatosis and insulin resistance in rats with diet-induced MASLD. Abx depletion of bacteria abrogated the ameliorating effects of DJB on MASLD. Fecal microbiota transplantation from rats that underwent DJB improved MASLD in high-fat diet-fed recipients by reshaping the gut microbiota, especially by significantly reducing the abundance of Clostridium. This, in turn, suppressed secondary BA biosynthesis and activated the hepatic BA receptor, farnesoid X receptor. Inhibition of farnesoid X receptor attenuated the ameliorative effects of post-DJB microbiota on MASLD.<br><br>CONCLUSIONS: DJB ameliorates MASLD by regulating gut microbiota and BA metabolism through hepatic farnesoid X receptor pathways.},
}
@article {pmid39812972,
year = {2025},
author = {de Oliveira, RVF and Garrido, LM and Padilla, G},
title = {Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39812972},
issn = {1678-4405},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2015/17177-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
abstract = {Despite meticulous precautions, contamination of genomic DNA samples is not uncommon, which can significantly compromise the analysis of microorganisms' whole-genome sequencing data, thus affecting all subsequent analyses. Thanks to advancements in software and bioinformatics techniques, it is now possible to address this issue and prevent the loss of the entire dataset obtained in a contaminated whole-genome sequencing, where the DNA of another bacterium is present. In this study, it was observed that the sequencing reads from Streptomyces sp. BRB040, generated using the HiSeq System platform (Illumina Inc., San Diego, USA), were contaminated with the DNA of Bacillus licheniformis. To eliminate the contamination in Streptomyces sp. BRB040, a combination of tools available on the Galaxy platform and other web-based resources were used (MeDuSa and Blast). The contaminated reads were treated as a metagenome to isolate the genome of the contaminating organism. They were assembled using the metaSPAdes, resulting in a large scaffold of 4.187 Mb, which was identified as Bacillus licheniformis. After the identification of the contaminating organism, its genome was used as a filter to remove sequencing reads that could align using then Bowtie 2 software for this step. Once the contaminated reads were removed a new assembly was performed using the Unicycler software, yielding 117 contigs with a total size of 7.9 Mb. The completeness of this genome was assessed through BUSCO, resulting in a completeness of 95.9%. We also used an alternative tool (BBduk) to eliminate contaminated reads and the resulting assembly by Unicycler generated 85 contigs with a total size of 8.3 Mb and completeness of 99.5%. These results were better than the assembly obtained via SPAdes, which generated less complete genomes (maximum of 97.8% completeness) compared to Unicycler and which was unable to perform an adequate assembly of the data obtained from decontamination by BBduk. When compared with the uncontaminated BRB040 genome, which has a total size of 8.2 Mb and completeness of 99.8%, this pipeline revealed that the assembly performed with the decontaminated reads via BBduk presented better results, with completeness 0.3% lower than the reference. The genome mining of both genomes using antiSMASH 7.0 revealed the number of 24 Biosynthetic Gene Clusters (BGCs) for BBduk data as well as in the control assembly of the BRB040. In silico decontamination process allows the genome mining of BGCs despite the loss of nucleotides. These findings show that contamination can be effectively removed from a genome using readily available online tools, while preserving a dataset suitable for extracting valuable insights into the secondary metabolism of the target organism. This approach is particularly beneficial in scenarios where resequencing samples is not immediately feasible.},
}
@article {pmid39812647,
year = {2025},
author = {Selami, N and Zitouni-Haouar, FE and Zerouki, C and Aibeche, C and Draou, N and Khelil, O and Choubane, S and Maatallah, M and Madani, I and Ouenzar, K and Zemmour, A and Kerkoud, M and Mnasri, B and Moumen, B and Vriet, C and Djabeur, A},
title = {Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006646},
pmid = {39812647},
issn = {1466-5034},
mesh = {*Pseudomonas/genetics/isolation &amp; purification/classification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Algeria ; *DNA, Bacterial/genetics ; *Nucleic Acid Hybridization ; *Endophytes/genetics/isolation &amp; purification/classification ; *Multilocus Sequence Typing ; *Sequence Analysis, DNA ; *Bacterial Typing Techniques ; *Root Nodules, Plant/microbiology ; *Base Composition ; Genome, Bacterial ; Fatty Acids ; },
abstract = {A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5[T] strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5[T] had the highest similarity to Pseudomonas granadensis LMG27940[T] (98.94%) and Pseudomonas gozinkensis IzPS32d[T] (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5[T] in a distinct branch alongside its closest relative, P. granadensis LMG27940[T]. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5[T] and its close relationship with P. granadensis LMG27940[T]. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940[T]. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5[T] represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5[T] belongs to a unique evolutionary line. The genome of RB5[T], with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5[T] strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5[T] includes C16:0, C17:0 cyclo and the summed features 3 consisting of C16:1 ω7c/C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5[T] was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5[T] (=DSM 117471[T]=LMG 33633[T]=CIP 112482[T]).},
}
@article {pmid39812555,
year = {2025},
author = {Bell, PT and Baird, T and Goddard, J and Olagoke, OS and Burke, A and Subedi, S and Davey, TR and Anderson, J and Sarovich, DS and Price, EP},
title = {Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0196024},
pmid = {39812555},
issn = {2165-0497},
support = {2021-04-CRG//Wishlist (Wishlist Inc.)/ ; AQIRF0362018//State of Queensland | Advance Queensland (AdvanceQld)/ ; AQIRF095-2020-CV//State of Queensland | Advance Queensland (AdvanceQld)/ ; },
mesh = {Humans ; Prospective Studies ; Male ; Female ; *Bacteria/genetics/isolation &amp; purification/classification ; Aged ; Middle Aged ; *Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; Pleural Effusion/microbiology/diagnosis ; Bacterial Infections/diagnosis/microbiology ; Feasibility Studies ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Pleural Diseases/diagnosis/microbiology ; Aged, 80 and over ; },
abstract = {Pleural infections are common and associated with substantial healthcare costs, morbidity, and mortality. Accurate diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Here, we undertook a prospective study examining the feasibility and performance of molecular methods for diagnosing suspected pleural infection. We prospectively characterized 26 consecutive clinically suspected pleural infections, and 10 consecutive patients with suspected non-infective pleural effusions, using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture. Molecular methods exhibited excellent diagnostic performance, with each method identifying 54% (14 out of 26) positive cases among the pleural infection cohort, versus 38% (10 out of 26) with culture. Metagenomics and bacterial metataxonomics unveiled complex polymicrobial infections that were not captured by culture. Dominant microbes included streptococci (Streptococcus intermedius, Streptococcus pyogenes, and Streptococcus mitis), Prevotella spp. (Prevotella oris and Prevotella pleuritidis), staphylococci (S. aureus and S. saprophyticus), and Klebsiella pneumoniae. However, we encountered challenges that complicated pleural infection interpretation, including: (i) uncertainties regarding microbial pathogenicity and the impact of prior antibiotic therapy on diagnostic performance; (ii) lack of a clinical diagnostic gold-standard for molecular performance comparisons; (iii) potential microbial contamination during specimen collection or processing; and (iv) difficulties distinguishing background microbial noise from true microbial signal in low-biomass specimens. This pilot study demonstrates the potential utility and value of molecular methods in diagnosing pleural infection and highlights key concepts and challenges that should be addressed when designing larger prospective trials.IMPORTANCEConfident pleural infection diagnosis is often challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Limitations of conventional diagnostic tests result in prolonged and inappropriately broad-spectrum antimicrobial use, encouraging antimicrobial resistance and leading to avoidable adverse effects. Here, we demonstrate the feasibility, utility, and challenges associated with the use of culture-independent molecular techniques for accurate pleural infection diagnosis in a real-world clinical setting. These data will help to inform the design of larger prospective clinical trials and identify potential obstacles to be overcome before next-generation sequencing technologies can be integrated into routine clinical practice.},
}
@article {pmid39812347,
year = {2025},
author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL},
title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2447815},
pmid = {39812347},
issn = {1949-0984},
support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/pathology ; *Dextran Sulfate ; Mice ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Female ; Specific Pathogen-Free Organisms ; Feces/microbiology ; Inflammatory Bowel Diseases/microbiology ; Male ; },
abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.},
}
@article {pmid39810418,
year = {2025},
author = {Yu, H and Liu, S and Zhang, D and Hu, R and Chen, P and Liu, H and Zhou, Q and Tan, W and Hu, N and He, Z and Ding, D and Yan, Q},
title = {Specific Enrichment of arsM-Carrying Microorganisms with Nitrogen Fixation and Dissimilatory Nitrate Reduction Function Enhances Arsenic Methylation in Plant Rhizosphere Soil.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {3},
pages = {1647-1660},
doi = {10.1021/acs.est.4c10242},
pmid = {39810418},
issn = {1520-5851},
mesh = {*Arsenic/metabolism ; *Rhizosphere ; *Nitrogen Fixation ; *Soil Microbiology ; *Nitrates/metabolism ; Methylation ; Soil Pollutants/metabolism ; Soil/chemistry ; },
abstract = {Plants can recruit microorganisms to enhance soil arsenic (As) removal and nitrogen (N) turnover, but how microbial As methylation in the rhizosphere is affected by N biotransformation is not well understood. Here, we used acetylene reduction assay, arsM gene amplicon, and metagenome sequencing to evaluate the influence of N biotransformation on As methylation in the rhizosphere of Vetiveria zizanioides, a potential As hyperaccumulator. V. zizanioides was grown in mining soils (MS) and artificial As-contaminated soils (AS) over two generations in a controlled pot experiment. Results showed that the content of dimethylarsinic acid in the rhizosphere was significantly positively correlated with the rate of N fixation and the activity of nitrite reductase. The As-methylating species (e.g., Flavisolibacter and Paraflavitalea) were significantly enriched in the root-associated compartments in the second generation of MS and AS. Notably, higher abundance of genes involved in N fixation (nifD, nifK) and dissimilatory nitrate reduction to ammonium (narG/H, nirB/D/K/S) was detected in the second generation of MS than in the first generation. The metabolic pathway analysis further demonstrated that N fixing-stimulative and DNRA-stimulative As-methylating species could provide ammonium to enhance the synthesis of S-adenosyl-l-methionine, serving as methyl donors for soil As methylation. This study highlights two important N conversion-stimulative As-methylating pathways and has important implications for enhancing phytoremediation in As-contaminated soils.},
}
@article {pmid39810263,
year = {2025},
author = {Nychas, E and Marfil-Sánchez, A and Chen, X and Mirhakkak, M and Li, H and Jia, W and Xu, A and Nielsen, HB and Nieuwdorp, M and Loomba, R and Ni, Y and Panagiotou, G},
title = {Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {10},
pmid = {39810263},
issn = {2049-2618},
mesh = {*Non-alcoholic Fatty Liver Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Machine Learning ; Metagenomics/methods ; Adult ; Obesity/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.<br><br>RESULTS: Here, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis. We identified highly specific microbiome signatures through building accurate machine learning models (accuracy&#x2009;=&#x2009;0.845-0.917) for NAFLD with high portability (generalizable) and low prediction rate (specific) when applied to other metabolic diseases, as well as through a community approach involving differential co-abundance ecological networks. Moreover, using these signatures coupled with further mediation analysis and metabolic dependency modeling, we propose synergistic defined microbial consortia associated with NAFLD phenotype in overweight and lean individuals, respectively.<br><br>CONCLUSION: Our study reveals robust and highly specific NAFLD signatures and offers a more realistic microbiome-therapeutics approach over individual species for this complex disease. Video Abstract.},
}
@article {pmid39810145,
year = {2025},
author = {Xiang, H and Zhang, L and Yang, L and Cai, M and Ma, Y and Zhang, Y},
title = {Asymptomatic lung abscess of aspergillus in a female without previous lung diseases or immunocompromise: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {66},
pmid = {39810145},
issn = {1471-2334},
support = {BRWEP2024W042180101//Beijing Research Ward Excellence Program/ ; },
mesh = {Humans ; Female ; Adult ; *Lung Abscess/microbiology/drug therapy/diagnosis ; *Aspergillus/isolation &amp; purification/genetics ; *Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy ; *Antifungal Agents/therapeutic use ; Tomography, X-Ray Computed ; Voriconazole/therapeutic use ; Lung/microbiology/diagnostic imaging/pathology ; },
abstract = {BACKGROUND: Chronic pulmonary abscess usually results from bacterial or mycobacterium infection, but rarely from aspergillosis. Chronic pulmonary aspergillosis is usually found in a person with structural lung disease or immunocompromise. Here, we report a case of chronic lung abscess of aspergillosis without immunocompromise, structural lung diseases or even clinical symptoms.<br><br>CASE PRESENTATION: A 43-year-old female was found a mass shadow with central liquid anechoic area in the apical posterior segment of the left upper lung lobe by chest computerized tomography for 1 month, but had no any systematic or respiratory complaints. The percutaneous abscess puncture was performed and 30 milliliters of yellow purulent fluid were aspirated from the liquid anechoic area. Then Aspergillus terreus was detected by both fluid culture and metagenomics next-generation sequencing. Interestingly, this patient had no history of tuberculosis or chronic pulmonary diseases. Other immunocompromised conditions were also denied through history inquest and laboratory tests. Ultimately, the catheterization and drainage of the lung abscess and 6 months of antifungal therapy with standard dose of voriconazole brought the woman a favorable outcome.<br><br>CONCLUSION: Aspergillus lung abscess can occasionally occur in a person without pre-existent lung cavity and immune suppression, which is prone to misdiagnosis because of the rarity and the symptom-free.},
}
@article {pmid39809974,
year = {2025},
author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB},
title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.},
journal = {Nature metabolism},
volume = {7},
number = {1},
pages = {16-34},
pmid = {39809974},
issn = {2522-5812},
mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology ; Risk Factors ; Prevalence ; Metabolomics ; Multiomics ; },
abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.},
}
@article {pmid39809928,
year = {2025},
author = {Lai, LM and Chen, QG and Liu, Y and Zhao, R and Cao, ML and Yuan, L},
title = {The value of metagenomic next-generation sequencing in the diagnosis of fever of unknown origin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1963},
pmid = {39809928},
issn = {2045-2322},
support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 2021B723//the Science and Technology Program of Jiangxi Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Fever of Unknown Origin/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Retrospective Studies ; Middle Aged ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Adolescent ; Metagenome ; Aged, 80 and over ; },
abstract = {Fever of unknown origin (FUO) caused by infection is a disease state characterized by complex pathogens and remains a diagnostic dilemma. Metagenomic next-generation sequencing (mNGS) technology is a promising diagnostic tool for identifying pathogenic microbes of FUO caused by infection. Little is known about the clinical impact of mNGS in the etiological diagnosis of FUO. This study focuses on the value of mNGS in the etiologic diagnosis of FUO by diagnostic performance, further clarifying the value of mNGS in clinical management. In a single-centre retrospective cohort study, 263 FUO patients who underwent both mNGS and culture at the First Affiliated Hospital of Nanchang University were enrolled from December 2020 to February 2023. The sensitivity and specificity of culture and mNGS were analyzed based on the final clinical diagnosis as the gold standard to assess the diagnostic value of mNGS in FUO cases. Among the 263 patients, 69.96%(184/263) cases were diagnosed as infectious diseases, of which lower respiratory tract infections were the most common, accounting for 53.26%(98/184). 30.04%(79/263) cases had a diagnosis of non-infectious disease. From these cases, mNGS identified 150 true-positive cases, 21 false-positive cases, 58 true-negative cases, and 34 false-negative cases. The sensitivity of mNGS in infection diagnosis was much higher than that of culture [81.52%(150/184) vs. 47.28%(87/184)], but the specificity was the opposite[73.42%(58/79) vs. 84.81%(67/79)]. mNGS had a receiver operating characteristic (ROC) curve of 0.775 for infectious disease, which was significantly higher than that of culture (0.661, P < 0.05). mNGS detection revealed that bacteria were the most commonly identified potential pathogens. The top causative pathogens identified were Acinetobacter baumannii. Of the 263 patients with FUO, clinical management of 48.67% (128/263) patients was positively affected by mNGS, and 51.33% (135/263) patients were not affected by mNGS(P = 0.1074). To sum up, infectious diseases are the principal cause of FUO. mNGS could significantly improve the detected pathogen spectrum of FUO caused by infection. However, the FUO disease spectrum is relatively broad, including a large number of non-infectious diseases. Therefore, Further investigation is warranted into the specific clinical scenarios for which mNGS may offer the greatest clinical diagnostic value.},
}
@article {pmid39809768,
year = {2025},
author = {Fahur Bottino, G and Bonham, KS and Patel, F and McCann, S and Zieff, M and Naspolini, N and Ho, D and Portlock, T and Joos, R and Midani, FS and Schüroff, P and Das, A and Shennon, I and Wilson, BC and O'Sullivan, JM and Britton, RA and Murray, DM and Kiely, ME and Taddei, CR and Beltrão-Braga, PCB and Campos, AC and Polanczyk, GV and Huttenhower, C and Donald, KA and Klepac-Ceraj, V},
title = {Early life microbial succession in the gut follows common patterns in humans across the globe.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {660},
pmid = {39809768},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Feces/microbiology ; Female ; Metagenome ; Male ; Bifidobacterium/genetics/isolation &amp; purification ; Infant, Newborn ; Faecalibacterium prausnitzii/genetics ; Child Development ; },
abstract = {Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that may be used alongside other measures of child development.},
}
@article {pmid39809763,
year = {2025},
author = {Armetta, J and Li, SS and Vaaben, TH and Vazquez-Uribe, R and Sommer, MOA},
title = {Metagenome-guided culturomics for the targeted enrichment of gut microbes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {663},
pmid = {39809763},
issn = {2041-1723},
support = {NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; no. ALTF 137-2018//European Molecular Biology Organization (EMBO)/ ; no. GNT1166180//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics/drug effects ; Humans ; *Metagenome ; *Phylogeny ; Culture Media/chemistry ; Bacteria/genetics/metabolism/classification ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Caffeine ; },
abstract = {The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.},
}
@article {pmid39809266,
year = {2025},
author = {Wang, D and Jiang, Y and Jiang, J and Pan, Y and Yang, Y and Fang, X and Liang, L and Li, H and Dong, Z and Fan, S and Ma, D and Zhang, XS and Li, H and He, Y and Li, N},
title = {Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia.},
journal = {Cell reports. Medicine},
volume = {6},
number = {1},
pages = {101919},
doi = {10.1016/j.xcrm.2024.101919},
pmid = {39809266},
issn = {2666-3791},
mesh = {*Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/metabolism/microbiology/genetics ; *gamma-Aminobutyric Acid/metabolism ; Humans ; Animals ; Female ; Male ; Mice ; Child ; Child, Preschool ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Escherichia/metabolism/genetics ; Feces/microbiology ; Glutamic Acid/metabolism ; Mice, Inbred C57BL ; Escherichia coli/genetics/metabolism ; Metabolome ; },
abstract = {Gut microbiota (GM) alterations have been implicated in autism spectrum disorder (ASD), yet the specific functional architecture remains elusive. Here, employing multi-omics approaches, we investigate stool samples from two distinct cohorts comprising 203 children with mild ASD or typical development. In our screening cohort, regression-based analysis for metabolomic profiling identifies an elevated γ-aminobutyric acid (GABA) to glutamate (Glu) ratio as a metabolic signature of ASD, independent of age and gender. In the validating cohort, we affirm the GABA/Glu ratio as an ASD diagnostic indicator after adjusting for geography, age, gender, and specific food-consuming frequency. Integrated analysis of metabolomics, 16S rRNA sequencing, and metagenomics reveals a correlation between overrepresented Escherichia and disrupted GABA metabolism. Furthermore, we observe social behavioral impairments in weaning mice transplanted with E. coli, suggesting a potential link to ASD symptomatology. Collectively, these findings provide insights into potential diagnostic and therapeutic strategies aimed at evaluating and restoring gut microbial neurotransmitter homeostasis.},
}
@article {pmid39809157,
year = {2024},
author = {Xu, H and Liu, Y and Niu, H and Cai, X and Zhan, F},
title = {Characteristics, symptoms, and outcomes of patients with Vibrio vulnificus infection in Hainan, China: A retrospective study.},
journal = {Medicine},
volume = {103},
number = {47},
pages = {e40706},
pmid = {39809157},
issn = {1536-5964},
mesh = {Humans ; Male ; *Vibrio Infections/epidemiology/diagnosis/therapy ; Female ; Retrospective Studies ; Middle Aged ; China/epidemiology ; Aged ; *Vibrio vulnificus/isolation &amp; purification ; Adult ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {With global temperatures on the rise and an expanding seafood trade, infections by Vibrio vulnificus, particularly in warm coastal areas like Hainan, China, are increasingly prevalent. These bacteria are notorious for causing grave infections with a high fatality rate. This study aims to dissect the clinical features, laboratory findings, treatment modalities, and patient outcomes associated with V vulnificus infections in Hainan Province. The medical records and clinical data of intensive care unit patients from Hainan General Hospital were retrospectively analyzed. Conventional sequencing and metagenomic sequencing were used to identify V vulnificus. The study involved 10 patients (9 males and 1 female) with a median age of 60.5 years, predominantly fishermen, with infections mainly occurring between May and October. Of note, 2 cases were linked to plant-related injuries. The typical manifestations included fever, pain, swelling, hemorrhagic vesicles, septic shock, and multi-organ dysfunction. It was found that delayed hospital admissions were associated with elevated Sequential Organ Failure Assessment and Acute Physiology and Chronic Health Evaluation II scores and increased mortality. Laboratory results indicated a robust inflammatory response, and interventions comprised antibiotic therapy and surgical procedures. A mortality rate of 50% was recorded. Vigilance for V vulnificus infections is crucial in coastal locales. The study endorses immediate and assertive treatment strategies, including the use of targeted antibiotics and surgical interventions, to enhance patient survival rates. A call for heightened awareness, intensified surveillance, and expanded research is essential to combat this life-threatening condition.},
}
@article {pmid39808116,
year = {2024},
author = {Zárate, A and Díaz-González, L and Taboada, B},
title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39808116},
issn = {1477-4054},
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Viral Proteins/genetics ; Humans ; Viruses/genetics/classification ; Genome, Viral ; Animals ; Eukaryota/genetics ; Artificial Intelligence ; Metagenome ; Algorithms ; },
abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.},
}
@article {pmid39807898,
year = {2025},
author = {Forry, SP and Servetas, SL and Dootz, JN and Hunter, ME and Kralj, JG and Filliben, JJ and Jackson, SA},
title = {A sensitivity analysis of methodological variables associated with microbiome measurements.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0069624},
pmid = {39807898},
issn = {2165-0497},
mesh = {*Metagenomics/methods ; *Feces/microbiology ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; DNA, Bacterial/genetics ; },
abstract = {The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, and reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of data sets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.IMPORTANCEMethod-specific bias is a well-recognized challenge in metagenomic sequencing characterization of microbiome samples, but rigorous bias quantification is challenging. This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. Quantification of the biases associated with each parameter revealed similar magnitudes of variation arising from real biological differences and from varied analysis procedures. Furthermore, these measurement biases varied substantially with taxa, even between closely related genera. However, computational correction of method bias using a reference material was demonstrated that significantly harmonized metagenomic sequencing results collected using different analysis protocols.},
}
@article {pmid39807869,
year = {2025},
author = {Sáenz, JS and Rios-Galicia, B and Seifert, J},
title = {Antiviral defense systems in the rumen microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0152124},
doi = {10.1128/msystems.01521-24},
pmid = {39807869},
issn = {2379-5077},
abstract = {The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the "pan-immune system" model, which appears to be common across different environments.},
}
@article {pmid39807864,
year = {2025},
author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS},
title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.},
journal = {mBio},
volume = {16},
number = {2},
pages = {e0373224},
pmid = {39807864},
issn = {2150-7511},
support = {R01 CA154426/CA/NCI NIH HHS/United States ; //Cancer Research UK (CRUK)/ ; R01CA154426//HHS | NIH | National Cancer Institute (NCI)/ ; },
mesh = {Humans ; *Virulence Factors/genetics ; *Colorectal Neoplasms/microbiology/genetics/pathology ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Fusobacterium/genetics/pathogenicity/metabolism ; Multigene Family ; Genome, Bacterial ; Lectins/genetics/metabolism ; Fusobacteria/genetics/metabolism/pathogenicity ; },
abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.},
}
@article {pmid39807156,
year = {2025},
author = {Song, H and Tithi, SS and Brown, C and Aylward, FO and Jensen, R and Zhang, L},
title = {Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18515},
pmid = {39807156},
issn = {2167-8359},
mesh = {*Genome, Viral/genetics ; *Metagenomics/methods ; *Software ; Contig Mapping/methods ; Molecular Sequence Annotation/methods ; Computational Biology/methods ; },
abstract = {Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform depth of coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprover annotates the gene content of the resulting sequence. Results show that Virseqimprover has good performances on correcting and extending viral contigs to their full lengths, hence can be a useful tool to improve the completeness and minimize the assembly errors of viral contigs. Both a web server and a conda package for Virseqimprover are provided to the research community free of charge.},
}
@article {pmid39807079,
year = {2025},
author = {Björnberg, A and Nestor, D and Peker, N and Sinha, B and Couto, N and Rossen, J and Sundqvist, M and Mölling, P},
title = {Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {1},
pages = {e13511},
pmid = {39807079},
issn = {1600-0463},
mesh = {Humans ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *DNA, Bacterial/genetics/blood ; Bacteremia/diagnosis/microbiology ; Reproducibility of Results ; },
abstract = {Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation. Results showed that bacterial reads were higher in WB than plasma. Differences for Staphylococcus aureus and Streptococcus pneumoniae were more pronounced compared to Escherichia coli. Plasma samples exhibited better method reproducibility, with more consistent droplet digital PCR results for human DNA. The study found that extraction was more efficient for Gram-positive bacteria than Gram-negative, suggesting that the human DNA depletion exerts a negative effect on Gram-negative bacteria. Overall, shotgun metagenomics needs further optimisation to improve bacterial DNA recovery and enhance pathogen detection sensitivity. This study highlights some critical steps in the methodology of shotgun metagenomic-based diagnosis of blood stream infections using Nanopore sequencing.},
}
@article {pmid39806507,
year = {2025},
author = {Zhang, D and Cao, Y and Dai, B and Zhang, T and Jin, X and Lan, Q and Qian, C and He, Y and Jiang, Y},
title = {The virome composition of respiratory tract changes in school-aged children with Mycoplasma pneumoniae infection.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {10},
pmid = {39806507},
issn = {1743-422X},
support = {No. Q202342//Scientific Research Program of Wuxi Health Commission/ ; No. 32201990//National Natural Science Foundation of China/ ; No. BK20210461//Natural Science Foundation of Jiangsu Province of China/ ; No. SBQN22013//Hospital-level project of Northern Jiangsu People's Hospital/ ; },
mesh = {Humans ; Child ; *Virome ; Male ; Female ; *Mycoplasma pneumoniae/genetics/isolation &amp; purification/classification ; *Pneumonia, Mycoplasma/epidemiology/microbiology/virology ; Viruses/classification/isolation &amp; purification/genetics ; Metagenomics ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Respiratory System/virology/microbiology ; COVID-19/virology/epidemiology ; Respiratory Tract Infections/virology/microbiology/epidemiology ; Adolescent ; },
abstract = {BACKGROUND: Mycoplasma pneumoniae (MP) is a common pathogen for respiratory infections in children. Previous studies have reported respiratory tract microbial disturbances associated with MP infection (MPI); however, since the COVID-19 pandemic, respiratory virome data in school-aged children with MPI remains insufficient. This study aims to explore the changes in the respiratory virome caused by MPI after the COVID-19 pandemic to enrich local epidemiological data.<br><br>METHODS: Clinical samples from 70 children with MPI (70 throat swab samples and 70 bronchoalveolar lavage fluid (BALF) samples) and 78 healthy controls (78 throat swab samples) were analyzed using viral metagenomics. Virus reads were calculated and normalized using MEGAN.6, followed by statistical analysis.<br><br>RESULTS: Principal Coordinate Analysis (PCoA) showed that viral community diversity is a significant difference between disease cohorts and healthy controls. After MPI, the number of virus species in the upper respiratory tract (URT) increased obviously, and the abundance of families Poxviridae, Retroviridae, and Iridoviridae, which infect vertebrates, rose evidently, particularly the species BeAn 58,085 virus (BAV). Meanwhile, phage alterations in the disease cohorts were predominantly characterized by increased Myoviridae and Ackermannviridae families and decreased Siphoviridae and Salasmaviridae families (p&#x2009;<&#x2009;0.01). In addition, some new viruses, such as rhinovirus, respirovirus, dependoparvovirus, and a novel gemykibvirus, were also detected in the BALF of the disease cohort.<br><br>CONCLUSIONS: This cross-sectional research highlighted the respiratory virome characteristics of school-aged children with MPI after the COVID-19 outbreak and provided important epidemiological information. Further investigation into the impact of various microorganisms on diseases will aid in developing clinical treatment strategies.},
}
@article {pmid39806455,
year = {2025},
author = {Liu, Z and Yao, X and Chen, C and Zhao, Y and Dong, C and Sun, L and Zhao, J and Zhang, B and Yu, Z and Cheng, D and Zhu, L and Hu, B},
title = {Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {8},
pmid = {39806455},
issn = {2049-2618},
support = {22206166//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 2020YFC1806903//National Key Research and Development Program of China/ ; 2023M733056//China Postdoctoral Science Foundation awards the fellowship/ ; ES202118//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute and Technology/ ; 2022HT0025//Zhejiang Province Ecological Environment Research and Results Promotion Project/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Metagenomics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Oxytetracycline/pharmacology ; Soil/chemistry ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.<br><br>RESULTS: Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10&#xa0;mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5&#xa0;mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.<br><br>CONCLUSION: The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.},
}
@article {pmid39806416,
year = {2025},
author = {Chen, L and Ye, Z and Li, J and Wang, L and Chen, Y and Yu, M and Han, J and Huang, J and Li, D and Lv, Y and Xiong, K and Tian, D and Liao, J and Seidler, U and Xiao, F},
title = {Gut bacteria Prevotellaceae related lithocholic acid metabolism promotes colonic inflammation.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {55},
pmid = {39806416},
issn = {1479-5876},
support = {81873556//National Natural Science Foundation of China/ ; 82170546//National Natural Science Foundation of China/ ; CCCF-QF-2022B67-3//China Crohn's &amp; Colitis Foundation/ ; 2023B02//Tongji Hospital Fund/ ; },
mesh = {Animals ; *Lithocholic Acid/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Colitis/microbiology/pathology/chemically induced/metabolism ; Humans ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Male ; Inflammation/pathology ; Feces/microbiology ; Female ; Colon/pathology/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Inflammatory Bowel Diseases/microbiology/pathology/metabolism ; Mice ; Signal Transduction ; Middle Aged ; },
abstract = {BACKGROUND: The conversion of primary bile acids to secondary bile acids by the gut microbiota has been implicated in colonic inflammation. This study investigated the role of gut microbiota related bile acid metabolism in colonic inflammation in both patients with inflammatory bowel disease (IBD) and a murine model of dextran sulfate sodium (DSS)-induced colitis.<br><br>METHODS: Bile acids in fecal samples from patients with IBD and DSS-induced colitis mice, with and without antibiotic treatment, were analyzed using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). The composition of the microbiota in fecal samples from IBD patients and DSS-colitis mice was characterized via Illumina MiSeq sequencing of the bacterial 16S rRNA gene V3-V4 region. Metagenomic profiling further identified metabolism-related gene signatures in stool samples from DSS-colitis mice. Histological analysis, quantitative PCR (qPCR) and Western Blotting were conducted on colonic samples from DSS-induced colitis mice to assess colonic inflammation, mucosal barrier integrity, and associated signaling pathways. The multivariate analysis of bile acids was conducted using Soft Independent Modelling of Class Analogy (SIMCA, Umetrics, Sweden). The relation between the relative abundance of specific phyla/genera and bile acid concentration was assess through Spearman's correlation analyses. Finally, lithocholic acid (LCA), the key bile acid, was administered via gavage to evaluate its effect on colonic inflammation and mucosal barrier integrity.<br><br>RESULTS: In patients with IBD, the composition of colonic bile acids and gut microbiota was altered. Moreover, changes in the gut microbiota further modulate the composition of bile acids in the intestine. As the gut microbiota continues to shift, the bile acid profile undergoes additional alterations. The aforementioned alterations were also observed in mice with DSS-induced colitis. The study revealed a correlation between dysbiosis of the gut microbiota and modifications in the profile of colonic bile acids, notably LCA observed in both patients with IBD and mice with DSS-induced colitis. Through multivariate analysis, LCA was identified as the key bile acid that significantly affects colonic inflammation and the integrity of mucosal barrier. Subsequent experiments confirmed that LCA supplementation effectively mitigated the inhibitory effects of gut microbiota on colitis progression in mice, primarily through the activation of the sphingosine-1-phosphate receptor 2 (S1PR2)/NF-&#x3ba;B p65 signaling pathway. Analysis of the microbiome and metagenomic data revealed changes in the gut microbiota, notably an increased abundance of an unclassified genus within the family Prevotellaceae in DSS-induced colitis mice. Furthermore, a positive correlation was observed between the relative abundance of Prevotellaceae and bile acid biosynthesis pathways, as well as colonic LCA level.<br><br>CONCLUSIONS: These findings suggest that LCA and its positively correlated gut bacteria, Prevotellaceae, are closely associated with intestinal inflammation. Targeting colonic inflammation may involve inhibiting LCA and members of the Prevotellaceae family as potential therapeutic strategies.},
}
@article {pmid39806046,
year = {2025},
author = {Sun, L and Liu, X and Zhou, L and Wang, H and Lian, C and Zhong, Z and Wang, M and Chen, H and Li, C},
title = {Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {46},
pmid = {39806046},
issn = {2399-3642},
support = {42276153, 42106134, 42106100, 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Mytilus/microbiology/genetics/immunology ; *Transcriptome ; *Microbiota ; Metagenomics ; Symbiosis/genetics ; Adaptation, Physiological/genetics ; Seawater/microbiology ; Metagenome ; },
abstract = {Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.},
}
@article {pmid39805953,
year = {2025},
author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C},
title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {313-331},
pmid = {39805953},
issn = {2058-5276},
mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; *Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/genetics/growth &amp; development ; Drug Resistance, Bacterial/genetics ; Mutation ; Escherichia coli/drug effects/genetics/growth &amp; development ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Acinetobacter baumannii/drug effects/genetics/growth &amp; development ; Klebsiella pneumoniae/drug effects/genetics/growth &amp; development ; Drug Resistance, Multiple, Bacterial/genetics ; Gram-Negative Bacteria/drug effects/genetics ; },
abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.},
}
@article {pmid39805403,
year = {2025},
author = {Wolf, PG and Welsh, C and Binion, B and Dai, H and Oliveira, ML and Hamm, A and Goldberg, S and Buobu, PS and Schering, T and Vergis, S and Kessee, N and Gomez, SL and Yazici, C and Maienschein-Cline, M and Byrd, DA and Gaskins, HR and Ridlon, JM and Mutlu, E and Greening, C and Tussing-Humphreys, L},
title = {Secondary Bile Acid Derivatives Are Contributors to the Fecal Bile Acid Pool and Associated With Bile Acid-Modulating Nutrients.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.12.035},
pmid = {39805403},
issn = {1541-6100},
abstract = {BACKGROUND: Accumulation of hydrophobic bile acids (BAs) is linked with cancer development. However, derivatives of deoxycholic acid (DCA) and lithocholic acid (LCA) produced via bacterial metabolism may mitigate the proinflammatory and cytotoxic effects of hydrophobic BAs. The impact of diet on secondary BA derivative production has not been determined.<br><br>OBJECTIVES: This study aimed to study the associations between BA-modulating nutrients and the composition of secondary BAs and their derivatives.<br><br>METHODS: Stool and blood were collected from 138 participants aged 45-75 y that self-identified as Black or non-Hispanic White. BAs were extracted from stool and serum and quantified using LC/ESI-MS/MS. Energy, macronutrients, micronutrients, and specific dietary nutrients were estimated from two 24-h diet recalls. The abundance of genes for microbial BA metabolism was assessed from stool metagenomes. Kendall &#x3c4; correlation and regression-based modeling were performed to determine associations between BA categories, microbial genes, and select energy-adjusted dietary variables (alcohol, calcium, coffee, fiber, fat, and protein).<br><br>RESULTS: Participants had a mean age of 60 y and a mean BMI of 31 kg/m[2]. BA derivatives were present in all participant stools, with lagodeoxycholic acid being the most abundant derivative quantified. Analysis of stool microbial metagenomes revealed the presence of genes for secondary BA derivative production in all participants. Protein is positively associated with the accumulation of secondary BAs. monounsaturated fatty acids (MUFA)s were negatively associated with high abundant derivatives of DCA in regression models. Total fiber and coffee intake were positively correlated with increased conversion of BAs to derivatives. Race and smoking status were significant predictors of associations between dietary variables and BA derivatives.<br><br>CONCLUSION: Protein, MUFAs, total fiber and coffee are significantly associated with concentrations of secondary BAs and their derivatives. Future work should account for social and structural influences on dietary intake and its relationship with BA-elicited cancer risk.},
}
@article {pmid39805250,
year = {2024},
author = {Bortoluzzi, C and Ghanbari, M and Gonzáles, JC and Bohórquez, JO and Paredes, R and Mauri, Y and Lozano-Poveda, CA},
title = {Precision biotic as an effective replacement of hydrolyzed yeast and butyrate in antibiotic free diets of broiler chickens raised under field conditions.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104664},
pmid = {39805250},
issn = {1525-3171},
abstract = {A total of 1,436,000 Ross 380 AP broiler chicks were included in the experiment, which was conducted in two cycles with 20 houses per cycle and 35,900 birds per house. The objective was to evaluate, under field conditions, the impact of a precision biotic (PB) on the growth performance and cecal microbiome of broiler chickens, in comparison to enzymatically hydrolyzed yeast (EHY) and butyrate (BT) in an antibiotic-free diet. Each cycle consisted of six (6) houses under PB supplementation, and 14 houses under the regular dietary program used by the integration. Body weight (BW), feed intake (FI), and feed conversion ratio (FCR) were assessed at processing age, ranging from 39 to 45 d. Birds had ad libitum access to water and feed. On day 29, cecal content from 7 birds per house (42 birds per treatment) were collected for microbiome analysis by applying shotgun metagenomics approach. The performance data were analyzed by ANCOVA, house was considered as the experimental unit for growth performance (n = 20; P < 0.05), and the bird for microbiome analysis (n = 84; P < 0.05). Both treatment groups performed below the strain target in terms of BW, but better in terms of FCR. There were no significant differences (P > 0.05) between both groups on the growth performance, indicating that PB effectively replaced EHY and BT without compromising growth. However, significant functional changes were observed in the microbiome of birds fed PB, with enrichment in the pathways related to carbon and nitrogen metabolism. These changes were associated with an increased carbon metabolism index (P = 0.05), which can lead to higher endogenous short-chain fatty acids (SCFAs) production. Overall, by potentially increasing SCFA production by the intestinal microbiome, PB supported the growth performance of chickens similar to that achieved with EHY and BT.},
}
@article {pmid39805166,
year = {2025},
author = {Memon, FU and Zhu, Y and Cui, Y and Feng, X and Ahmad, S and Zeng, P and Nabi, F and Hao, D and Huang, Z and Tettamanti, G and Tian, L},
title = {Gut microbial communities and transcriptional profiles of black soldier fly (Hermitia illucens) larvae fed on fermented sericulture waste.},
journal = {Waste management (New York, N.Y.)},
volume = {194},
number = {},
pages = {158-168},
doi = {10.1016/j.wasman.2025.01.011},
pmid = {39805166},
issn = {1879-2456},
abstract = {Sericulture waste poses significant challenges to industrial and environmental safety. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect protein. This study aimed to develop a microbial fermented method for utilizing sericulture waste to feed BSFL and explore the underlying mechanisms. Our results showed that all fermented sericulture waste groups had positive effects on body weight, survival rate, substrate consumption rate, and substrate conversion rate. Metagenomic analysis revealed a notable increase in the abundances of commensal genera, including Sedimentibacter, Clostridium, Enterococcus, Bacteroides, and Bacillus, in the gut of BSFL fed on sericulture waste fermented with the most effective combination of microbial strains (B. subtilis, B. licheniformis, and E. faecalis). In contrast, BSFL reared on unfermented sericulture waste exhibited higher abundances of potentially pathogenic and harmful genera, including Providencia, Klebsiella, Escherichia, Brucella, and Enterobacter. Clusters of orthologous genes (COG) analysis indicated that altered microbial communities in the fermented group mainly participated in metabolic pathways, defense mechanism, and signal transduction mechanism. Transcriptome analysis further revealed that the upregulated genes were functionally associated with key metabolic pathways and immune mechanisms in the fermented group. These findings underscore the pivotal role of selected microbial fermentation in utilizing sericulture waste as BSFL feed, providing a sustainable solution for organic waste management.},
}
@article {pmid39805015,
year = {2025},
author = {Chuckran, PF and Estera-Molina, K and Nicolas, AM and Sieradzki, ET and Dijkstra, P and Firestone, MK and Pett-Ridge, J and Blazewicz, SJ},
title = {Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {3},
pages = {e2413032122},
pmid = {39805015},
issn = {1091-6490},
support = {SCW1632//U.S. Department of Energy (DOE)/ ; DE-SC0020163//U.S. Department of Energy (DOE)/ ; DE-SC0016247//U.S. Department of Energy (DOE)/ ; SCW1589//U.S. Department of Energy (DOE)/ ; SCW1421//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/growth &amp; development ; *Codon Usage ; *Soil/chemistry ; *Genome Size ; Metagenome ; Codon/genetics ; Genome, Bacterial ; Transcription, Genetic ; Nucleotides/genetics ; },
abstract = {In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with [18]O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.},
}
@article {pmid39804694,
year = {2025},
author = {Puller, V and Plaza Oñate, F and Prifti, E and de Lahondès, R},
title = {Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.},
journal = {Microbial genomics},
volume = {11},
number = {1},
pages = {},
pmid = {39804694},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Computer Simulation ; Benchmarking ; Bacteria/classification/genetics ; Metagenomics/methods ; Microbiota/genetics ; },
abstract = {Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not to customize databases but to translate results to a common reference to use the tools with their native environment. Specifically, we conducted two realistic simulations of gut microbiome samples, each based on a specific taxonomic profiler, and used two different taxonomic references to project their results, namely the Genome Taxonomy Database and the Unified Human Gastrointestinal Genome. To demonstrate the importance of using such a framework, we evaluated four established profilers as well as the impact of the simulations and that of the common taxonomic references on the perceived performance of these profilers. Finally, we provide guidelines to enhance future profiler comparisons for human microbiome ecosystems: (i) use or create realistic simulations tailored to your biological context (BC), (ii) identify a common feature space suited to your BC and independent of the catalogues used by the profilers and (iii) apply a comprehensive set of metrics covering accuracy (sensitivity/precision), overall representativity (richness/Shannon) and quantification (UniFrac and/or Aitchison distance).},
}
@article {pmid39804671,
year = {2025},
author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV},
title = {Long-term climate establishes functional legacies by altering microbial traits.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39804671},
issn = {1751-7370},
mesh = {*Soil Microbiology ; *Carbon Cycle ; *Metagenomics ; Soil/chemistry ; Droughts ; Climate ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Microbiota ; Climate Change ; Seasons ; Carbon/metabolism ; },
abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.},
}
@article {pmid39804518,
year = {2025},
author = {Claytor, JD and Lin, DL and Magnaye, KM and Guerrero, YS and Langelier, CR and Lynch, SV and El-Nachef, N},
title = {Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {39804518},
issn = {1573-2568},
abstract = {BACKGROUND: Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods.<br><br>AIM: We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis.<br><br>METHODS: We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT.<br><br>RESULTS: All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P&#x2009;=&#x2009;0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO.<br><br>CONCLUSION: Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.},
}
@article {pmid39804408,
year = {2025},
author = {Macdonald, JFH and Han, Y and Astafyeva, Y and Bergmann, L and Gurschke, M and Dirksen, P and Blümke, P and Schneider, YKH and Alawi, M and Lippemeier, S and Andersen, JH and Krohn, I},
title = {Exploring Tetraselmis chui microbiomes-functional metagenomics for novel catalases and superoxide dismutases.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {6},
pmid = {39804408},
issn = {1432-0614},
support = {AquaHealth FKZ 031B0945C//Bundesministerium f&#xfc;r Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {*Superoxide Dismutase/genetics/metabolism ; *Metagenomics ; *Antioxidants/metabolism ; *Catalase/metabolism/genetics ; *Microbiota ; Microalgae/genetics/enzymology ; Chlorophyta/genetics/enzymology ; Bacteria/genetics/enzymology/classification/isolation &amp; purification ; },
abstract = {The focus on microalgae for applications in several fields, e.g. resources for biofuel, the food industry, cosmetics, nutraceuticals, biotechnology, and healthcare, has gained increasing attention over the last decades. In this study, we investigate the microbiome of the cultured microalga Tetraselmis chui (T. chui) to highlight their potential for health benefits. In this context, biomolecules like antioxidants play a crucial role in the well-being of living organisms as they metabolise harmful reactive oxygen species (ROS) to reduce oxidative stress. Impaired processing of ROS leads to damaged cells and increases the risk of cancer, inflammatory diseases, and diabetes, among others. Here, we identify, characterise, and test bacterial antioxidants derived from the T. chui microbiome metagenome dataset. We identified 258 genes coding for proteins with potential antioxidant activity. Of those, four novel enzymes are expressed and identified as two superoxide dismutases (SOD), TcJM_SOD2 and TcIK_SOD3, and two catalases (CAT), TcJM_CAT2 and TcIK_CAT3. Extensive analyses characterised all implemented enzymes as active even in concentrations down to 25 ng*ml[-1] for the SODs and 15 ng*ml[-1] for the CATs. Furthermore, sequence-based analyses assign TcJM_SOD2 and TcIK_SOD3 to iron superoxide dismutases (Fe SODs) and TcJM_CAT2 and TcIK_CAT3 to heme-containing catalases. These candidates are phylogenetically classified within the phylum Pseudomonadota. Regarding the biotechnological potential, a toxicity assay did not indicate any harmful effects. The introduced enzymes may benefit medical applications and expand the potential of microalgae microbiomes. KEY POINTS: • Omics-based discoveries of antioxidant enzymes from Tetraselmis chui microbiome • Two superoxide dismutases and two catalases are identified and tested for activity • Enzyme sensitivity highlights biotechnological potential of microalgae microbiomes.},
}
@article {pmid39803536,
year = {2025},
author = {Kettenburg, G and Ranaivoson, HC and Andrianianina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Picornaviridae and Caliciviridae diversity in Madagascar fruit bats is driven by cross-continental genetic exchange.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.31.630946},
pmid = {39803536},
issn = {2692-8205},
abstract = {Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Divergent Caliciviridae and Picornaviridae (families within the Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Bats live in close proximity to and are consumed widely as a food source by humans in Madagascar, providing opportunities for zoonotic transmission. Prior work in Madagascar has described numerous evolutionarily divergent bat viruses, some with zoonotic potential. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum , Pteropus rufus , and Rousettus madagascariensis), we recovered 13 full-length and 37 partial-length genomic sequences within the order Picornavirales (36 Picornaviridae and 14 Caliciviridae sequences), which we identify and describe here. We find evidence that genetic exchange between mainland African bat and Madagascar bat Picornavirales likely shaped the diversification patterns of these novel sequences through recombination events between closely related Picornavirales ; thus far, high host fidelity appears to have limited these viruses from spilling over into other species.},
}
@article {pmid39803511,
year = {2024},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Protists as mediators of complex microbial and viral associations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39803511},
issn = {2692-8205},
support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; },
abstract = {Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments. Our findings reveal unique microbiome compositions and hint at an intricate network of complex interactions and associations with bacterial symbionts and viruses. We observed stark differences between ciliates and amoebae in terms of microbiome and virome compositions, highlighting the specificity of protist-microbe interactions. Over 115 of the recovered microbial genomes were affiliated with known endosymbionts of eukaryotes, including diverse members of the Holosporales, Rickettsiales, Legionellales, Chlamydiae, Dependentiae , and more than 250 were affiliated with possible host-associated bacteria of the phylum Patescibacteria. We also identified more than 80 giant viruses belonging to diverse viral lineages, of which some were actively expressing genes in single cell transcriptomes, suggesting a possible association with the sampled protists. We also revealed a wide range of other viruses that were predicted to infect eukaryotes or host-associated bacteria. Our results provide further evidence that protists serve as mediators of complex microbial and viral associations, playing a critical role in ecological networks. The frequent co-occurrence of giant viruses and diverse microbial symbionts in our samples suggests multipartite associations, particularly among amoebae. Our study provides a preliminary assessment of the microbial diversity associated with lesser-known protist lineages and paves the way for a deeper understanding of protist ecology and their roles in environmental and human health.},
}
@article {pmid39803498,
year = {2024},
author = {Arp, G and Jiang, A and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, M and Li, Y and Hall, B and Jiang, X},
title = {Gut Bacteria Encode Reductases that Biotransform Steroid Hormones.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39803498},
issn = {2692-8205},
support = {R35 GM155208/GM/NIGMS NIH HHS/United States ; },
abstract = {The metabolism of steroids by the gut microbiome affects hormone homeostasis, impacting host development, mental health, and reproductive functions. In this study, we identify the Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, We show that 5β-reductase and Δ[6]-3-ketosteroid reductase have evolved to specialize in converting diverse 3-keto steroid hormones into their 5β- and Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the multi-step conversion of pregnenolone, a steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations, being enriched in females over males. These findings provide the molecular basis for studying microbial steroid metabolism in the gut, offering insights into its potential impact on hormonal health in hosts, especially in the context of women's health.},
}
@article {pmid39802822,
year = {2025},
author = {French, RK and Anderson, S and Cain, K and Digby, A and Greene, TC and Miskelly, CM and Muller, CG and Taylor, MW and Recovery Team, K and Geoghegan, JL and Holmes, EC},
title = {Diversity and cross-species transmission of viruses in a remote island ecosystem: implications for wildlife conservation.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veae113},
pmid = {39802822},
issn = {2057-1577},
abstract = {The ability of viruses to emerge in new species is influenced by aspects of host biology and ecology, with some taxa harbouring a high diversity and abundance of viruses. However, how these factors shape virus diversity at the ecosystem scale is often unclear. To better understand the pattern and determinants of viral diversity within an ecosystem, and to describe the novel avian viruses infecting an individual avian community, we performed a metagenomic snapshot of the virome from the entire avian community on remote Pukenui/Anchor Island in Aotearoa New Zealand. Through total RNA sequencing of 18 bird species, we identified 50 avian viruses from 9 viral families, of which 96% were novel. Of note, passerines (perching birds) exhibited high viral abundance and diversity, with viruses found across all nine viral families identified. We also identified numerous viruses infecting seabirds on the Island, including megriviruses, hepaciviruses, and hepatoviruses, while parrots exhibited an extremely low diversity of avian viruses. Within passerines, closely related astroviruses and hepatoviruses, and multiple identical hepe-like viruses, were shared among host species. Phylogenetic reconciliation analysis of these viral groups revealed a mixture of co-divergence and cross-species transmission, with virus host-jumping relatively frequent among passerines. In contrast, there was no evidence for recent cross-species virus transmission in parrots or seabirds. The novel pegiviruses and a flavivirus identified here also pose intriguing questions regarding their origins, pathogenicity, and potential impact on vertebrate hosts. Overall, these results highlight the importance of understudied remote island ecosystems as refugia for novel viruses, as well as the intricate interplay between host ecology and behaviour in shaping viral communities.},
}
@article {pmid39802798,
year = {2024},
author = {Blank, RB and Bu, K and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Clemente, JC and Scher, JU},
title = {Multi-omic Biomarkers Distinguish Rheumatoid Arthritis in Discordant Monozygotic Twins.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39802798},
support = {UL1 TR001445/TR/NCATS NIH HHS/United States ; R03 AR072182/AR/NIAMS NIH HHS/United States ; UC2 AR081034/AR/NIAMS NIH HHS/United States ; T32 AR069515/AR/NIAMS NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; },
abstract = {BACKGROUND: Although genetic factors have been identified in the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other features contribute to disease development. Further, the relative contribution of such non-genetic elements in identical twins have not been characterized. Here, we aimed to measure differentiating host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multi-omics approach.<br><br>METHODS: Eight pairs of MZ twins discordant for RA (n=16) were enrolled. Gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and other plasma proteins were measured in both plasma and feces. Levels of short and medium-chain fatty acids from serum and feces were quantified using gas chromatography mass spectrometry (GC-MS).<br><br>RESULTS: While overall microbiome diversity and composition did not significantly differ between twins, we observed a decrease in Blautia faecis in affected twins. Affected twins had higher concentrations of both fecal and plasma citrullinated and non-citrullinated autoantibodies, as well as significantly lower concentrations of fecal butyrate and propionate.<br><br>CONCLUSION: Multi-omics biomarkers differentiate MZ twins discordant for RA. Blautia faecis, which is associated with reduced inflammatory cytokine expression, was decreased in RA twins. Similarly, short-chain fatty acids, known to have immune modulatory effects, were decreased in affected twins, suggesting further bi-directional interactions between inflammation at the gut barrier and disease state. If confirmed in other cohorts, exhaustive multi-omics approaches may improve our understanding of RA pathogenesis and potentially contribute to novel diagnostics and co-adjuvant therapies.},
}
@article {pmid39802519,
year = {2025},
author = {Yan, C and Qiu, J and Pan, X and Huang, X and Pan, L and Wang, C and Mao, M},
title = {Mixed Pulmonary Infection, Asthma, and Nephrotic Syndrome in a Patient Diagnosed with Selective IgA Deficiency: A Case Report.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {127-132},
pmid = {39802519},
issn = {1178-7031},
abstract = {Patients with selective IgA deficiency could have various clinical presentations ranging from asymptomatic to severe respiratory or gastrointestinal tract infection, as well as autoimmune disease and allergic reactions. Selective IgA deficiency is relatively common in Caucasians, but it is rare in the Asian population, meaning it could be easily missed in the clinic. In this study, we report a 26-year-old man with a history of asthma and nephrotic syndrome. He presented with symptoms of pulmonary infection, and his condition quickly deteriorated to respiratory failure that required endotracheal intubation and mechanical ventilation. Sputum smear; sputum, blood, and bronchoalveolar lavage fluid culture; and metagenomic sequencing examination identified multiple mixed pathogens, including Mycobacterium chelonae-abscessus, Pseudomonas aeruginosa, Candida parapsilosis, Acinetobacter baumannii, and Klebsiella cepacia. Finally, he was diagnosed with selective IgA deficiency after a laboratory test detected an extremely low serum IgA level (<0.06 g/L). The patient died of septic shock and multiorgan failure despite aggressive management with a combination of antibiotics and supportive care. We report this case to remind clinicians about this rare disease in the Asian population. Patients with multisystem illnesses that are related to immune dysregulation, such as asthma or nephrotic syndrome, should be tested for immune system disorder. Rare and mixed pathogens should be considered during antibiotic selection in patients with selective IgA deficiency.},
}
@article {pmid39801738,
year = {2024},
author = {Harmak, Z and Kone, AS and Ghouzlani, A and Ghazi, B and Badou, A},
title = {Beyond Tumor Borders: Intratumoral Microbiome Effects on Tumor Behavior and Therapeutic Responses.},
journal = {Immune network},
volume = {24},
number = {6},
pages = {e40},
pmid = {39801738},
issn = {1598-2629},
abstract = {The human body contains a diverse array of microorganisms, which exert a significant impact on various physiological processes, including immunity, and can significantly influence susceptibility to various diseases such as cancer. Recent advancements in metagenomic sequencing have uncovered the role of intratumoral microbiome, which covertly altered the development of cancer, the growth of tumors, and the response to existing treatments through multiple mechanisms. These mechanisms involve mainly DNA damage induction, oncogenic signaling pathway activation, and the host's immune response modulation. To explore novel therapeutic options and effectively target and regulate the intratumoral microbiome, a comprehensive understanding of these processes is indispensable. Here, we will explore various potential actions of the intratumoral microbiome concerning the initiation and progression of tumors. We will examine its impact on responses to chemotherapy, radiotherapy, and immunotherapy. Additionally, we will discuss the current state of knowledge regarding the use of genetically modified bacteria as a promising treatment option for cancer.},
}
@article {pmid39801456,
year = {2025},
author = {Torozan, DA and Laczny, CC and Roomp, K and Wilmes, P and Fleckenstein, J and Schneider, JG},
title = {Metagenomic Profiling of Oral Microbiome Dynamics During Chemoradiotherapy in Head and Neck Squamous Cell Carcinoma Patients.},
journal = {Cancer medicine},
volume = {14},
number = {1},
pages = {e70589},
pmid = {39801456},
issn = {2045-7634},
support = {863664//H2020 European Research Council/ ; },
mesh = {Humans ; Male ; *Chemoradiotherapy/adverse effects ; Female ; Middle Aged ; *Squamous Cell Carcinoma of Head and Neck/microbiology/therapy ; *Microbiota/radiation effects ; Aged ; *Metagenomics/methods ; *Head and Neck Neoplasms/microbiology/therapy ; *Saliva/microbiology ; Prospective Studies ; Mouth/microbiology ; Adult ; Case-Control Studies ; Metagenome ; },
abstract = {BACKGROUND: We explored the interaction between the oral microbiome and the development of radiation-induced mucositis in patients with head and neck squamous cell cancer (HNSCC) undergoing chemoradiotherapy (CRT). We prospectively studied the oral microbiome and compared it to healthy controls. Additionally, we compared patients with low-grade (LGM) vs. high-grade mucositis (HGM).<br><br>METHODS: Ten HNSCC patients scheduled for CRT were included. Saliva samples were characterized prior to, during, and nine months after CRT using metagenomic sequencing. We similarly characterized samples from seven healthy controls. We assessed alpha and beta diversity and examined abundances at different taxonomic levels between (sub)groups.<br><br>RESULTS: Patients exhibited significantly reduced alpha diversity compared to controls at all times (p &#x27e8; 0.05). Differential abundance of taxa between patients and controls was observed at baseline. In patients, the relative abundance of Staphylococcus aureus and Escherichia coli increased significantly during CRT. Capnocytophaga spp. was associated with the definitive CRT patients' subgroup. At baseline, two fungal families (Melampsoraceae and Herpotrichiellaceaea) were more abundant in patients who later developed HGM. No differentially abundant taxa were found between LGM vs. HGM during irradiation.<br><br>CONCLUSION: Our findings support the hypothesis that CRT, as well as HNSCC itself, influences the composition of the oral microbiome. Microbial markers found in patients who later developed HGM should be evaluated using independent cohorts to qualify their specific biomarker potential.},
}
@article {pmid39800795,
year = {2025},
author = {Pagac, MP and Davient, B and Plado, LA and Lam, HYI and Lee, SM and Ravikrishnan, A and Chua, WLE and Muralidharan, S and Sridharan, A and Irudayaswamy, AS and Srinivas, R and Wearne, S and Mohamed Naim, AN and Ho, EXP and Ng, HQA and Kwah, JS and Png, E and Bendt, AK and Wenk, MR and Torta, F and Nagarajan, N and Common, J and Chong, YS and Tham, EH and Shek, LP and Loo, EXL and Chambers, J and Yew, YW and Loh, M and Dawson, TL},
title = {Life stage impact on the human skin ecosystem: lipids and the microbial community.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {13},
pmid = {39800795},
issn = {2055-5008},
mesh = {Humans ; *Skin/microbiology ; Female ; Adult ; *Microbiota ; *Oxylipins/metabolism ; *Lipid Metabolism ; *Lipidomics/methods ; Child ; Malassezia ; Keratinocytes/microbiology/metabolism ; Middle Aged ; Male ; Metagenomics/methods ; Sebum/metabolism ; Interleukin-6/metabolism ; Interleukin-1beta/metabolism ; Aged ; Coculture Techniques ; Adolescent ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Young Adult ; Host Microbial Interactions ; Ecosystem ; },
abstract = {Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin. Co-culturing Malassezia with keratinocytes demonstrated a link between 9,10-DiHOME and pro-inflammatory cytokines IL-1β and IL-6 production. We also observed strong correlations between other skin oxylipins and microbial taxa, highlighting life stage differences in sebum production and microbial community composition. Our findings imply a complex host-microbe communication system mediated by lipid metabolism occurring on human skin, warranting further research into its role in skin health and disease and paving the way towards novel therapeutic targets and treatments.},
}
@article {pmid39800316,
year = {2025},
author = {He, S and Xue, W and Wu, X and Liang, Z and Gao, J and Qin, W and Wei, H and Zhou, L and Yuan, H and Xie, L},
title = {The application value of targeted next-generation sequencing using bronchoalveolar lavage fluid samples in community-acquired pneumonia in children.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {31},
number = {3},
pages = {102610},
doi = {10.1016/j.jiac.2025.102610},
pmid = {39800316},
issn = {1437-7780},
abstract = {BACKGROUND: The precise identification of pathogens responsible for community-acquired pneumonia (CAP) in children is essential for effective treatment. However, the performance of targeted next-generation sequencing (tNGS) in the detection of pathogens associated with CAP in children remains unclear.<br><br>METHODS: In this study, 216 children diagnosed with CAP were enrolled, and bronchoalveolar lavage fluid (BALF) samples underwent detection through tNGS, culture, and multiplex quantitative polymerase chain reaction (qPCR).<br><br>RESULTS: In 208 children, tNGS identified a total of 389 strains of microorganisms, including 111 Mycoplasma pneumoniae, 123 bacteria, 127 viruses, and 28 fungi. Among the cases, 89 presented as single-pathogen detection, while 119 exhibited multiple pathogens co-detection. The positive detection rates of bacteria and fungi through tNGS were significantly higher than those achieved through the traditional culture method, with rates of 56.9&#xa0;% vs 8.3&#xa0;% for bacteria and 13.0&#xa0;% vs 4.2&#xa0;% for fungi, respectively. The overall agreement between tNGS and multiplex qPCR ranged from 89.4&#xa0;% to 99.1&#xa0;%, with Kappa values ranging from 0.541 to 0.912 (P&#xa0;=&#xa0;0.000).<br><br>CONCLUSIONS: The tNGS technique demonstrates rapid and effective capabilities in identifying a wide array of pathogens with a detection sensitivity that surpasses traditional culture methodologies while exhibiting a high degree of consistency with multiplex qPCR in detecting respiratory viruses. The tNGS detection method can serve as an important complement to traditional diagnostic approaches; however, caution must be exercised when interpreting tNGS findings due to its heightened sensitivity which may lead to identification of pathogens that are not necessarily responsible for causing disease.},
}
@article {pmid39800299,
year = {2025},
author = {Pang, S and Cai, X and Yang, L and Zhou, J and Li, X and Xia, S},
title = {Microbial synergy mechanism of hydrogen flux influence on hydrogen-based partial denitrification coupled with anammox in a membrane biofilm reactor.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120827},
doi = {10.1016/j.envres.2025.120827},
pmid = {39800299},
issn = {1096-0953},
abstract = {The hydrogen-based partial denitrification coupled with anammox (H2-PDA) biofilm system effectively achieves low-carbon and high-efficiency biological nitrogen removal. However, the effects and biological interaction mechanism of H2 flux with the H2-PDA system have not yet been understood. This study assessed the effects of H2 flux on interactions among anammox bacteria (AnAOB), denitrifying bacteria (DB), and sulfate-reducing bacteria (SRB) coexisting in a H2-PDA system. Results showed the simultaneous removal of 40 mg/L ammonium nitrogen (NH4[+]-N) and 50 mg/L nitrate nitrogen (NO3[-]-N) in the H2-PDA system at a flux of 0.13-0.14 e[-] eq/(m[2]·d) without additional organic carbon. Candidatus_Brocadia was involved in H2 oxidation and was negatively associated with the heterotrophic Thauera genus (DB). The expression of nirS and dsrA was increased to 5.6 × 10[5] copies/gSS and 2.1 × 10[5] copies/gSS, respectively, with excessive H2 flux (0.17 e[-] eq/(m[2]·d). This study provides technical guidance for understanding and applying the H2-PDA technology for low-carbon wastewater treatment.},
}
@article {pmid39799988,
year = {2025},
author = {Chen, L and Wu, Z and Niu, J and Wang, Y and Cai, M and Xi, J and Cui, Y and Cheng, L and Fan, X},
title = {Simultaneous nitrogen removal and phosphorus recovery in granular sludge-based partial denitrification/anammox-hydroxyapatite precipitation (PD/A-HAP) process under low C/N ratio and dissolved oxygen limitation.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132045},
doi = {10.1016/j.biortech.2025.132045},
pmid = {39799988},
issn = {1873-2976},
mesh = {*Phosphorus/metabolism ; *Nitrogen ; *Sewage/microbiology ; *Denitrification ; *Durapatite/chemistry ; *Oxygen/metabolism ; *Carbon ; Bioreactors ; Chemical Precipitation ; Water Purification/methods ; Oxidation-Reduction ; Anaerobiosis ; },
abstract = {This study integrates partial denitrification/Anammox (PD/A) with hydroxyapatite (HAP) crystallization in a single reactor, achieving simultaneous nitrogen and phosphorus removal along with phosphorus recovery. By adjusting pH, sludge concentration, low COD/TN ratio, and applying moderate dissolved oxygen stress, the system operated stably and promoted the synergistic growth of HAP and biomass. Results showed a nitrogen removal efficiency (NRE) of 94.13 % and a phosphorus removal efficiency (PRE) of 73.6 %. Metagenomic analysis revealed that under dissolved oxygen stress, The abundance of Candidatus Brocadia increased from 1 % to 26.1 %, significantly boosting anammox activity. indicating enhanced microbial activity. The upregulation of related genes (sdh, suc, hzs) further boosted AnAOB activity. HAP was identified as the main inorganic component of the granule. This process shows strong potential for nitrogen and phosphorus removal with resource recovery in wastewater treatment.},
}
@article {pmid39799815,
year = {2025},
author = {Zhao, S and Zhang, H and Zhu, Y and Xing, Z and Chen, W and Dong, B and Zheng, Z and Ji, C and Xue, Y and Liu, X},
title = {Residual heavy metals and antibiotic pollution in abandoned breeding areas along the northeast coast of Hainan Island, China.},
journal = {Marine pollution bulletin},
volume = {212},
number = {},
pages = {117518},
doi = {10.1016/j.marpolbul.2024.117518},
pmid = {39799815},
issn = {1879-3363},
abstract = {To assess the environmental status of an abandoned aquaculture and breeding area in the northeast coast of the Hainan Island, surface and well water, sediment and surface soils were sampled and analyzed for conventional physicochemical properties, heavy metals and antibiotics. Metagenome tests were also conducted to determine the composition and diversity of the microbial community in typical habitats. Affected by the discharge of wastewater from higher-place pond aquaculture, coastal freshwater rivers have undergone significant salinization, Cl[-] and Na[+] were as high as 4.51 × 10[3] and 1.42 × 10[3] mg/L. The 3 hand-pumped wells surveyed were also suffered from varying degrees of salinization and heavy metal pollution, especially the threat of arsenic pollution. Compared with the local background values, significantly higher valves of Cu, Zn, As and Cd were observed in the surface soil and sediment, and the average concentrations for Cu, Zn, As and Cd are 5.71, 17.6, 15.4 and 0.09 mg/kg respectively. For As，the Nemerow index ranges from 7 to 16 and the geoaccumulation index is between 2 and 4, indicating moderate to severe pollution levels in surface soil. 14 antibiotics were detected in the soil and sediment samples, and the highest total amount was 73 μg/kg, with tetracycline being the dominant antibiotic. Sediment and forest soil showed different microbial community and the genetic diversity index of sediment was lower than that of the forest soils. For typical vegetation soil, the genetic diversity followed the order as P. elliottii × P. caribaea > Eucalyptus > C. equisetifolia. Among the soil and sediment samples, the highest abundances of antibiotic resistance genes (ARGs) were associated with elfamycin, peptide, rifamycin, and the most common antibiotic resistance mechanisms were antibiotic target alteration (54.5 %), antibiotic efflux (27.6 %) and antibiotic target replacement (12.1 %). The metal resistance genes (MRGs) for Cu, Fe, and Zn resistance were the main MRGs in the samples. This study identified the potential ecological environment risk factors in the abandoned coastal breeding areas, and suggested continuous monitoring and assessment of the residual pollutant abatement processes in the future.},
}
@article {pmid39799800,
year = {2025},
author = {Floyd, B and Gaston, F and Saadoon, R and Shaikh, N and Bakir, M},
title = {Disseminated histoplasmosis in a 4-month-old infant presenting with prolonged fever and pancytopenia: A case report.},
journal = {Journal de mycologie medicale},
volume = {35},
number = {1},
pages = {101532},
doi = {10.1016/j.mycmed.2025.101532},
pmid = {39799800},
issn = {1773-0449},
abstract = {BACKGROUND: Histoplasmosis is the most prevalent endemic mycosis in the United States, typically affecting immunocompromised individuals. Diagnosis of histoplasmosis in immunocompetent patients is rare, particularly among young infants, with only a few cases reported.<br><br>CASE PRESENTATION: We present a 4-month-old female with a history of prematurity who initially presented with 11 days of fever. She visited her local emergency department, where she was diagnosed with Rhino/enterovirus bronchiolitis. Pancytopenia was noted at that time, attributed to viral bone marrow suppression. Persistent fever and pancytopenia led to her transfer to our hospital for further evaluation and treatment. On admission, she exhibited hepatosplenomegaly, pancytopenia, elevated procalcitonin, and lactate dehydrogenase levels. Additionally, T cell deficiency was observed. Initially, there was concern for hemophagocytic lymphohistiocytosis; however, bone marrow biopsy and aspirate confirmed T cell deficiency. As fever persisted on day 19, further investigations were conducted, including a positive beta-D-glucan assay. Subsequent urine and serum Histoplasma antigen tests were positive, with metagenomic sequencing confirming the diagnosis of histoplasmosis. Treatment comprised one week of amphotericin B followed by three months of oral itraconazole. Resolution of fever, pancytopenia, T cell deficiency, and hepatosplenomegaly occurred, and the patient has shown no signs of recurrence to date.<br><br>CONCLUSIONS: This case serves as a reminder to clinicians regarding the necessity of considering disseminated histoplasmosis in young infants who present with fever of unknown origin, pancytopenia, and hepatosplenomegaly, despite its rarity. Failure to do so can lead to fatal outcomes.},
}
@article {pmid39799674,
year = {2025},
author = {Li, Y and Qin, W and Xin, X and Tang, C and Huang, Y and He, X and Chen, L and Yu, G and Yu, F},
title = {Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137173},
doi = {10.1016/j.jhazmat.2025.137173},
pmid = {39799674},
issn = {1873-3336},
abstract = {This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.},
}
@article {pmid39799113,
year = {2025},
author = {Tyagi, A and Choi, YY and Shan, L and Vinothkanna, A and Lee, ES and Chelliah, R and Barathikannan, K and Raman, ST and Park, SJ and Jia, AQ and Choi, GP and Oh, DH},
title = {Limosilactobacillus reuteri fermented brown rice alleviates anxiety improves cognition and modulates gut microbiota in stressed mice.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {5},
pmid = {39799113},
issn = {2396-8370},
support = {4299990913942//the fourth Brain Korea (BK) 21 Plus Project/ ; 4299990913942//the fourth Brain Korea (BK) 21 Plus Project/ ; },
abstract = {Chronic stress disrupts gut microbiota homeostasis, contributing to anxiety and depression. This study explored the effects of Limosilactobacillus reuteri fermented brown rice (FBR) on anxiety using an ICR mouse chronic mild stress (CMS) model. Anxiety was assessed through body weight, corticosterone levels, neurotransmitter profiles, and behavioral tests. A four-week FBR regimen reduced corticosterone, restored neurotransmitters like gamma-aminobutyric acid (GABA) and serotonin, and improved anxiety-related behaviors. Metagenomic (16S rRNA) and metabolomic analyses revealed enhanced amino acid metabolism, energy metabolism, and short-chain fatty acid (SCFA) production in FBR-treated mice. FBR-enriched beneficial gut bacteria, aligning the microbiota profile with that of non-stressed mice. FBR also modulated GABA receptor-related gene expression, promoting relaxation. Network pharmacology identified quercetin, GABA, glutamic acid, phenylalanine, and ferulic acid as bioactive compounds with neuroprotective potential. These findings highlight FBR's potential as a gut-brain axis-targeted therapeutic for anxiety and stress-related disorders.},
}
@article {pmid39798925,
year = {2025},
author = {Aleksandrova, RR and Nieuwenhuis, LM and Karmi, N and Zhang, S and Swarte, JC and Björk, JR and Gacesa, R and Blokzijl, H and Connelly, MA and Weersma, RK and Lisman, T and Festen, EAM and de Meijer, VE and , },
title = {Gut microbiome dysbiosis is not associated with portal vein thrombosis in patients with end-stage liver disease: a cross-sectional study.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2024.12.036},
pmid = {39798925},
issn = {1538-7836},
abstract = {BACKGROUND: Portal vein thrombosis (PVT) is a common complication in patients with end-stage liver disease (ESLD). The portal vein in patients with ESLD is proposedly an inflammatory vascular bed due to translocation of endotoxins and cytokines from the gut. We hypothesized that a proinflammatory gut microbiome and elevated trimethylamine N-oxide (TMAO), a driver of thrombosis, may contribute to PVT development.<br><br>OBJECTIVES: We investigated whether gut microbiome diversity, bacterial species, metabolic pathways, and TMAO levels are associated with PVT in patients with ESLD.<br><br>METHODS: Fecal samples, plasma samples, and data from patients with ESLD and healthy controls were collected through the TransplantLines Biobank and Cohort Study. PVT was defined as a thrombus in the portal vein within a year prior to or after fecal sample collection. Fecal samples were analyzed using Shotgun Metagenomic Sequencing, and TMAO levels were measured in plasma using a Vantera Clinical Analyzer.<br><br>RESULTS: One hundred two patients with ESLD, of which 23 with PVT, and 246 healthy controls were included. No significant difference in gut microbiome diversity was found between patients with PVT and without PVT (P&#xa0;= .18). Both ESLD groups had significantly lower alpha diversity than controls. Bacteroides fragilis and 3 Clostridiales species were increased in patients with PVT compared with without PVT. TMAO levels between the 3 groups were not significantly different.<br><br>CONCLUSION: We observed profound differences in gut microbiota between patients with ESLD and controls, but minimal differences between patients with ESLD with or without PVT. In our cohort, a gut-derived proinflammatory state was not associated with presence of PVT in patients with ESLD.},
}
@article {pmid39798664,
year = {2025},
author = {Wu, Y and Liu, X and Yin, M and Pei, Y and Cui, Y and Li, J and Zhu, Y and Guo, W and Li, D},
title = {Combining metagenomic sequencing and molecular docking to understand signaling molecule degradation characteristics of quorum quenching consortia.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120815},
doi = {10.1016/j.envres.2025.120815},
pmid = {39798664},
issn = {1096-0953},
abstract = {Quorum quenching consortia (QQC) enriched by special substrates for bioaugmentation is a promising QQ technology to reduce biofouling, sludge yield, and sludge bulking. However, the effect of substrate type on the performance of QQC is still a research gap. This study selected three different substrates, regular AHLs (N-octanoyl-l-homoserine lactone, C8), 3-oxo-AHLs (3-oxo-octanoyl)-l-homoserine lactone, 3-oxo-C8), and AHLs analogs (γ-caprolactone, GCL) to enrich three QQC (C8-QQC, 3OC8-QQC, GCL-QQC). Combining metagenomic sequencing, protein prediction, and molecular docking to fill the above gaps from the perspective of bacteria and enzymes. The performance of the three QQC decreased with the increasing complexity of the molecular structure of the substrates. This decline was attributed to more complex substrate enriched with more bacteria, lacking QQ genes in the QQC. All QQC degraded N-acetyl-l-homoserine lactones (AHLs) via acylase and lactonase. C8-QQC and 3OC8-QQC showed stronger degradation capabilities for N-(3-oxo-hexanoyl)-L-homoserine lactone (3OC6) compared to N-hexanoyl-L-homoserine lactone (C6), whereas GCL-QQC exhibited stronger degradation for C6. Molecular docking results showed that in 3OC8-QQC and C8-QQC, most enzymes exhibited stronger degradation capabilities for long-chain and 3OAHLs. However, in GCL-QQC, more QQ enzymes showed stronger degradation for C6 than for 3OC6, explaining the observed differences in AHL degradation. β-Oxidation metabolic pathways in bins revealed differences in their abilities to metabolize octanoic acid from C8 and 3-oxo-octanoic acid from 3OC8, which influenced their abundance in the respective QQC. The study findings offer insights into the relationship between substrates and QQC performance at the gene and protein levels.},
}
@article {pmid39798656,
year = {2025},
author = {Xing, F and Ma, X and Sun, B and Wang, T and Lian, F and Wang, L and Fu, Z},
title = {Enhancing anammox granular sludge for mainstream anammox process by adding iron-loaded diatomite: Performance and intrinsic mechanism.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120806},
doi = {10.1016/j.envres.2025.120806},
pmid = {39798656},
issn = {1096-0953},
abstract = {Iron-loaded diatomite (Fe-DE) was developed as the innovative material to enhance anammox granular sludge (AnGS) and mainstream anammox performance. By adding Fe-DE with the Fe:DE ratio of 1:20 and the dosage of 3 g/L, the start-up period of mainstream anammox process was shortened from 29 d to 17 d and its nitrogen removal rate was increased from 0.234 kg N/(m[3]·d) to 0.437 kg N/(m[3]·d). AnGS generated more hydrophobic functional groups and redox substances, forming the robust particle structure and improving the electron transfer of anammox reaction. In addition, the key genes PleC, PleD and TrpE/G, related to quorum sensing, increased from 502.69, 91.18 and 18.25 CPM to 532.84, 103.66 and 19.96 CPM. The key genes hzs and hdh related to anammox process also increased by 30.76% and 24.26%. As a result, formation of AnGS was promoted and the enrichment level of Candidatus Brocadia was improved. This study provides a novel insight into the development of innovative material for enhancing mainstream anammox process.},
}
@article {pmid39798650,
year = {2025},
author = {Zhang, X and Guo, W and Zhang, Z and Gao, P and Tang, P and Liu, T and Yao, X and Li, J},
title = {Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120807},
doi = {10.1016/j.envres.2025.120807},
pmid = {39798650},
issn = {1096-0953},
abstract = {Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.},
}
@article {pmid39798533,
year = {2025},
author = {Mao, X and Yin, X and Yang, Y and Gao, F and Li, S and Shi, X and Deng, Y and Li, L and Leung, KMY and Zhang, T},
title = {Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city.},
journal = {Water research},
volume = {274},
number = {},
pages = {123102},
doi = {10.1016/j.watres.2025.123102},
pmid = {39798533},
issn = {1879-2448},
abstract = {Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD5), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.},
}
@article {pmid39798461,
year = {2025},
author = {Silvester, R and Perry, WB and Webster, G and Rushton, L and Baldwin, A and Pass, DA and Healey, N and Farkas, K and Craine, N and Cross, G and Kille, P and Weightman, AJ and Jones, DL},
title = {Metagenomics unveils the role of hospitals and wastewater treatment plants on the environmental burden of antibiotic resistance genes and opportunistic pathogens.},
journal = {The Science of the total environment},
volume = {961},
number = {},
pages = {178403},
doi = {10.1016/j.scitotenv.2025.178403},
pmid = {39798461},
issn = {1879-1026},
mesh = {*Wastewater/microbiology ; *Waste Disposal, Fluid ; *Metagenomics ; *Hospitals ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; },
abstract = {Antimicrobial resistance (AMR) is a global health challenge, with hospitals and wastewater treatment plants (WWTPs) serving as significant pathways for the dissemination of antibiotic resistance genes (ARGs). This study investigates the potential of wastewater-based epidemiology (WBE) as an early warning system for assessing the burden of AMR at the population level. In this comprehensive year-long study, effluent was collected weekly from three large hospitals, and treated and untreated wastewater were collected monthly from three associated community WWTPs. Metagenomic analysis revealed a significantly higher relative abundance and diversity of ARGs in hospital wastewater than in WWTPs. Notably, ARGs conferring resistance to clinically significant antibiotics such as β-lactams, aminoglycosides, sulfonamides, and tetracyclines were more prevalent in hospital effluents. Conversely, resistance genes associated with rifampicin and MLS (macrolides-lincosamide-streptogramin) were more commonly detected in the WWTPs, particularly in the treated effluent. Network analysis identified the potential bacterial hosts, which are the key carriers of these ARGs. The study further highlighted the variability in ARG removal efficiencies across the WWTPs, with none achieving complete elimination of ARGs or a significant reduction in bacterial diversity. Additionally, ARG profiles remained relatively consistent in hospital and community wastewater throughout the study, indicating a persistent release of a baseload of ARGs and pathogenic bacteria into surface waters, potentially polluting aquatic environments and entering the food chain. The study underscores the need for routine WBE surveillance, enhanced wastewater treatment strategies, and hospital-level source control measures to mitigate AMR dissemination into the environment.},
}
@article {pmid39798326,
year = {2025},
author = {Tang, Q and Zhao, Y and Li, X and Zhang, J and Li, J and Zhao, C and Pang, Y and Li, W and Huang, Q and Xiong, J and Qian, K and Liu, Z and Guo, J},
title = {Glyphosate and spinetoram alter viral communities with different effects on antibiotic resistance genes in the bumblebee gut.},
journal = {Journal of environmental management},
volume = {374},
number = {},
pages = {124079},
doi = {10.1016/j.jenvman.2025.124079},
pmid = {39798326},
issn = {1095-8630},
mesh = {Animals ; *Glyphosate ; Bees/virology/drug effects ; *Drug Resistance, Microbial/genetics ; Glycine/analogs &amp; derivatives/pharmacology/toxicity ; },
abstract = {Limited research investigating the impact of pesticides on antibiotic resistance genes (ARGs) and viral community in the gut of wild animals. In this study, we employed metagenomic to investigate the effects of glyphosate and spinetoram on the gut viral communities, ARGs, and their interactions in a key wild pollinator, bumblebees. The results showed that both 2.5 mg/L glyphosate and 2.5 mg/L spinetoram did not significantly alter the α-diversity of the ARGs (p > 0.05). However, spinetoram significantly enriched core ARG subtypes, such as Bado_rpoB_RIF, Bbif_ileS_MUP, and CRP, and total abundance of ARGs (p < 0.05). In contrast, glyphosate had no significant impact on ARG subtypes or total abundance (p > 0.05). The mantel test (R = 0.455, p = 0.020) and Procrustes analysis (M[2] = 0.095, p = 0.069) revealed a significant correlation between the bacterial community and ARGs. Although glyphosate and spinetoram had no significant effect on the relative abundance of mobile ARGs (p > 0.05), both significantly altered the alpha diversity (p < 0.05) and compositional structure (one-way PERMANOVA, p = 0.003) of the gut viral communities, with glyphosate increasing the abundance of lytic phages (p < 0.05). Notably, a phage and host relationship network constructed revealed no evidence of phage-mediated ARGs transduction, but five associations between lytic phages and antibiotic-resistant bacteria (ARB) were identified. Furthermore, glyphosate and spinetoram exposure significantly reduced the total relative abundance of these five lytic phages in the viral community (p < 0.001), indicating that phages primarily function in lysing ARBs. These findings suggest that glyphosate may inhibit the enrichment of ARGs by increasing the abundance of lytic phages, while spinetoram may promote the enrichment of total ARGs by affecting the bacterial community.},
}
@article {pmid39798310,
year = {2025},
author = {Zhou, HZ and Wang, BQ and Ma, YH and Sun, YY and Zhou, HL and Song, Z and Zhao, Y and Chen, W and Min, J and Li, JW and He, T},
title = {The combination of metagenomics and metabolomics reveals the effect of nitrogen fertilizer application driving the remobilization of immobilization remediation cadmium and rhizosphere microbial succession in rice.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137117},
doi = {10.1016/j.jhazmat.2025.137117},
pmid = {39798310},
issn = {1873-3336},
abstract = {The remobilization of cadmium (Cd) in contaminated farmland soil due to nitrogen fertilizer addition has raised significant concerns regarding the effectiveness of immobilization remediation. This study investigated the effects of ammonia nitrogen (NH4[+]-N) and nitrogen (NO3[-]-N) application (100 kg/ha) on the remobilization of immobilization of remediation Cd (bound to clay palygorskite) during various growth stages of rice through field experiments. Our findings revealed that increased organic acid secretion (e.g., benzoic acid and malic acid) from rice roots, induced by NH4[+]-N, significantly enhanced the NH4NO3-extractable Cd content. Consequently, the concentration of Cd in brown rice varied from 39.84 to 43.25 μg/kg to 78.31-90.44 μg/kg. While NO3[-]-N exhibited a relatively weaker capacity for Cd remobilization (Cd content in brown rices: 50.17-65.23 μg/kg). Meanwhile, the organic acid secretion in roots inhibited the expression of most functional genes (e.g., nifK and napA), leading to shifts in microbial communities and functional metabolism (e.g., Cd[2+] exporting). According to the results of metagenome-assembled genome (MAG) composition, specific MAGs with fewer functional annotations were enriched under NH4[+]-N treatment, may further increased risk of Cd exposure in rice by stimulating amt expression. Interaction analysis of metabolic products and microbial communities indicated acids linked to branched-chain amino acid (BCAA) metabolism and urea cycle might serve as a potentially key process influencing microbial dynamics.},
}
@article {pmid39798223,
year = {2025},
author = {Larsson, SC and Ericson, U and Dekkers, KF and Arage, G and Rašo, LM and Sayols-Baixeras, S and Hammar, U and Baldanzi, G and Nguyen, D and Nielsen, HB and Holm, JB and Risérus, U and Michaëlsson, K and Sundström, J and Smith, JG and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Ahmad, S},
title = {Meat intake in relation to composition and function of gut microbiota.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {45},
number = {},
pages = {124-133},
doi = {10.1016/j.clnu.2024.12.034},
pmid = {39798223},
issn = {1532-1983},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Male ; Female ; Middle Aged ; Adult ; Diet/methods/statistics &amp; numerical data ; Meat/microbiology ; Aged ; Red Meat/microbiology ; Metagenomics/methods ; Biomarkers/blood ; },
abstract = {OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.<br><br>DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.<br><br>RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.<br><br>CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.},
}
@article {pmid39797569,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
pmid = {39797569},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}
@article {pmid39797470,
year = {2025},
author = {Záhonová, K and Kaur, H and Furgason, CC and Smirnova, AV and Dunfield, PF and Dacks, JB},
title = {Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70029},
pmid = {39797470},
issn = {1462-2920},
support = {e-INFRA CZ (90254)//the Ministry of Education, Youth and Sports of the Czech Republic/ ; CRDPJ 542973-19//Natural Sciences and Engineering Research Council of Canada/ ; RES0021028//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Alberta ; *Metagenomics/methods ; *Oil and Gas Fields ; *Eukaryota/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Phylogeny ; },
abstract = {The Canadian province of Alberta contains substantial oilsands reservoirs, consisting of bitumen, clay and sand. Extracting oil involves separating bitumen from inorganic particles using hot water and chemical diluents, resulting in liquid tailings waste with ecotoxicologically significant compounds. Ongoing efforts aim to reclaim tailings-affected areas, with protist colonisation serving as one assessment method of reclamation progress. Oilsands-associated protist communities have mainly been evaluated using amplicon sequencing of the 18S rRNA V4 region; however, this barcode may overlook important protist groups. This study examined how community assessment methods between the V4 and V9 regions differ in representing protist diversity across four oilsands-associated environments. The V9 barcode identified more operational taxonomical units (OTUs) for Discoba, Metamonada and Amoebozoa compared with the V4. A comparative shotgun metagenomics approach revealed few eukaryotic contigs but did recover a complete Paramicrosporidia mitochondrial genome, only the second publicly available from microsporidians. Both V4 and V9 markers were informative for assessing community diversity in oilsands-associated environments and are most effective when combined for a comprehensive taxonomic estimate, particularly in anoxic environments.},
}
@article {pmid39797441,
year = {2025},
author = {McCorison, CB and Kim, T and Donato, JJ and LaPara, TM},
title = {Proximity-Ligation Metagenomic Sequence Analysis Reveals That the Antibiotic Resistome Makes Significant Transitions During Municipal Wastewater Treatment.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70036},
pmid = {39797441},
issn = {1462-2920},
support = {//Minnesota Environment and Natural Resources Trust Fund/ ; },
mesh = {*Wastewater/microbiology ; *Metagenomics ; *Bioreactors/microbiology ; *Sewage/microbiology ; *Bacteria/genetics/drug effects/classification ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Water Purification ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; },
abstract = {Shotgun and proximity-ligation metagenomic sequencing were used to generate thousands of metagenome assembled genomes (MAGs) from the untreated wastewater, activated sludge bioreactors, and anaerobic digesters from two full-scale municipal wastewater treatment facilities. Analysis of the antibiotic resistance genes (ARGs) in the pool of contigs from the shotgun metagenomic sequences revealed significantly different relative abundances and types of ARGs in the untreated wastewaster compared to the activated sludge bioreactors or the anaerobic digesters (p < 0.05). In contrast, these results were statistically similar when comparing the ARGs in the pool of MAGs, suggesting that proximity-ligation metagenomic sequencing is particularly useful for pairing ARGs with their hosts but less adept at discerning quantitative differences in ARG types and relative abundances. For example, numerous MAGs of the genera Acinetobacter, Enterococcus, Klebsiella and Pseudomonas were identified in the untreated wastewater, many of which harboured plasmid-borne and/or chromosomal-borne ARGs; none of these MAGs, however, were detected in the activated sludge bioreactors or anaerobic digesters. In conclusion, this research demonstrates that the antibiotic resistome undergoes significant transitions in both the relative abundance and the host organisms during the municipal wastewater treatment process.},
}
@article {pmid39796619,
year = {2025},
author = {Johnson, AJ and Alvear, A and Knights, D and Chow, LS and Bantle, AE},
title = {A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
pmid = {39796619},
issn = {2072-6643},
support = {KL2TR002492//National Institutes of Health, National Center of Advancing Translational Sciences/ ; UL1TR002494//National Institutes of Health, National Center for Advancing Translational Sciences/ ; K23DK115906/DK/NIDDK NIH HHS/United States ; 17SFR-2YR50LC//Healthy Foods, Healthy Lives Institute at the University of Minnesota/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome ; Male ; *Feces/microbiology ; Female ; Adult ; Obesity/microbiology ; Middle Aged ; Body Composition ; Fasting ; Time Factors ; },
abstract = {OBJECTIVE: TRE is an emerging approach in obesity treatment, yet there is limited data on how it influences gut microbiome composition in humans. Our objective was to characterize the gut microbiome of human participants before and after a TRE intervention. This is a secondary analysis of a previously published clinical trial examining the effects of time-restricted eating (TRE).<br><br>METHODS: In a previously published, 12-week randomized controlled trial, Chow et al. evaluated the effects of an 8-h TRE intervention on body composition in human participants. Chow et al. demonstrated significant reductions in weight, lean mass, and visceral fat in the TRE group compared to those following time-unrestricted eating (non-TRE). Stool samples were collected by a subset of those participants using home kits at both baseline and post-intervention for shotgun metagenomic sequencing for this secondary analysis. Microbiome community composition was compared before and after intervention as alpha and beta diversity.<br><br>RESULTS: Sixteen participants provided stool samples (eight in the TRE group and eight in the non-TRE group). Stool samples were collected from all participants at at least one time point, but both pre- and post-treatment samples were available from only five participants who completed both baseline and post-treatment collections. In alignment with the findings of Chow et al., the participants in the TRE group of the secondary analysis who collected microbiome sample(s) successfully reduced their eating window from an average of 15.3 &#xb1; 0.8 h at baseline to 9.3 &#xb1; 1.7 h during the intervention (mean &#xb1; SD, p < 0.001) and the non-TRE group's eating window remained unchanged. While the TRE group lost weight and visceral fat mass, no effect of the TRE intervention was observed on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-Curtis, PERMANOVA), even after controlling for weight and visceral fat changes.<br><br>CONCLUSIONS: Our analysis did not detect any significant differences in gut microbiome composition or diversity indices between participants undergoing a TRE intervention and those in the control group. The study's findings are limited by a small sample size, short duration, and the collection of stool samples at only two time points. Future studies with larger sample sizes, longer durations, and more frequent sampling, and collection of detailed dietary data are needed to better understand the relationship between TRE and gut microbiome dynamics.},
}
@article {pmid39796584,
year = {2024},
author = {Firrman, J and Deyaert, S and Mahalak, KK and Liu, L and Baudot, A and Joossens, M and Poppe, J and Cameron, SJS and Van den Abbeele, P},
title = {The Bifidogenic Effect of 2'Fucosyllactose Is Driven by Age-Specific Bifidobacterium Species, Demonstrating Age as an Important Factor for Gut Microbiome Targeted Precision Medicine.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
pmid = {39796584},
issn = {2072-6643},
support = {8072-41000-102-00D//United States Department of Agriculture/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Trisaccharides/pharmacology ; *Bifidobacterium/drug effects ; Infant ; *Feces/microbiology ; Aged ; Adult ; Child, Preschool ; *Precision Medicine ; Middle Aged ; Child ; Female ; Male ; Age Factors ; Young Adult ; Adolescent ; Milk, Human/chemistry ; Oligosaccharides/pharmacology ; Lactose ; },
abstract = {BACKGROUND: The human gut microbiota develops in concordance with its host over a lifetime, resulting in age-related shifts in community structure and metabolic function. Little is known about whether these changes impact the community's response to microbiome-targeted therapeutics. Providing critical information on this subject, faecal microbiomes of subjects from six age groups, spanning from infancy to 70-year-old adults (n = six per age group) were harvested. The responses of these divergent communities to treatment with the human milk oligosaccharide 2'-fucosyllactose (2'FL), fructo-oligosaccharides (FOS), and lactose was investigated using the Ex vivo SIFR[®] technology that employs bioreactor fermentation and is validated to be predictive of clinical findings. Additionally, it was evaluated whether combining faecal microbiomes of a given age group into a single pooled microbiome produced similar results as the individual microbiomes.<br><br>RESULTS: First, marked age-dependent changes in community structure were identified. Bifidobacterium levels strongly declined as age increased, and Bifidobacterium species composition was age-dependent: B. longum, B. catenulatum/pseudocatenulatum, and B. adolescentis were most prevalent for breastfed infants, toddlers/children, and adults, respectively. Metabolomic analyses (LA-REIMS) demonstrated that these age-dependent differences particularly impacted treatment effects of 2'FL (more than FOS/lactose). Further analysis revealed that while 2'FL enhanced production of short-chain fatty acids (SCFAs) and exerted potent bifidogenic effects, regardless of age, the specific Bifidobacterium species enhanced by 2'FL, as well as subsequent cross-feeding interactions, were highly age-dependent. Furthermore, single-pooled microbiomes produced results that were indicative of the average treatment response for each age group. Nevertheless, pooled microbiomes had an artificially high diversity, thus overestimating treatment responses (especially for infants), did not recapitulate interindividual variation, and disallowed for the correlative analysis required to unravel mechanistic actions.<br><br>CONCLUSIONS: Age is an important factor in shaping the gut microbiome, with the dominant taxa and their metabolites changing over a lifetime. This divergence affects the response of the microbiota to therapeutics, demonstrated in this study using 2'FL. These results evidence the importance of screening across multiple age groups separately to provide granularity of how therapeutics impact the microbiome and, consequently, human health.},
}
@article {pmid39796532,
year = {2024},
author = {Paterson, S and Majchrzak, M and Gómez-Garre, D and Ortega-Hernández, A and Sánchez-González, S and de la Fuente, M&#xc1; and Gómez-Cortés, P and Hernández-Ledesma, B},
title = {Role of Simulated Nannochloropsis gaditana Digests in Shaping Gut Microbiota and Short-Chain Fatty Acid Levels.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
pmid = {39796532},
issn = {2072-6643},
support = {PID2021-122989OB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PIPF-2022/BIO-24996//Comunidad Aut&#xf3;noma de Madrid/ ; },
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Fatty Acids, Volatile/metabolism ; *Microalgae ; *Fermentation ; Stramenopiles/metabolism ; RNA, Ribosomal, 16S ; Bacteria/metabolism/classification/genetics ; Colon/microbiology/metabolism ; },
abstract = {The connection between gut microbiota and factors like diet is crucial for maintaining intestinal balance, which in turn impacts the host's overall health. Nannochloropsis gaditana microalgae is a sustainable source of bioactive compounds, mainly known for its used in aquaculture and extraction of bioactive lipids, with potential health benefits whose effects on human gut microbiota are still unknown. Therefore, the goal of this work was to assess the impact of N. gaditana on human gut microbiota composition and derived metabolites by combining the INFOGEST protocol and in vitro colonic fermentation process to evaluate potential effects on human gut microbiota conformation through 16S rRNA gene sequencing and its metabolic functionality. The results have demonstrated the ability of the digests from N. gaditana to significantly modify gut microbiota composition, promoting an increase in beneficial bacterial genera such as Akkermansia, Butyricicoccus, Eisenbergiella, Lachnoclostridium, and Marvinbryantia, in contrast to inulin, after 48 h of colonic fermentation. Additionally, the digests increased the levels of both major and minor short-chain fatty acids (SCFAs), particularly butyric and valeric acids, considered as intestinal biomarkers, and increased ammonium production. This research has demonstrated, for the first time, the potential of N. gaditana microalgae as a sustainable agent for influencing the composition and functionality of human gut microbiota.},
}
@article {pmid39796518,
year = {2024},
author = {Vega-Rojas, A and Haro, C and Molina-Abril, H and Guil-Luna, S and Santos-Marcos, JA and Gutierrez-Mariscal, FM and Garcia-Fernandez, H and Caballero-Villarraso, J and Rodriguez-Ariza, A and Lopez-Miranda, J and Perez-Martinez, P and Hervas, A and Camargo, A},
title = {Gut Microbiota Interacts with Dietary Habits in Screenings for Early Detection of Colorectal Cancer.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
pmid = {39796518},
issn = {2072-6643},
support = {PI-0055-2021//Consejer&#xed;a de Salud y Consumo/ ; PI-0156-2016//Consejer&#xed;a de Salud y Consumo/ ; AGL2015-67896-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; n.a.//European Union/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI19/00299//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; C1-0001-2022//Andalusian Health Service/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Male ; Female ; Middle Aged ; *Feeding Behavior ; *Colonoscopy ; Aged ; Adenocarcinoma/microbiology ; Occult Blood ; Diet ; Colonic Polyps/microbiology/diagnosis ; Feces/microbiology ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbiota interacts with nutrients, which may be relevant to assigning a microbial signature to colorectal cancer (CRC). We aim to evaluate the potential of gut microbiota combined with dietary habits in the early detection of pathological findings related to CRC in the course of a screening program.<br><br>METHODOLOGY: The colonoscopy performed on 152 subjects positive for fecal occult blood test showed that 6 subjects had adenocarcinoma, 123 had polyps, and 23 subjects had no pathological findings. Gut microbiota was analyzed by 16S metagenomic. Caret package was used to build the classification models in R.<br><br>RESULTS: Random forest (RF) classifier models were used to test the potential of gut microbiota alone or combined with dietary habits as a biomarker to discern between individuals with CRC-related lesions (polyps or adenocarcinoma) versus individuals without pathological findings. RF classifier models yielded an area under the curve of 0.790 using gut microbiota data, 0.710 using dietary habits data, and 0.804 in the combined model including gut microbiota and dietary habits data. The abundance of Suterella, Oscillospirales, Proteobacteria, and Burkholderiales was highly discriminant between groups, together with the consumption of fruit and vegetables and the consumption of carbonated and/or sweetened beverages.<br><br>CONCLUSIONS: Our results suggest that the interaction between gut microbiota and dietary habits is relevant when a microbial signature is used as a marker in CRC. Moreover, gut microbiota signature and information about the dietary habits of the individuals seem to be important for improving screening programs for the early detection of CRC.},
}
@article {pmid39796476,
year = {2024},
author = {Andersen, CJ and Fernandez, ML},
title = {Emerging Biomarkers and Determinants of Lipoprotein Profiles to Predict CVD Risk: Implications for Precision Nutrition.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
pmid = {39796476},
issn = {2072-6643},
mesh = {Humans ; *Cardiovascular Diseases/blood/prevention &amp; control ; *Biomarkers/blood ; *Lipoproteins/blood ; Precision Medicine/methods ; Risk Factors ; Heart Disease Risk Factors ; Nutritional Status ; Risk Assessment ; },
abstract = {Biomarkers constitute a valuable tool to diagnose both the incidence and the prevalence of chronic diseases and may help to inform the design and effectiveness of precision nutrition interventions. Cardiovascular disease (CVD) continues to be the foremost cause of death all over the world. While the reasons that lead to increased risk for CVD are multifactorial, dyslipidemias, plasma concentrations of specific lipoproteins, and dynamic measures of lipoprotein function are strong biomarkers to predict and document coronary heart disease incidence. The aim of this review is to provide a comprehensive evaluation of the biomarkers and emerging approaches that can be utilized to characterize lipoprotein profiles as predictive tools for assessing CVD risk, including the assessment of traditional clinical lipid panels, measures of lipoprotein efflux capacity and inflammatory and antioxidant activity, and omics-based characterization of lipoprotein composition and regulators of lipoprotein metabolism. In addition, we discuss demographic, genetic, metagenomic, and lifestyle determinants of lipoprotein profiles-such as age, sex, gene variants and single-nucleotide polymorphisms, gut microbiome profiles, dietary patterns, physical inactivity, obesity status, smoking and alcohol intake, and stress-which are likely to be essential factors to explain interindividual responses to precision nutrition recommendations to mitigate CVD risk.},
}
@article {pmid39796430,
year = {2025},
author = {Chen, Q and He, S and Li, M and Sui, Y and Kong, B and Wen, R},
title = {Metagenomic Reveals the Role of Autochthonous Debaryomyces hansenii in the Fermentation and Flavor Formation of Dry Sausage.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39796430},
issn = {2304-8158},
support = {U22A20547//Baohua Kong/ ; 32172232//Qian Chen/ ; },
abstract = {The effect of Debaryomyces hansenii SH4, a typical aroma enhancer, on flavor formation of the dry fermented sausage was investigated using gas chromatography-mass spectrometry and metagenomic sequencing. The results showed that inoculation with D. hansenii SH4 promoted volatile compound formation from carbohydrate and amino acid metabolism and accelerated ester synthesis. The enzymes, genes, and microorganisms involved in the formation pathway of volatile compounds based on microbial metabolism were predicted and constructed into a metabolic pathway network. D. hansenii, Lactobacillus curvatus, Lactobacillus sakei, Lactobacillus plantarum, Leuconostoc fallax, Weissella minor, and Staphylococcus and Candida species were found to be the predominant functional microbes for flavor development in dry sausage. This study established a new insight into the metagenome-based bioinformatic effects of D. hansenii SH4 as a starter culture on the microbial synthesis of key volatile compounds in dry sausage.},
}
@article {pmid39796346,
year = {2024},
author = {Román-Camacho, JJ and Santos-Dueñas, IM and García-García, I and García-Martínez, T and Peinado, RA and Mauricio, JC},
title = {Correlating Microbial Dynamics with Key Metabolomic Profiles in Three Submerged Culture-Produced Vinegars.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39796346},
issn = {2304-8158},
support = {PID2021-127766OB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
abstract = {Although vinegar is a product obtained by a well-known bioprocess from a technical point of view, the complex microbiota responsible for its production and their involvement in the organoleptic profiles are not clear yet. In this work, three acetification profiles in submerged culture using both synthetic and raw materials from Andalusia (Spain) were characterized by metagenomic (16S rRNA amplicon sequencing) and metabolomic tools (stir-bar sorptive extraction with thermo-desorption coupled to gas chromatography-mass spectrometry (SBSE-TD-GC-MS) and high-performance liquid chromatography (HPLC)). A total of 29 phyla, 208 families, and many more genera were identified, comprising bacteria and archaea as well as 75 metabolites, including minor volatile compounds, amino acids, biogenic amines, and other nitrogenous compounds. It can be concluded that Komagataeibacter and Acetobacter were not only the predominant genera but also the ones that most influenced vinegar metabolite profiles by using different metabolic strategies for mutual collaboration, and together with other microbial groups, some of them were previously practically unknown in vinegar. These results can be of interest not only to deepen the basic knowledge about vinegar but also to the vinegar industry by elucidating microbial succession and the key associated metabolites.},
}
@article {pmid39796296,
year = {2024},
author = {Lee, JH and Son, H and Subramaniyam, S and Lim, HJ and Park, S and Choi, RY and Kim, IW and Seo, M and Kweon, HY and Kim, Y and Kim, SW and Choi, JS and Shin, Y},
title = {Impact of Edible Insect Polysaccharides on Mouse Gut Microbiota: A Study on White-Spotted Flower Chafer Larva (Protaetia brevitarsis seulensis) and Silkworm Pupa (Bombyx mori).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39796296},
issn = {2304-8158},
support = {PJ01673101//the Cooperative Research Program for Agriculture Science and Technology Development (Project no. PJ01673101)/ ; },
abstract = {The increasing global population and the environmental consequences of meat consumption have led to the exploration of alternative sources of protein. Edible insects have gained attention as a sustainable and nutritionally rich meat alternative. We investigated the effects of two commonly consumed insects, Protaetia brevitarsis seulensis larva and Bombyx mori pupa, on beneficial gut microbiota growth, using whole 16s metagenome sequencing to assess diet-associated changes. Seven-week-old female C57BL/6J mice were administered the edible insects, along with fracto-oligosaccharide (FOS) as a positive control and sham (phosphate buffer saline (PBS)) as a negative control, to assess the relative abundance of insect-diet-associated gut microbes. In total, 567 genera and 470 species were observed, and among these, 15 bacterial genera were differentially abundant in all three groups. These results show that among the two insects, Bombyx mori pupa polysaccharides have a greater ability to regulate beneficial probiotics and next-generation probiotics. In particular, Lactococcus garvieae, which has promising effects on the gastrointestinal tracts of humans and animals, was significantly enriched in both Protaetia brevitarsis seulensis larva and Bombyx mori pupa polysaccharides, similar to fracto-oligosaccharide. The results suggest that the consumption of these insects, particularly polysaccharides, can enhance the growth of beneficial gut microbes, potentially leading to improved overall health in healthy populations.},
}
@article {pmid39796082,
year = {2024},
author = {Kim, DG and Lee, CM and Lee, YS and Yoon, SH and Kim, SY},
title = {Isolation of a Novel Low-Temperature-Active and Organic-Solvent-Stable Mannanase from the Intestinal Metagenome of Hermetia illucens.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
pmid = {39796082},
issn = {1422-0067},
support = {Project No. PJ008604//Rural Development Administration/ ; },
mesh = {*Mannans/metabolism ; Animals ; Phylogeny ; Metagenome ; Diptera/microbiology ; Mannosidases/metabolism/genetics/chemistry ; Gastrointestinal Microbiome ; Substrate Specificity ; Amino Acid Sequence ; Galactans/metabolism ; Enzyme Stability ; Cold Temperature ; Plant Gums/chemistry/metabolism ; Hydrogen-Ion Concentration ; Intestines/microbiology ; Solvents/chemistry ; Recombinant Proteins/metabolism/genetics/chemistry ; Galactose/analogs &amp; derivatives ; },
abstract = {The black soldier fly, Hermetia illucens, is a voracious scavenger of various organic materials; therefore, it could be exploited as a biological system for processing daily food waste. In order to survey novel hydrolytic enzymes, we constructed a fosmid metagenome library using unculturable intestinal microorganisms from H. illucens. Through functional screening of the library on carboxymethyl cellulose plates, we identified a fosmid clone, the product of which displayed hydrolytic activity. Sequence analysis of the fosmid revealed a novel mannan-degrading gene, ManEM6, composed of 1185 base pairs encoding 394 amino acids, with a deduced 20-amino-acid N-terminal signal peptide sequence. The conceptual translation of ManEM6 exhibited the highest identity (78%) to endo-1,4-β-mannosidase from Dysgonomonas mossii. Phylogenetic and domain analyses indicated that ManEM6 encodes a novel mannanase with a glycoside hydrolase family 26 domain. The recombinant protein rManEM6 showed its highest activity at 40 °C and pH 7.0, and it remained stable in the range of pH 5-10.0. rManEM6 hydrolyzed substrates with β-1,4-glycosidic mannoses, showing maximum enzymatic activity toward locust bean gum galactomannan, while it did not hydrolyze p-nitrophenyl-β-pyranosides, demonstrating endo-form mannosidase activity. rManEM6 was highly stable under stringent conditions, including those of polar organic solvents, as well as reducing and denaturing reagents. Therefore, ManEM6 may be an attractive candidate for the degradation of mannan under high-organic-solvent and protein-denaturing processes in the food and feed industries.},
}
@article {pmid39795878,
year = {2024},
author = {Niecwietajewa, I and Banasiewicz, J and Zaremba-Wróblewski, G and Majewska, A},
title = {Exploring the Link Between Infections and Primary Osteoarthritis: A Next-Generation Metagenomic Sequencing Approach.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
pmid = {39795878},
issn = {1422-0067},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Osteoarthritis, Knee/microbiology/genetics ; Female ; Male ; Aged ; Prospective Studies ; Pilot Projects ; Middle Aged ; Synovial Fluid/microbiology ; Synovial Membrane/microbiology ; Metagenome ; },
abstract = {This prospective pilot study examined the association between microorganisms and knee osteoarthritis by identifying pathogens in the synovial membrane, synovial fluid, and blood samples from two patients with primary bilateral knee osteoarthritis, using metagenomic next-generation sequencing (mNGS). Intraoperatively, during routine knee arthroplasty procedures, we collected the following 12 samples from each patient: two synovial membrane samples, two synovial fluid samples, and two venous blood samples. After DNA isolation and library construction, each sample was subjected to deep whole-genome sequencing using the DNBSEQT17 platform with the read length PE150 as the default. Metagenomic sequencing data were mapped to the NCBI NT database to determine species abundance. The predominant species in all samples tested were classified under the Enterobacterales order, the most abundant being Yersinia enterocolitica. The second and third most common microorganisms detected were Escherichia coli and autotrophic, Gram-negative bacteria Synechococcus sp., which is a bioaerosol component, indicating a risk of inhalation of the toxic metabolites of this latter microorganism. This article provides an initial exploration of mNGS use to study the etiopathogenetic mechanisms of knee osteoarthritis (OA). While our analysis identified bacterial DNA, particularly from Yersinia, further cross-sectional studies in larger populations with and without OA are needed to determine the role of these agents in OA pathogenesis.},
}
@article {pmid39795003,
year = {2024},
author = {Kaszab, E and Sós, E and Bali, K and Sós-Koroknai, V and Perge, E and Ursu, K and Marton, S and Hoitsy, M and Kemenesi, G and Bányai, K},
title = {Near-Complete Avipoxvirus Genome Assembled from Skin Lesions of Dead Eurasian Crane (Grus grus).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {1},
pages = {},
pmid = {39795003},
issn = {2076-2615},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00010//National Research, Development and Innovation Office/ ; },
abstract = {Avian pox is a globally spread viral disease affecting a wide spectrum of wild and domesticated bird species. The disease is caused by a diverse group of large DNA viruses, namely, avipoxviruses (genus Avipoxvirus, family Poxviridae). In this study, gross pathological examination and histopathological examination of skin lesions and several organs suggested acute poxvirus infection of a Eurasian crane (Grus grus, Linnaeus, 1758). Avipoxvirus infection was confirmed by testing wart-like lesions via gene-specific PCR assay and sequencing the obtained amplicon. Phylogenetic analysis of the gene encoding the DNA polymerase revealed that the crane poxvirus clustered in clade A, subclade A3. A large fragment of the poxvirus genome (306,477 bp in length) was assembled from the DNA of a skin specimen. Our study reaffirms previous findings that even complex virus genomes can be determined from a metagenomic assemblage generated directly from avian tissue samples without prior virus isolation, a promising approach for the epidemiologic surveillance of avipoxvirus infections in wild birds and domestic poultry.},
}
@article {pmid39795000,
year = {2024},
author = {Dai, Z and Xie, B and Xie, C and Xiang, J and Wang, X and Li, J and Zheng, R and Wang, Y},
title = {Comparative Metagenomic Analysis of the Gut Microbiota of Captive Pangolins: A Case Study of Two Species.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {1},
pages = {},
pmid = {39795000},
issn = {2076-2615},
support = {2021C02044//Key R&amp;D Program Projects in Zhejiang Province/ ; },
abstract = {Pangolins, one of the most trafficked mammals, face significant health challenges in captivity, including digestive disorders and immune dysfunctions. These issues are closely linked to alterations in their gut microbiota, which play vital roles in the host metabolism, immunity, and overall health. This study investigated the differences in the gut microbiota composition and function between two pangolin species, Chinese pangolins (Manis pentadactyla) and Malayan pangolins (Manis javanica), under identical captive conditions to better understand their ecological adaptability and health implications. Using metagenomic sequencing, fecal samples from eight adult captive pangolins were analyzed, including four male Malayan pangolins and three male and one female Chinese pangolins. Comparative analyses of the alpha and beta diversities, microbial community structure, and functional profiles were performed. Both species harbored gut microbiota dominated by Firmicutes, Bacteroidetes, and Proteobacteria. However, the Chinese pangolins exhibited higher microbial diversity (Shannon index, p = 0.042; Simpson index, p = 0.037) and lower relative abundance of Proteobacteria compared with the Malayan pangolins. A functional analysis revealed significant differences in the metabolic pathways, where the Chinese pangolins demonstrated a higher potential for fiber degradation, whereas the Malayan pangolins exhibited elevated levels of antibiotic resistance genes and pathogenic taxa, such as Escherichia coli. These findings suggest that captivity duration and environmental stress likely contribute to the observed differences, with the Malayan pangolins experiencing greater dysbiosis due to longer captivity periods. This study provides valuable insights into the role of gut microbiota in pangolin health and offers a foundation for improving conservation strategies and captive care protocols.},
}
@article {pmid39794871,
year = {2025},
author = {Samodova, D and Stankevic, E and Søndergaard, MS and Hu, N and Ahluwalia, TS and Witte, DR and Belstrøm, D and Lubberding, AF and Jagtap, PD and Hansen, T and Deshmukh, AS},
title = {Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {5},
pmid = {39794871},
issn = {2049-2618},
support = {74550801//European Foundation for the Study of Diabetes/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Saliva/microbiology ; *Proteomics/methods ; Male ; Middle Aged ; Female ; *Microbiota ; Biomarkers/metabolism ; Bacterial Proteins/genetics ; Adult ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Computational Biology/methods ; Salivary Proteins and Peptides/metabolism ; Case-Control Studies ; Aged ; },
abstract = {BACKGROUND: Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.<br><br>RESULTS: We conducted ultrafast, in-depth MS-based proteomic and metaproteomic profiling of saliva from 15 newly diagnosed T2D individuals and 15 age-/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Abundance of peptides for bacterial genera such as Neisseria and Corynebacterium were altered showing biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management.<br><br>CONCLUSIONS: This study presents a comprehensive mapping of salivary proteins and microbial communities, serving as a foundational resource for enhancing understanding of T2D pathophysiology. The identified biomarkers hold promise for advancing diagnostics and therapeutic approaches in T2D and its associated long-term complication Video Abstract.},
}
@article {pmid39794645,
year = {2025},
author = {Dirks, RAM and Sosef, NP and Zwartkruis-Nahuis, JTM and Thijssen, MMA and Jansen, CCC and Boxman, ILA},
title = {A Metagenomic Survey of Virological Hazards in Market-Ready Oysters.},
journal = {Food and environmental virology},
volume = {17},
number = {1},
pages = {16},
pmid = {39794645},
issn = {1867-0342},
mesh = {Animals ; *Metagenomics ; *Ostreidae/virology ; *Food Contamination/analysis ; *Shellfish/virology ; Norovirus/genetics/classification/isolation &amp; purification ; Metagenome ; Netherlands ; Genome, Viral ; Viruses/genetics/classification/isolation &amp; purification ; Food Safety ; },
abstract = {Viral contamination of bivalve molluscs, such as oysters, is a well-recognized food safety risk. The aim of this study was to assess virological hazards in market-ready oysters on the Dutch market. Non-targeted metagenome analysis was first performed on norovirus spiked-in samples showing linear and sensitive detection of norovirus GI.2 and GII.4 down to 14 and 5 genome copies per reaction, respectively. Subsequently, metagenomic measurements were performed to detect vertebrate viral genomes present in 24 undepurated B-area samples and 144 market-ready oyster samples taken in November up to and including February of the years 2015-2021. Genome sequences from fifteen viral species were identified in market-ready oysters which are associated with infections in humans and were detected above the genomic coverage threshold (5%) applied. Among these, the two genera from the Caliciviridae family, norovirus and sapovirus were detected at high prevalence (44 and 30%). Additionally, adeno-associated dependoparvovirus A and B as well as Aichi virus A and B (ribo)nucleic acids were detected (42, 33, 6, and 11%). Nucleic acids from virus species in oysters included potentially hazardous Picobirnavirus, Anellovirus, and multiple Circoviridae and Genomoviridae species. By integrating metagenome analysis into the monitoring process, researchers, food producers and regulatory bodies can gain valuable insights into the viral communities present in the food chain. This allows for the detection of potential pathogenic hazards at an early stage, providing an opportunity for tailored monitoring programs and targeted interventions to maintain the sanitary quality of the production area and safeguard public health.},
}
@article {pmid39794618,
year = {2025},
author = {Nguyen, HP and Le, BT and Nguyen, HN and Nguyen, TT and Duong, TH and Hoang, TC and Duy, NPT and Nguyen, MV and Duong, LN and Le, LQ and Pham, TT},
title = {Demonstration of adapted packed-bed bioreactor for accurate and rapid estimation of biochemical oxygen demand: insights into the influence of microbial community structure and functions.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {2},
pages = {31},
pmid = {39794618},
issn = {1573-0972},
support = {NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; },
mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology/chemistry ; *Biological Oxygen Demand Analysis ; *Microbial Consortia ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Biodegradation, Environmental ; Cocos/microbiology ; Glucose/metabolism ; Azo Compounds/metabolism ; Metagenome ; },
abstract = {This study demonstrated a novel approach to accurately estimate 5-day biochemical oxygen demand (BOD5) in textile wastewater using a microbial consortium from food processing wastewater fixed on coconut fibers. Although glucose-glutamic acid (GGA) has been widely known as the most preferred substrates for microbial respiration, its calibration surprisingly resulted in an overestimation of BOD5 in textile wastewater due to its lower utilization rate compared to that of textile wastewater. After being adapted with a new nutrient environment composed of GGA and textile wastewater, the adapted packed-bed bioreactors (PBBRs) was capable of accurate estimation of BOD5 in textile wastewater using GGA standard solution. Metagenomic analysis revealed the dominance of the genera Enterobacter, Acinetobacter, Chryseobacterium, and Comamonas in the adapted microbial community, which are recognized for their significant potential in azo dye degradation. The imputed metagenome showed an enhanced showed an enhanced abundance of "Amino Acid Degradation" and "Carbohydrate Degradation" functions, confirming the improved ability of adapted community to utilization of GGA in the standard solution. These findings suggest that adaptation of exogenous microbial consortium to a nutrient environment composed of GGA and target wastewater may shift the community to that dominated by strains having both utilization ability of GGA and target compounds which, in turn, enhance the accuracy of the adapted PBBRs for estimation of BOD5 in target wastewater.},
}
@article {pmid39794474,
year = {2025},
author = {Yin, Q and da Silva, AC and Zorrilla, F and Almeida, AS and Patil, KR and Almeida, A},
title = {Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {541-553},
pmid = {39794474},
issn = {2058-5276},
support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Enterobacteriaceae/genetics/classification/isolation &amp; purification ; Metagenome ; Enterobacteriaceae Infections/microbiology ; Feces/microbiology ; Machine Learning ; },
abstract = {Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.},
}
@article {pmid39794073,
year = {2025},
author = {Kitsios, GD and Morris, A},
title = {Blurred Lines on the Dysbiosis Spectrum: Pneumocystis Colonization vs Infection by Metagenomics.},
journal = {Chest},
volume = {167},
number = {1},
pages = {3-5},
doi = {10.1016/j.chest.2024.08.038},
pmid = {39794073},
issn = {1931-3543},
}
@article {pmid39793869,
year = {2025},
author = {Xu, W and Wu, L and Geng, M and Zhou, J and Bai, S and Nguyen, DV and Ma, R and Wu, D and Qian, J},
title = {Biochar@MIL-88A(Fe) accelerates direct interspecies electron transfer and hydrogen transfer in waste activated sludge anaerobic digestion: Exploring electron transfer and biomolecular mechanisms.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120810},
doi = {10.1016/j.envres.2025.120810},
pmid = {39793869},
issn = {1096-0953},
abstract = {Adding additives exogenously is an effective strategy to enhance methanogenic activity and improve AD stability. Corn straw-based biochar@MIL-88A(Fe) (BM) was synthesized herewith and used as an exogenous additive to boost methane (CH4) production. After adding BM at 250 mg/g WAS VS, the accumulative CH4 production and maximum CH4 yield increased by 1.2 and 1.9 times, respectively, with CH4 comprising 88% of the biogas. BM accelerated electron transfer through its unsaturated sites and surface functional groups, while also enhancing metabolic functions for facilitating enzymatic activities and converting organic substrates. The abundance of syntrophic bacteria and methanogen were higher after BM addition. BM-mediated DIET and IHT pathways effectively oxidized propionate and butyrate, promoting methane generation. Higher expression of key genes involved in methane production correlated with shifts in microbial structure and increased CH4 yield after BM dosage. The invention of BM may provide more solutions for addressing low energy recovery during AD.},
}
@article {pmid39793775,
year = {2025},
author = {Li, X and Ning, L and Zhao, H and Gu, C and Han, Y and Xu, W and Si, Y and Xu, Y and Wang, R and Ren, Q},
title = {Jiawei Ermiao Granules (JWEMGs) clear persistent HR-HPV infection though improving vaginal microecology.},
journal = {Journal of ethnopharmacology},
volume = {341},
number = {},
pages = {119342},
doi = {10.1016/j.jep.2025.119342},
pmid = {39793775},
issn = {1872-7573},
mesh = {Female ; Humans ; *Vagina/microbiology/drug effects/pathology ; *Papillomavirus Infections/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Adult ; Middle Aged ; Microbiota/drug effects ; Antiviral Agents/pharmacology ; Cytokines/metabolism ; Young Adult ; },
abstract = {Jiawei Ermiao Granules (JWEMGs), a traditional Chinese herbal formulation, has been widely used in China for the treatment of human papillomavirus (HPV) infections. However, the underlying mechanisms through which it exerts its antiviral effects remain poorly understood.<br><br>AIM OF THE STUDY: This study aimed to investigate the potential mechanisms by which JWEMGs modulate vaginal microecology and clear HPV infections, utilizing clinical trials, metagenomic sequencing, and in vitro models.<br><br>MATERIALS AND METHODS: Clinical indicators related to vaginal microecology, such as vaginal pH, cleanliness, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, were evaluated in 65 patients with high-risk HPV (HR-HPV) infection. The study examined the impact of two courses of oral JWEMGs on these clinical parameters. Additionally, metagenomic sequencing was performed on vaginal lavage samples from 33 patients to assess the alteration of the vaginal microbiome following JWEMGs treatment. Immunohistochemistry was used to detect ALPK1 expression in cervical exfoliated cells, and ELISA was employed to measure cytokine levels in vaginal lavage fluid. JWEMGs intervention was applied to HaCaT-HPV E6/E7 cells to evaluate its effects on restoring &#x3b1;-kinase 1 (ALPK1) expression and promoting the secretion of cytokines and chemokines.<br><br>RESULTS: Treatment with JWEMGs significantly improved several clinical indicators, including cleanliness, pH, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, in HR-HPV-infected patients. Furthermore, JWEMGs therapy led to an increased abundance of Lactobacillus species, especially Lactobacillus crispatus, and a marked reduction in Gardnerella species. JWEMGs treatment also significantly promoted ALPK1 expression in cervical exfoliated cells and augmented the secretion of key cytokines, including IL-6, IL-8, and TNF-&#x3b1;. In parallel, in vitro results showed that JWEMGs substantially enhanced IL-6, IL-8, TNF-&#x3b1;, CCL2, CCL5, and CCL7 secretion in HaCaT-HPV E6/E7 cells, which correlated with the activation of the ALPK1/NF-&#x3ba;B signaling pathway.<br><br>CONCLUSION: In conclusion, JWEMGs treatment effectively remodels the vaginal microbiota and bolsters mucosal immunity in the lower genital tract, thereby improving the vaginal microecology in HR-HPV-infected individuals. In vitro findings further demonstrated that JWEMGs promote cytokine and chemokine expression, activating the ALPK1/NF-&#x3ba;B pathway.},
}
@article {pmid39793486,
year = {2025},
author = {Eckermann, H and Lustermans, H and Parnanen, K and Lahti, L and de Weerth, C},
title = {Maternal pre- and postnatal stress and maternal and infant gut microbiota features.},
journal = {Psychoneuroendocrinology},
volume = {172},
number = {},
pages = {107273},
doi = {10.1016/j.psyneuen.2024.107273},
pmid = {39793486},
issn = {1873-3360},
abstract = {BACKGROUND: Maternal stress can have short and long term adverse (mental) health effects for the mother and her child. Previous evidence suggests that the gut microbiota may be a potential mediator and moderator for the effects of stress via various pathways. This study explored the maternal microbiota trajectory during pregnancy as well as the association between pre- and postnatal maternal stress and features of the maternal and infant gut microbiota during and after pregnancy. In line with previous research, we hypothesized that maternal stress would be positively related to maternal and infant microbiota volatility and that infants of highly stressed mothers would show a relative increase in Proteobacteria and a relative decrease in Bifidobacterium.<br><br>METHODS: We collected maternal stool samples at 18 and 32 weeks of pregnancy and 8 months postpartum. Infant stools samples were obtained at 2, 6 and 12 weeks and 8 months postpartum. All samples were analyzed using shotgun metagenome sequencing. We also collected several measures of maternal stress (self-reported depression, anxiety, and stress, and hair cortisol and cortisone), most at the same time points as the microbiota samples.<br><br>RESULTS: Our data indicated that the maternal microbiota does not undergo drastic changes from the second to the third trimester of pregnancy but that the postpartum microbiota differs significantly from the prenatal microbiota. Furthermore, we identified associations between several stress measures and maternal and infant gut microbiota features at different time points including positive and negative associations with alpha diversity, beta diversity and individual microbial phyla and species relative abundances. Also, the maternal stress composite score, the perceived stress score and the log-ratio of hair cortisol and cortisone were all positively associated with infant microbiota volatility.<br><br>CONCLUSION: Our study provides evidence that maternal prenatal and postnatal stress is related to both the maternal and the infant microbiota. Collectively, this and previous studies indicate that maternal stress does not uniformly associate with most gut microbial features. Instead, the associations are highly time point specific. Regarding infant microbiota volatility, we have consistently found a positive association between stress and infant microbiota volatility. This warrants future research investigating this link in more depth.},
}
@article {pmid39793467,
year = {2025},
author = {Cardacino, A and Turco, S and Balestra, GM},
title = {Seasonal dynamics of kiwifruit microbiome: A case study in a KVDS-affected orchard.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128044},
doi = {10.1016/j.micres.2024.128044},
pmid = {39793467},
issn = {1618-0623},
mesh = {*Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Seasons ; *Actinidia/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Plant Roots/microbiology ; Italy ; Metagenomics ; Temperature ; },
abstract = {Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.},
}
@article {pmid39793444,
year = {2025},
author = {Verheijden, RJ and van Eijs, MJM and Paganelli, FL and Viveen, MC and Rogers, MRC and Top, J and May, AM and van de Wijgert, JHHM and Suijkerbuijk, KPM and , },
title = {Gut microbiome and immune checkpoint inhibitor toxicity.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {216},
number = {},
pages = {115221},
doi = {10.1016/j.ejca.2025.115221},
pmid = {39793444},
issn = {1879-0852},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/adverse effects ; Male ; Female ; Middle Aged ; Aged ; Prospective Studies ; *Neoplasms/drug therapy/microbiology ; Dysbiosis/chemically induced/microbiology ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.<br><br>METHODS: Stool samples of cancer patients treated with anti-PD-1&#x202f;&#xb1;&#x202f;anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.<br><br>FINDINGS: We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2&#x202f;%) compared to those who did not (4.8&#x202f;%; odds ratio 1.40; 95&#x202f;%CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.<br><br>INTERPRETATION: Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.},
}
@article {pmid39793291,
year = {2025},
author = {Jahanshahi, DA and Barzani, MRR and Bahram, M and Ariaeenejad, S and Kavousi, K},
title = {Metagenomic exploration and computational prediction of novel enzymes for polyethylene terephthalate degradation.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117640},
doi = {10.1016/j.ecoenv.2024.117640},
pmid = {39793291},
issn = {1090-2414},
mesh = {*Polyethylene Terephthalates/chemistry ; *Biodegradation, Environmental ; *Metagenomics ; *Soil Microbiology ; *Soil Pollutants/analysis ; Machine Learning ; Enzymes/metabolism/genetics ; },
abstract = {As a global environmental challenge, plastic pollution raises serious ecological and health concerns owing to the excessive accumulation of plastic waste, which disrupts ecosystems, harms wildlife, and threatens human health. Polyethylene terephthalate (PET), one of the most commonly used plastics, has contributed significantly to this growing crisis. This study offers a solution for plastic pollution by identifying novel PET-degrading enzymes. Using a combined approach of computational analysis and metagenomic workflow, we identified a diverse array of genes and enzymes linked to plastic degradation. Our study identified 1305,282 unmapped genes, 36,000 CAZymes, and 317 plastizymes in the soil samples were heavily contaminated with plastic. We extended our approach by training machine learning models to discover candidate PET-degrading enzymes. To overcome the scarcity of known PET-degrading enzymes, we used a Generative Adversarial Network (GAN) model for dataset augmentation and a pretrained deep Evolutionary Scale Language Model (ESM) to generate sequence embeddings for classification. Finally, 21 novel PET-degrading enzymes were identified. These enzymes were further validated through active site analysis, amino acid composition analysis, and 3D structure comparison. Additionally, we isolated bacterial strains from contaminated soils and extracted plastizymes to demonstrate their potential for environmental remediation. This study highlights the importance of biotechnological solutions for plastic pollution, emphasizing scalable, cost-effective processes and the integration of computational and metagenomic methods.},
}
@article {pmid39791120,
year = {2024},
author = {Huang, H and Yang, Y and Wang, X and Wen, B and Yang, X and Zhong, W and Wang, Q and He, F and Li, J},
title = {Gut virome dysbiosis impairs antitumor immunity and reduces 5-fluorouracil treatment efficacy for colorectal cancer.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1501981},
pmid = {39791120},
issn = {2234-943X},
abstract = {INTRODUCTION: Despite the established influence of gut bacteria, the role of the gut virome in modulating colorectal cancer (CRC) patient chemotherapy response remains poorly understood. In this study, we investigated the impact of antiviral (AV) drug-induced gut virome dysbiosis on the efficacy of 5-FU in CRC treatment.<br><br>METHODS: Using a subcutaneous CRC mouse model, we assessed tumor growth and immune responses following AV treatment, fecal microbiota transplantation (FMT), and 5-FU administration.<br><br>RESULTS: AV therapy reduced the abundance of gut DNA and RNA viruses, leading to accelerated tumor growth, shortened survival, and diminished chemotherapy efficacy. FMT restored the gut virome, improving tumor suppression and extending the survival of 5-FU-treated mice. Metagenomic sequencing revealed significant changes in virome composition, AV treatment expanded Kahnovirus, Petivirales, and Enterogokushovirus, whereas FMT enriched Peduovirus STYP1, Mahlunavirus rarus, and Jouyvirus ev207. AV treatment reduced the number of dendritic cells and CD8+ T cells in peripheral blood and tumor tissues, impairing antitumor immunity, FMT reversed these deficiencies. To further investigate the underlying mechanisms, we examined the TLR3-IRF3-IFN-&#x3b2; pathway, essential for recognizing viral RNA and triggering immune responses. AV treatment downregulated this pathway, impairing immune cell recruitment and reducing chemotherapy efficacy, while activation of TLR3 with Poly(I:C) restored pathway function and enhanced the effectiveness of 5-FU.<br><br>DISCUSSION: These findings suggest the importance of maintaining gut virome integrity or activating TLR3 as adjunct strategies to enhance chemotherapy outcomes in CRC patients.},
}
@article {pmid39790984,
year = {2025},
author = {Paiva, P and Teixeira, LMC and Wei, R and Liu, W and Weber, G and Morth, JP and Westh, P and Petersen, AR and Johansen, MB and Sommerfeldt, A and Sandahl, A and Otzen, DE and Fernandes, PA and Ramos, MJ},
title = {Unveiling the enzymatic pathway of UMG-SP2 urethanase: insights into polyurethane degradation at the atomic level.},
journal = {Chemical science},
volume = {16},
number = {5},
pages = {2437-2452},
pmid = {39790984},
issn = {2041-6520},
abstract = {The recently discovered metagenomic urethanases UMG-SP1, UMG-SP2, and UMG-SP3 have emerged as promising tools to establish a bio-based recycling approach for polyurethane (PU) waste. These enzymes are capable of hydrolyzing urethane bonds in low molecular weight dicarbamates as well as in thermoplastic PU and the amide bond in polyamide employing a Ser-Ser cis -Lys triad for catalysis, similar to members of the amidase signature protein superfamily. Understanding the catalytic mechanism of these urethanases is crucial for enhancing their enzymatic activity and improving PU bio-recycling processes. In this study, we employed hybrid quantum mechanics/molecular mechanics methods to delve into the catalytic machinery of the UMG-SP2 urethanase in breaking down a model PU substrate. Our results indicate that the reaction proceeds in two stages: STAGE 1 - acylation, in which the enzyme becomes covalently bound to the PU substrate, releasing an alcohol-leaving group; STAGE 2 - deacylation, in which a catalytic water hydrolyzes the enzyme:ligand covalent adduct, releasing the product in the form of a highly unstable carbamic acid, expected to rapidly decompose into an amine and carbon dioxide. We found that STAGE 1 comprises the rate-limiting step of the overall reaction, consisting of the cleavage of the substrate's urethane bond by its ester moiety and the release of the alcohol-leaving group (overall Gibbs activation energy of 20.8 kcal mol[-1]). Lastly, we identified point mutations that are expected to enhance the enzyme's turnover for the hydrolysis of urethane bonds by stabilizing the macrodipole of the rate-limiting transition state. These findings expand our current knowledge of urethanases and homolog enzymes from the amidase signature superfamily, paving the way for future research on improving the enzymatic depolymerization of PU plastic materials.},
}
@article {pmid39789504,
year = {2025},
author = {Duan, J and Ding, J and Wei, Y and Zhang, Y and You, Z and Li, D and Chen, C},
title = {Metagenomic analysis identifying a polymicrobial pulmonary infection in a non-HIV immunocompromised patient: a case report.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {12},
pmid = {39789504},
issn = {1471-2466},
support = {2019WS113//the Medical Science and Technology Development Foundation of Department of Health of Shandong Province/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Immunocompromised Host ; *Metagenomics ; *Coinfection/diagnosis ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Pneumocystis carinii/isolation &amp; purification/genetics ; Nocardia/isolation &amp; purification/genetics ; Tomography, X-Ray Computed ; Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Polymicrobial pulmonary infections, common in immunocompromised patients, often manifest more severe symptoms than monomicrobial infections. Clinical diagnosis delays may lead to mortality, emphasizing the importance of fast and accurate diagnosis for these patients. Metagenomic next-generation sequencing (mNGS), as an unbiased method capable of detecting all microbes, is a valuable tool to identify pathogens, particularly in cases where infections are difficult to diagnosis using conventional methods.<br><br>CASE PRESENTATION: A 50-year-old male patient was admitted due to cough, expectoration and dyspnea. CT scan revealed diffuse inflammatory and cavernous lung lesion, and blood examination suggested a polymicrobial infection. However, no etiology was found by routine examination. mNGS of bronchoalveolar lavage fluid(BALF)simultaneously detected the presence of Pneumocystis jirovecii (P.jirovecii), Aspergillus fumigates (A.fumigates), Nocardia farcinica (N.farcinica), Salmonella enterica subsp. enterica (S.enterica subsp. enterica), and cytomegalovirus (CMV). The patient was successfully treated with compound sulfamethoxazole (SMZ-TMP), cefoperazone/sulbactam (SCF), moxifloxacin (MXF), voriconazole (VCZ), and ganciclovir. The patient recovered after two weeks of anti-infection therapy and maintained good health at a six-month follow-up.<br><br>CONCLUSION: For immunocompromised patients with multiple infections and atypical symptoms, mNGS emerged as a reliable approach to pathogen detection and guiding antibiotic therapy.},
}
@article {pmid39789442,
year = {2025},
author = {Tu, Y and Deng, M and Zhang, X and Xiang, T and Wu, D},
title = {Dabie bandavirus and Mycoplasma pneumoniae co-infection: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {47},
pmid = {39789442},
issn = {1471-2334},
support = {82000601//National Natural Science Foundation of China/ ; 20224BAB206022, 20232A CB216004//Natural Science Foundation of Jiangxi Province/ ; },
mesh = {Humans ; Male ; *Coinfection/microbiology/virology ; Middle Aged ; *Mycoplasma pneumoniae/isolation &amp; purification/genetics ; *Pneumonia, Mycoplasma/complications/drug therapy/diagnosis/microbiology ; Severe Fever with Thrombocytopenia Syndrome/diagnosis/virology ; Immunoglobulin M/blood ; },
abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by Dabie bandavirus (DBV). We report a case of DBV and Mycoplasma pneumoniae (MP) co-infection.<br><br>CASE PRESENTATION: Here we reported a 57-year-old healthy male who was admitted with the presentations of fever, cough, hemoptysis, and hypotension. Laboratory investigations revealed thrombocytopenia, leukopenia, and organ dysfunction of liver and kidney. Seroconversion from Mycoplasma IgM antibody to IgG was recorded, and SFTS was confirmed through metagenomic next-generation sequencing. In addition, hemophagocytic lymphohistiocytosis was diagnosed in the context of DBV and MP coinfection. The patient exhibited a rapid recovery following treatment with omadacycline and essential symptomatic and supportive treatment.<br><br>CONCLUSIONS: We firstly reported a case with DBV and MP coinfection, which reminded us that the symptoms of DBV infection were bewildering and easy to miss diagnosis when it was co-infection with other etiologies.},
}
@article {pmid39789436,
year = {2025},
author = {Cao, T and Guo, Y and Lin, L and Wang, D and Liu, Z and Zou, X and Ke, Y and Lv, Z},
title = {Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {11},
pmid = {39789436},
issn = {1471-2180},
support = {JCYJ20210324124014040//Shenzhen Science and Technology Program/ ; JCYJ20210324124201004//Shenzhen Science and Technology Program/ ; SZSM202011008//Sanming Project of Medicine in Shenzhen/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Hypoglycemia/genetics/chemically induced ; Blood Glucose/metabolism/drug effects ; Sulfonamides/pharmacology ; Bacteria/drug effects/genetics/classification/isolation &amp; purification ; Male ; Metagenomics ; },
abstract = {BACKGROUND: Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice.<br><br>METHODS: Mice were orally administered folpet at 0, 1, 10, and 100&#xa0;mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism.<br><br>RESULTS: Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment.<br><br>CONCLUSIONS: Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.},
}
@article {pmid39788986,
year = {2025},
author = {Patova, A and Ribeiro, PA and Murillo, FJ and Riesgo, A and Taboada, S and Pomponi, SA and Rapp, HT and Kenchington, E and Xavier, JR},
title = {Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1540},
pmid = {39788986},
issn = {2045-2322},
mesh = {*Metagenomics ; *Porifera/genetics/metabolism ; Atlantic Ocean ; *Ecosystem ; *Aquatic Organisms/genetics/metabolism ; *Conservation of Natural Resources ; Hunting/statistics &amp; numerical data ; Animal Distribution ; Animals ; Polymorphism, Single Nucleotide/genetics ; Nova Scotia ; },
abstract = {Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.},
}
@article {pmid39788961,
year = {2025},
author = {Banerjee, G and Papri, SR and Huang, H and Satapathy, SK and Banerjee, P},
title = {Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {39},
pmid = {39788961},
issn = {2052-4463},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Liver Transplantation ; *Metagenome ; High-Throughput Nucleotide Sequencing ; Akkermansia ; Fatty Liver/microbiology ; },
abstract = {Recurrence of metabolic dysfunction-associated steatotic liver disease (MASLD) after liver transplantation (LT) is a continuing concern. The role of gut microbiome dysbiosis in MASLD initiation and progression has been well established. However, there is a lack of comprehensive gut microbiome shotgun sequence data for patients experiencing MASLD recurrence after LT. In this data descriptor, we describe a dataset of deep metagenomic sequences of a well-defined LT recipient population. Community-based analysis revealed a high abundance of Akkermansia muciniphila, consistently observed in most patient samples with a low (0-2) MASLD Activity Score (NAS). We constructed 357 metagenome-assembled genomes (MAGs), including 220 high-quality MAGs (>90% completion). The abundance of different species of Bacteroides MAGs dominated in patient samples with NAS > 5 ("definite MASH"). In contrast, the MAGs of A. muciniphila, Akkermansia sp., and Blutia sp. dominated in samples from patients without MASH (NAS = 0-2). In addition, the phylogenetic analysis of A. muciniphila and Akkermansia sp. MAGs identified two new phylogroups of Akkermansia that are distinct from the previously reported three phylogroups.},
}
@article {pmid39788783,
year = {2025},
author = {Franz, K and Markó, L and Mähler, A and Chakaroun, R and Heinitz, S and Schlögl, H and Sacher, J and Steckhan, N and Dechend, R and Adams, N and Andersen, M and Glintborg, D and Viehweger, M and Bahr, LS and Forslund-Startceva, SK},
title = {Sex hormone-dependent host-microbiome interactions and cardiovascular risk (XCVD): design of a longitudinal multi-omics cohort study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e087982},
pmid = {39788783},
issn = {2044-6055},
mesh = {Humans ; *Cardiovascular Diseases/microbiology/epidemiology ; Longitudinal Studies ; Male ; Female ; *Gonadal Steroid Hormones/metabolism/blood ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Transgender Persons ; Research Design ; Heart Disease Risk Factors ; Adult ; Sex Reassignment Procedures ; Multiomics ; },
abstract = {INTRODUCTION: Cardiovascular diseases (CVDs) present differently in women and men, influenced by host-microbiome interactions. The roles of sex hormones in CVD outcomes and gut microbiome in modifying these effects are poorly understood. The XCVD study examines gut microbiome mediation of sex hormone effects on CVD risk markers by observing transgender participants undergoing gender-affirming hormone therapy (GAHT), with findings expected to extrapolate to cisgender populations.<br><br>METHODS AND ANALYSES: This observational, longitudinal cohort study includes baseline, 1- and 2-year follow-ups with transgender participants beginning GAHT. It involves comprehensive phenotyping and microbiome genotyping, integrating computational analyses of high-dimensional data. Microbial diversity will be assessed using gut, skin, and oral samples via 16S rRNA and shotgun metagenomic sequencing of gut samples. Blood measurements will include sex hormones, CVD risk markers, cardiometabolic parameters, cytokines, and immune cell counts. Hair samples will be analysed for cortisol. Participants will complete online questionnaires on physical activity, mental health, stress, quality of life, fatigue, sleep, pain, and gender dysphoria, tracking medication use and diet to control for confounders. Statistical analyses will integrate phenomic, lifestyle, and multi-omic data to model health effects, testing gut microbiome mediation of CVD risk as the endocrine environment shifts between that typical for cisgender men to women and vice versa.<br><br>ETHICS AND DISSEMINATION: The study adheres to Good Clinical Practice and the Declaration of Helsinki. The protocol was approved by the Charit&#xe9; Ethical Committee (EA1/339/21). Signed informed consent will be obtained. Results will be published in peer-reviewed journals and conferences and shared as accessible summaries for participants, community groups, and the public, with participants able to view their data securely after public and patient involvement review for accessibility.<br><br>TRIAL REGISTRATION NUMBER: The XCVD study was registered on ClinicalTrials.gov (NCT05334888) as 'Sex-differential host-microbiome CVD risk - a longitudinal cohort approach (XCVD)" on 4 April 2022. Data set link can be found at https://classic.<br><br>CLINICALTRIALS: gov/ct2/show/NCT05334888.},
}
@article {pmid39786931,
year = {2025},
author = {Ni, B and Xiao, L and Lin, D and Zhang, TL and Zhang, Q and Liu, Y and Chen, Q and Zhu, D and Qian, H and Rillig, MC and Zhu, YG},
title = {Increasing pesticide diversity impairs soil microbial functions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {2},
pages = {e2419917122},
pmid = {39786931},
issn = {1091-6490},
support = {41991332//MOST | National Natural Science Foundation of China (NSFC)/ ; 42307027//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; },
mesh = {*Soil Microbiology ; *Pesticides ; *Bacteria/genetics/metabolism/classification/drug effects ; *Soil/chemistry ; *Fertilizers ; *Nitrogen/metabolism ; Phosphorus/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Agriculture/methods ; Metagenomics/methods ; Microbiota/drug effects ; },
abstract = {Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.},
}
@article {pmid39781513,
year = {2025},
author = {Wagatsuma, R and Nishikawa, Y and Hosokawa, M and Takeyama, H},
title = {vClean: assessing virus sequence contamination in viral genomes.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqae185},
pmid = {39781513},
issn = {2631-9268},
mesh = {*Genome, Viral/genetics ; *Metagenomics/methods ; Machine Learning ; Viruses/genetics/isolation &amp; purification ; DNA Contamination ; Software ; Sequence Analysis, DNA/methods ; },
abstract = {Recent advancements in viral metagenomics and single-virus genomics have improved our ability to obtain the draft genomes of environmental viruses. However, these methods can introduce virus sequence contaminations into viral genomes when short, fragmented partial sequences are present in the assembled contigs. These contaminations can lead to incorrect analyses; however, practical detection tools are lacking. In this study, we introduce vClean, a novel automated tool that detects contaminations in viral genomes. By applying machine learning to the nucleotide sequence features and gene patterns of the input viral genome, vClean could identify contaminations. Specifically, for tailed double-stranded DNA phages, we attempted accurate predictions by defining single-copy-like genes and counting their duplications. We evaluated the performance of vClean using simulated datasets derived from complete reference genomes, achieving a binary accuracy of 0.932. When vClean was applied to 4693 genomes of medium or higher quality derived from public ocean metagenomic data, 1604 genomes (34.2%) were identified as contaminated. We also demonstrated that vClean can detect contamination in single-virus genome data obtained from river water. vClean provides a new benchmark for quality control of environmental viral genomes and has the potential to become an essential tool for environmental viral genome analysis.},
}
@article {pmid39781512,
year = {2025},
author = {Sato, N and Katayama, K and Miyaoka, D and Uematsu, M and Saito, A and Fujimoto, K and Uematsu, S and Imoto, S},
title = {stana: an R package for metagenotyping analysis and interactive application based on clinical data.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqae191},
pmid = {39781512},
issn = {2631-9268},
mesh = {Humans ; *Software ; *Gastrointestinal Microbiome/genetics ; Crohn Disease/genetics/microbiology ; Metagenomics/methods ; Parkinson Disease/genetics ; Kidney Failure, Chronic/genetics ; Metagenome/genetics ; },
abstract = {Metagenotyping of metagenomic data has recently attracted increasing attention as it resolves intraspecies diversity by identifying single nucleotide variants. Furthermore, gene copy number analysis within species provides a deeper understanding of metabolic functions in microbial communities. However, a platform for examining metagenotyping results based on relevant grouping data is lacking. Here, we have developed the R package, stana, for the processing and analysis of metagenotyping results. The package consists of modules for preprocessing, statistical analysis, functional analysis and visualization. An interactive analysis environment for exploring the metagenotyping results was also developed and publicly released with over 1000 publicly available metagenome samples related to human diseases. Three examples exploring the relationship between the metagenotypes of the gut microbiome and human diseases are presented-end-stage renal disease, Crohn's disease and Parkinson's disease. The results suggest that stana facilitated the confirmation of the original study's findings and the generation of a new hypothesis. The GitHub repository for the package is available at https://github.com/noriakis/stana.},
}
@article {pmid39781508,
year = {2024},
author = {Park, SS and Park, SH and Jeong, HT and Shin, MS and Kim, MK and Kim, BK and Yoon, HS and Kim, SH and Kim, TW},
title = {The effect of treadmill exercise on memory function and gut microbiota composition in old rats.},
journal = {Journal of exercise rehabilitation},
volume = {20},
number = {6},
pages = {205-212},
pmid = {39781508},
issn = {2288-176X},
abstract = {Aging is associated with declines in memory function and significant change in gut microbiota. In this study, we investigated how exercise affects age-related memory decline and inflammation, and gut microbiota diversity. Bl6 mice were divided into control, control and exercise, old, and old and exercise groups. Treadmill exercise was performed once a day, 5 days a week for 8 consecutive weeks. Short-term memory was assessed using step-through test and spatial learning memory was assessed using Morris water maze task. Enzyme-linked immunosorbent assay was performed for the proinflammatory cytokines, tumor necrosis factor (TNF)-α and interleukin (IL)-6, in the hippocampus. Western blot analysis was conducted for the neurotrophic factors, brain-derived neurotrophic factor (BDNF) and tyrosine kinase B (TrkB), in the hippocampus. In addition, fecal samples were collected for sequencing and metagenomic analysis. Old rats showed decline in short-term memory and spatial learning memory. Increment of TNF-α and IL-6 concentration with decrement of BDNF and TrkB expression were observed in the old rats. Decreased diversity of gut microbiota composition and decreased beneficial gut microbiota were found in the old rats. However, treadmill exercise improved short-term memory, decreased TNF-α and IL-6 concentration, and increased BDNF and TrkB expression in the old rats. Treadmill exercise also increased the diversity of gut microbiota composition and affected the increase of beneficial gut microbiota in the old rats. In conclusion, treadmill exercise reduced age-related inflammatory markers and effectively improved memory decline while enhancing the diversity and abundance of beneficial gut microbiota.},
}
@article {pmid39780485,
year = {2024},
author = {Wei, A and Zhan, H and Xiao, Z and Zhao, W and Jiang, X},
title = {A novel framework for phage-host prediction via logical probability theory and network sparsification.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39780485},
issn = {1477-4054},
support = {62372205//National Natural Science Foundation of China/ ; ZDI145-56//National Language Commission Key Research Project/ ; KJ02502022-0450//Fundamental Research Funds for Central Universities/ ; 2022CFB289//Natural Science Foundation of Hubei Province of China/ ; CCNU24JC032//Self-determined Research Funds of CCNU from the Colleges' Basic Research and Operation of MOE/ ; },
mesh = {*Bacteriophages/genetics ; Probability Theory ; Algorithms ; Host-Pathogen Interactions ; Computational Biology/methods ; Bacteria/virology/genetics ; },
abstract = {Bacterial resistance has emerged as one of the greatest threats to human health, and phages have shown tremendous potential in addressing the issue of drug-resistant bacteria by lysing host. The identification of phage-host interactions (PHI) is crucial for addressing bacterial infections. Some existing computational methods for predicting PHI are suboptimal in terms of prediction efficiency due to the limited types of available information. Despite the emergence of some supporting information, the generalizability of models using this information is limited by the small scale of the databases. Additionally, most existing models overlook the sparsity of association data, which severely impacts their predictive performance as well. In this study, we propose a dual-view sparse network model (DSPHI) to predict PHI, which leverages logical probability theory and network sparsification. Specifically, we first constructed similarity networks using the sequences of phages and hosts respectively, and then sparsified these networks, enabling the model to focus more on key information during the learning process, thereby improving prediction efficiency. Next, we utilize logical probability theory to compute high-order logical information between phages (hosts), which is known as mutual information. Subsequently, we connect this information in node form to the sparse phage (host) similarity network, resulting in a phage (host) heterogeneous network that better integrates the two information views, thereby reducing the complexity of model computation and enhancing information aggregation capabilities. The hidden features of phages and hosts are explored through graph learning algorithms. Experimental results demonstrate that mutual information is effective information in predicting PHI, and the sparsification procedure of similarity networks significantly improves the model's predictive performance.},
}
@article {pmid39780272,
year = {2025},
author = {Albert, E and Kis, IE and Kiss, K and K-Jánosi, K and Révész, T and Biksi, I},
title = {Serotype distribution and antimicrobial susceptibility of Streptococcus suis isolates from porcine diagnostic samples in Hungary, 2020-2023.},
journal = {Porcine health management},
volume = {11},
number = {1},
pages = {3},
pmid = {39780272},
issn = {2055-5660},
abstract = {BACKGROUND: Streptococcus suis (S. suis) is a major swine pathogen and a significant zoonotic agent, causing substantial economic losses in the swine sector and having considerable public health importance. The control and management of S. suis-related conditions has become increasingly challenging due to the multitude of involved serotypes with varying antimicrobial resistance patterns. Here, we report the serological distribution and antimicrobial susceptibility of S. suis isolates isolated form clinical samples of Hungarian large-scale swine farms.<br><br>RESULTS: Between 2020 and 2023, altogether 296 S. suis isolates were obtained from diseased pigs of 64 Hungarian pig operations. Serotyping of the isolates was carried out by using molecular methods (cps-typing). The isolated strains belonged to 24 single cps-types. The most frequently detected cps-types during the four years of this passive survey were 9 (19.6%), 2 (19.3%), 1/2 (18.9%) and 7 (14.5%). The brain, spleen, endocardial valve thrombus and lung proved to be the most frequent site of S. suis strain isolation, and animals 29-75&#xa0;days of age were affected in the highest proportion. Antimicrobial susceptibility testing of the isolates was performed by determining the minimal inhibitory concentration for 15 antimicrobial agents of veterinary and human importance using a commercial microdilution assay. More than 90% of the tested isolates proved to be susceptible to the examined beta-lactams, cephalosporins and florfenicol, as well as to rifampicin, trimethoprim/sulfamethoxazole and vancomycin. Phenotypic resistance profiles (resistotypes) of clindamycin-tetracyclin (3.8%), clindamycin-erythromycin-tetracyclin (8.4%) and clindamycin-erythromycin-tetracyclin-trimethoprim / sulfamethoxazole (3.8%) were most frequently detected. Vancomycin resistance was observed in the case of 1 S. suis strain.<br><br>CONCLUSIONS: The dominance of S. suis cps-types 9, 2, 1/2 and 7 in Hungary over the four years of this study aligns with previous reports from several countries worldwide. The presence of highly susceptible S. suis isolates suggests a prudent antibiotic usage and treatment practice in the surveyed Hungarian swine operations. In contrary, the presence of several resistotypes could indicate the problem of antibiotic resistance in the future.},
}
@article {pmid39779932,
year = {2025},
author = {Wei, Y and Zhu, Y and Yang, L and Chen, C and Yue, M and Mao, Z and Wang, Y and Li, Q and Li, Y and Lv, J and Xue, W},
title = {Effects of oil pollution on the growth and rhizosphere microbial community of Calamagrostis epigejos.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1278},
pmid = {39779932},
issn = {2045-2322},
support = {22NYYF029//Xi'an Agricultural Technology R&amp;D Projects/ ; S2024-JC-YB-2574//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2020ZDLSF06-01//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2021K-25//Strategic Reserve Talent Training Program of Shaanxi Academy of Sciences/ ; 2023JH-NJGG-0167//Xi'an Science Technology Bureau Fund/ ; KRDL K6-2207039//the Project of the First Investigation of Wild Plants Resources in Xi'an/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Fungi/genetics ; *Bacteria/genetics/classification ; *Archaea/genetics/growth &amp; development/metabolism ; Petroleum Pollution/adverse effects ; Petroleum ; Microbiota/drug effects ; Soil Pollutants ; },
abstract = {Bacteria, fungi, archaea, and viruses are reflective organisms that indicate soil health. Investigating the impact of crude oil pollution on the community structure and interactions among bacteria, fungi, archaea, and viruses in Calamagrostis epigejos soil can provide theoretical support for remediating crude oil pollution in Calamagrostis epigejos ecosystems. In this study, Calamagrostis epigejos was selected as the research subject and subjected to different levels of crude oil addition (0 kg/hm[2], 10 kg/hm[2], 40 kg/hm[2]). Metagenomic sequencing technology was employed to analyze the community structure and diversity of soil bacteria, fungi, archaea, and viruses. Additionally, molecular ecological network analysis was integrated to explore species interactions and ecosystem stability within these microbial communities. The functional profiles of soil microorganisms were elucidated based on data from the KEGG database. Results demonstrated a significant increase in petroleum hydrocarbon content, polyphenol oxidase activity, hydrogen peroxide enzyme activity, and acid phosphatase activity upon crude oil addition, while β-glucosidase content, fiber disaccharide hydrolase content, and tiller number decreased (P < 0.05). Proteobacteria and Actinobacteria were identified as dominant bacterial phyla; Ascomycota, Basidiomycota, and Mucoromycota were found to be dominant fungal phyla; Thaumarchaeota emerged as a dominant archaeal phylum; and Uroviricota represented a dominant viral phylum. The diversity of soil bacterial, fungal, archaeal, and viral communities increased with higher amounts of added crude oil. Ecological network analysis revealed a robust collaborative relationship among bacterial, fungal, archaeal, and viral community species in the control treatment (CK), while strong competitive relationships were observed among these species in the treatments with 10% (F10) and 40% (F40) crude oil concentrations. Structural equation modeling analysis indicated significant positive correlations between fungal community, viral community, enzyme activity, and plant growth; conversely, bacterial and archaeal communities showed significant negative correlations with plant growth (P < 0.05). Correlation analysis identified acid phosphatase as the primary environmental factor influencing soil microbial function. Acid phosphatase levels along with tiller number, aboveground biomass, and petroleum hydrocarbons significantly influenced the fungal community (P < 0.05), while underground biomass had a significant impact on the archaeal community (P < 0.05). Acid phosphatase levels along with cellulose-hydrolyzing enzymes, tiller number, and petroleum hydrocarbons exhibited significant effects on the viral community (P < 0.05). This study investigated variations in bacterial, fungal, archaeal, and viral communities under different crude oil concentrations as well as their driving factors, providing a theoretical foundation for evaluating Calamagrostis epigejos' potential to remediate crude oil pollution.},
}
@article {pmid39779925,
year = {2025},
author = {He, X and Hu, M and Xu, Y and Xia, F and Tan, Y and Wang, Y and Xiang, H and Wu, H and Ji, T and Xu, Q and Wang, L and Huang, Z and Sun, M and Wan, Y and Cui, P and Liang, S and Pan, Y and Xiao, S and He, Y and Song, R and Yan, J and Quan, X and Wei, Y and Hong, C and Liao, W and Li, F and El-Omar, E and Chen, J and Qi, X and Gao, J and Zhou, H},
title = {The gut-brain axis underlying hepatic encephalopathy in liver cirrhosis.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {39779925},
issn = {1546-170X},
support = {82372305//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Up to 50-70% of patients with liver cirrhosis develop hepatic encephalopathy (HE), which is closely related to gut microbiota dysbiosis, with an unclear mechanism. Here, by constructing gut-brain modules to assess bacterial neurotoxins from metagenomic datasets, we found that phenylalanine decarboxylase (PDC) genes, mainly from Ruminococcus gnavus, increased approximately tenfold in patients with cirrhosis and higher in patients with HE. Cirrhotic, not healthy, mice colonized with R. gnavus showed brain phenylethylamine (PEA) accumulation, along with memory impairment, symmetrical tremors and cortex-specific neuron loss, typically found in patients with HE. This accumulation of PEA was primarily driven by decreased monoamine oxidase-B activity in both the liver and serum due to cirrhosis. Targeting PDC or PEA reversed the neurological symptoms induced by R. gnavus. Furthermore, fecal microbiota transplantation from patients with HE to germ-free cirrhotic mice replicated these symptoms and further corroborated the efficacy of targeting PDC or PEA. Clinically, high baseline PEA levels were linked to a sevenfold increased risk of HE after intrahepatic portosystemic shunt procedures. Our findings expand the understanding of the gut-liver-brain axis and identify a promising therapeutic and predictive target for HE.},
}
@article {pmid39779716,
year = {2025},
author = {Gałęcka, I and Rychlik, A and Całka, J},
title = {Influence of selected dosages of plastic microparticles on the porcine fecal microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1269},
pmid = {39779716},
issn = {2045-2322},
support = {2020/37/N/NZ7/01383//Narodowe Centrum Nauki/ ; The Regional Initiative of Excellence Program//Minister of Science Poland/ ; },
mesh = {Animals ; Swine ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Female ; Plastics ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Studies conducted so far have shown that nano- and microplastic may disturb the intestinal microenvironment by interacting with the intestinal epithelium and the gut microbiota. Depending on the research model used, the effect on the microbiome is different-an increase or decrease in selected taxa resulting in the development of dysbiosis. Dysbiosis may be associated with intestinal inflammation, development of mental disorders or diabetes. The aim of the study was to analyze the intestinal microbiome in 15 gilts divided into 3 research groups (n = 5; control group, receiving micropartices at a dose 0.1 g/day (LD) and 1 g/day (HD)). Feaces were collected before and after 28 days of exposure to PET microplastics. The analysis of the intestinal microbiome was performed using next-generation sequencing. Alpha and beta diversity indices were compared, showing, that repetition affected only the abundance indices in the control and LD groups, but not in the HD group. The relationships between the number of reads at the phylum, genus and species level and the microplastic dose were calculated using statistical methods (r-Pearson correlation, generalized regression model, analysis of variance). The statistical analysis revealed, that populations of Family XIII AD3011 group, Coprococcus, V9D2013 group, UCG-010 and Sphaerochaeta increased with increasing MP-PET dose. The above-mentioned taxa are mainly responsible for the production of short-chain fatty acids (SCFA). It may be assumed, that SCFA are one of the mechanisms involved in the response to oral exposure to MP-PET.},
}
@article {pmid39779308,
year = {2025},
author = {Nguyen-Tiêt, A and Puente-Sánchez, F and Bertilsson, S and Aalto, SL},
title = {Identifying Bacteria Responsible for Non-Sulphate-Based Hydrogen Sulphide Production in Aquaculture.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70024},
doi = {10.1111/1462-2920.70024},
pmid = {39779308},
issn = {1462-2920},
support = {1051-00044B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Hydrogen Sulfide/metabolism ; *Aquaculture ; *Cysteine/metabolism ; *Bacteria/metabolism/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; Bioreactors/microbiology ; Sulfates/metabolism ; Phylogeny ; Metagenome ; Metagenomics ; },
abstract = {The unintended microbiological production of hydrogen sulphide (H2S) poses a significant challenge in engineered systems, including sewage treatment plants, landfills and aquaculture systems. Although sulphur-rich amino acids and other substrates conducive to non-sulphate-based H2S production are frequently present, the capacity and potential of various microorganisms to perform sulphate-free H2S production remain unclear. In this study, we identify the identity, activity and genomic characteristics of bacteria that degrade cysteine to produce H2S in anaerobic enrichment bioreactors seeded with material from aquaculture systems. Our comparison with canonical sulphate-reducing bacteria reveals that both sulphur sources contribute to microbial H2S production, with cysteine facilitating a more rapid process compared to sulphate. 16S rRNA amplicon sequencing and metagenomic analysis identified four bacterial families-Dethiosulfatibacteraceae, Fusobacteriaceae, Vibrionaceae and Desulfovibrionaceae-as central to non-sulphate H2S production. Metagenome- and metatranscriptome-assembled genomes elucidated the primary cysteine degradation pathway mediated by cysteine desulphidase cyuA and indicated that some bacteria may also utilise cysteine as a carbon source in sulphate-based H2S production.},
}
@article {pmid39779118,
year = {2025},
author = {Wang, C and Bin, Z and Wang, L and Zhu, G and Tang, S and Chen, Y and Xiao, D and Guo, X},
title = {Metagenomic and metabolomic profiling analyses to unravel the formation mechanism of n-propanol during the first and second round of Jiangxiangxing Baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {200},
number = {},
pages = {115459},
doi = {10.1016/j.foodres.2024.115459},
pmid = {39779118},
issn = {1873-7145},
mesh = {*Fermentation ; *Metabolomics/methods ; *1-Propanol/metabolism ; *Metagenomics/methods ; Lactobacillus/metabolism/genetics ; Alcoholic Beverages/microbiology ; Pichia/metabolism/genetics ; Saccharomyces cerevisiae/metabolism/genetics ; Food Microbiology ; Microbiota ; },
abstract = {N-propanol is one of the higher alcohols, a moderate amount of n-propanol is beneficial for the harmony of the liquor body, whereas excessive or repeated intake will lead to discomfort and pose significant harm to human health. In actual production process of Jiangxiangxing Baijiu, the n-propanol content of the base baijiu in first round (FR) is far higher than that of second round (SR). Nevertheless, the formation mechanism and the key n-propanol producing microbials remain unclear and this limits the quality control of baijiu fermentation. Here, we combined metagenomics and metabolomics to verify the biosynthesis pathway of n-propanol and to identify characteristic microorganisms in FR and SR. The results showed that the preliminary period of pit fermentation was critical for the accumulation of n-propanol. FR was enriched in Lactobacillus plantarum, Lactobacillus ponits, Lactobacillus brevis and Lactobacillus panis, while it was harbored greater abundances of Pichia kudriazevii, Saccharomyces cerevisiae and Lactobacillus acetotolerans in SR. Function analysis combined with KEGG providing comprehensive evidence for the main synthetic pathways of n-propanol in Jiangxiangxing baijiu, and L. panis was key microbial. In addition, the experiments of inoculating L. panis and L. acetotolerans in situ indicated L. panis was mainly responsible for n-propanol production while L. acetotolerans not conducive to the production of n-propanol. Besides, the bioturbation effect on microbiota and flavor compounds were also analyzed. These results are useful for elucidating the mechanism of flavor formation in baijiu fermentation and promoting the further application of bioturbation technology in the traditional fermentation industry.},
}
@article {pmid39778648,
year = {2025},
author = {Bellanco, A and Requena, T and Martínez-Cuesta, MC},
title = {Polysorbate 80 and carboxymethylcellulose: A different impact on epithelial integrity when interacting with the microbiome.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {196},
number = {},
pages = {115236},
doi = {10.1016/j.fct.2025.115236},
pmid = {39778648},
issn = {1873-6351},
mesh = {*Polysorbates/pharmacology ; *Carboxymethylcellulose Sodium/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Emulsifying Agents ; Bacteria/drug effects/classification/genetics/metabolism ; },
abstract = {The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.},
}
@article {pmid39778631,
year = {2025},
author = {Harriman, D and Ng, A and Bronowski, M and Kazakov, H and Nguan, C and Dang, T and Sherwood, K and Miller, A and Lange, D},
title = {Characterizing the urobiome and associated metabolic profiles during acute rejection in renal transplant patients: A pilot study.},
journal = {Transplant immunology},
volume = {89},
number = {},
pages = {102170},
doi = {10.1016/j.trim.2024.102170},
pmid = {39778631},
issn = {1878-5492},
abstract = {Characteristic alterations in the urinary microbiome, or urobiome, are associated with renal transplant pathology. To date, there has been no direct study of the urobiome during acute allograft rejection. The goal of this study was to determine if unique urobiome alterations are present during acute rejection in renal transplant recipients. We performed shotgun metagenomic sequencing of 32 mid-stream urine samples obtained from 15 transplant recipients pre-transplant, 1- and 3-months post-transplant, and at time of rejection discovered with for-cause biopsy. Within individuals, there was a 40-60 % difference in urobiome composition from pre-to-post-transplant in both rejectors and non-rejectors. The taxa Ureaplasma was enriched in rejectors compared to non-rejectors. However, a greater number of microbial genes were enriched in non-rejectors compared to rejectors, except for genes associated with tetracycline resistance, the lysophosphatidic acid synthesis pathway, and tryptophanyl-tRNA synthetase. Together, our findings suggest that the urobiome is significantly altered post-transplant with certain taxa and/or microbial genes potentially associated with acute allograft rejection/inflammation.},
}
@article {pmid39778056,
year = {2025},
author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A},
title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70010},
pmid = {39778056},
issn = {1462-2920},
support = {//Max-Planck-Gesellschaft/ ; },
mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; },
abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.},
}
@article {pmid39777846,
year = {2025},
author = {Liu, R and He, X and Ren, G and Li, DW and Zhao, M and Lehtovirta-Morley, L and Todd, JD and Zhang, XH and Liu, J},
title = {Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70018},
doi = {10.1111/1462-2920.70018},
pmid = {39777846},
issn = {1462-2920},
support = {41976101//National Natural Science Foundation of China/ ; 92051115//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; 202141009//Fundamental Research Funds for the Central Universities/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3//Laoshan Laboratory/ ; LSKJ202203206//Laoshan Laboratory/ ; ZR2022YQ38//Natural Science Foundation of Shandong Province/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; },
mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Phylogeny ; Oceans and Seas ; Metagenome ; Ecosystem ; Seawater/microbiology ; Metagenomics ; Ammonia/metabolism ; Genome, Archaeal ; },
abstract = {Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.},
}
@article {pmid39777550,
year = {2025},
author = {Byers, AK and Wakelin, SA and Condron, L and Black, A},
title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {167},
pmid = {39777550},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; },
abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.},
}
@article {pmid39777544,
year = {2025},
author = {Qiao, L and Zheng, X and Zhao, J and Wu, B and Hao, Y and Li, X and Helal, MMU and Zheng, J},
title = {Genetic dissection of flag leaf morphology traits and fine mapping of a novel QTL (Qflw.sxau-6BL) in bread wheat (Triticum aestivum L.).},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {138},
number = {1},
pages = {21},
pmid = {39777544},
issn = {1432-2242},
support = {202302140601001//Key Research and Development Project of Shanxi Province/ ; 202201140601025-2//Grant Science and Technology special project in Shanxi Province/ ; 202303021222043//Youth Project of Shanxi Province/ ; 2023CYJSTX02//Modern Agro-industry Technology Research System/ ; },
mesh = {*Triticum/genetics/anatomy &amp; histology/growth &amp; development ; *Quantitative Trait Loci ; *Chromosome Mapping/methods ; *Plant Leaves/anatomy &amp; histology/genetics/growth &amp; development ; *Phenotype ; Genetic Linkage ; Genetic Markers ; Haploidy ; Genotype ; },
abstract = {Total 60-QRC for FLM traits were detected by meta-genomics analysis, nine major and stable QTL identified by DH population and validated, and a novel QTL Qflw.sxau-6BL was fine mapped. The flag leaf is an "ideotypic" morphological trait providing photosynthetic assimilates in wheat. Although flag leaf morphology (FLM) traits had been extensively investigated through genetic mapping, there is a desire for FLM-related loci to be validated in multi-environments and fine mapping. In order to identify the stable genomic regions for FLM traits, we conducted a meta-genomic analysis based on reports from 2008 to 2024. Experimentally, a doubled haploid (DH) population was used to assess the genetic regions associated with FLM traits in nine environments. The meta-genomic analysis extracted 60 QTL-rich clusters (QRC), 45 of which were verified in marker-trait association (MTA) study. Nine major and stable QTL were found being associated with FLM traits across three-to-seven environments including BLUP, with phenotypic variance explained (PVE) ranging from 5.05 to 34.95%. The KASP markers of the nine QTL were validated (P < 0.005) in more than three environments using a panel of diverse wheat collections from Shanxi Province in China. Two co-located major and stable QTL viz. Qflw.sxau-6B.5 and Qfla.sxau-6B.4 were found novel and contributed to increase FLW by 12.09-19.21% and FLA by 5.45-13.28%. They also demonstrated high recombination rates in LD analysis based on the resequencing of 145 wheat landmark cultivars. The fine mapping of Qflw.sxau-6BL narrowed it down to a 1.27 Mb region as a result of the combined genotypic and phenotypic analysis for secondary mapping population. Comparing to NIL-ND3338, the NIL-LF5064 showed higher FLW by 20.45-27.37%, thousand-grain weight by 1.88-2.57% and grain length by 0.47-2.30% across all environments. The expression analysis of 11 tissues revealed seven highly expressed genes within the fine map region. This study provides a genetic basis for the FLM traits for further map-based cloning of FLW genes in wheat.},
}
@article {pmid39777507,
year = {2025},
author = {Shelton, AN and Yu, FB and Grossman, AR and Bhaya, D},
title = {Abundant and active community members respond to diel cycles in hot spring phototrophic mats.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39777507},
issn = {1751-7370},
support = {2125965//NSF/ ; 1921429//BBSRC-NSF/BIO/ ; //Office of Science of the U.S. Department of Energy/ ; },
mesh = {*Hot Springs/microbiology ; Metagenome ; Photosynthesis ; Phototrophic Processes ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics ; Microbiota ; Transcriptome ; },
abstract = {Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets. Metagenome-assembled genomes comprised 71 taxa (in 19 different phyla), of which 12 core taxa were present at high abundance in both springs. The eight most active taxa identified by metatranscriptomics were an oxygenic cyanobacterium (Synechococcus sp.), five anoxygenic phototrophs from three different phyla, and two understudied heterotrophs from phylum Armatimonadota. In all eight taxa, a significant fraction of genes exhibited a diel expression pattern, although peak timing varied considerably. The two abundant heterotrophs exhibit starkly different peak timing of expression, which we propose is shaped by their metabolic and genomic potential to use carbon sources that become differentially available during the diel cycle. Network analysis revealed pathway expression patterns that had not previously been linked to diel cycles, including ribosome biogenesis and chaperones. This provides a framework for analyzing metabolically coupled communities and the dominant role of the diel cycle.},
}
@article {pmid39777151,
year = {2024},
author = {Nhung, PTT and Le, HTT and Nguyen, QH and Huyen, DT and Quyen, DV and Song, LH and Van Thuan, T and Tran, TTT},
title = {Identifying fecal microbiota signatures of colorectal cancer in a Vietnamese cohort.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1388740},
pmid = {39777151},
issn = {1664-302X},
abstract = {BACKGROUND: Colorectal cancer (CRC) is among the top three causes of global cancer mortality. In Vietnam, CRC is the third leading cause of death in women and the fourth cause of cancer mortality in men. A large number of metagenomic studies have reported the relationship between altered composition and function of the gut microbiota with CRC, but this relationship in low- and middle-income countries including Vietnam (with an estimated population of 100.3 million people in 2023, ranking 16th largest country by population in the world) is not well-explored.<br><br>METHODS: We collected clinical data and fecal samples from 43 CRC patients and 44 healthy control subjects. The total community DNA of microorganisms was extracted from the fecal samples and analyzed for microbiota composition using Illumina MiSeq amplicon sequencing targeting the V3-V4 region of the 16S rRNA gene.<br><br>RESULTS: We identified a significant difference in the overall fecal microbiota composition between CRC patients and healthy controls, and we detected several CRC-associated microbial signatures in fecal samples of Vietnamese patients with CRC, which overlapped with signatures from other countries and meta-analyses. Although patients with (n = 8) and without (n = 35) type 2 diabetes (T2D) exhibited distinct gut microbiota composition compared to healthy controls, increased relative abundances of putatively pathogenic species including Parvimonas micra, Peptostreptococcus stomatis, and Prevotella intermedia were consistent biomarkers for CRC. In contrast, several health-associated species were significantly depleted in CRC patients such as Lactobacillus johnsonii and Bifidobacterium longum in CRC/non-T2D patients, Ruminococcus species, Bacteroides uniformis, and Phascolarctobacterium faecium in CRC/T2D patients, and Butyricicoccus pullicaecorum in both CRC groups combined.<br><br>CONCLUSION: Our findings confirm alterations in gut microbiota composition in CRC in a pilot Vietnamese cohort and highlight several gut microbial taxa that may have inhibitory or driver roles in CRC. This and future studies will enable the development of cancer diagnostics and treatment strategies for CRC in Vietnam, with a focus on targeting the microbiota.},
}
@article {pmid39776843,
year = {2024},
author = {Zhang, X and Wu, Z and Shao, S},
title = {Pulmonary mucormycosis in an immunocompetent young female: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1491489},
pmid = {39776843},
issn = {2296-858X},
abstract = {Mucormycosis is considered a rare but highly lethal fungal infection, often occurring in patients with poorly controlled diabetes or immunosuppression. Pulmonary mucormycosis progresses rapidly and is often associated with pulmonary infarction and hemoptysis. In this case report, we presented a young, immunocompetent female patient with newly diagnosed diabetes who was diagnosed early with Rhizopus delemar infection through metagenomic next-generation sequencing. Despite early diagnosis, the infection progressed rapidly, invading the tracheal cartilage and upper mediastinal soft tissue, ultimately leading to the patient's unfortunate demise.},
}
@article {pmid39776838,
year = {2024},
author = {Li, MJ and Zhou, SF and Zhang, Y and Zhang, Y and Fu, WB},
title = {Unveiling the dark side of Prevotella: a case of fatal pneumonia from a common probiotic.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1382134},
pmid = {39776838},
issn = {2296-858X},
abstract = {Prevotella is often considered a Bacteroides complex associated with a healthy plant-based diet that acts as a "probiotic" throughout the body's entire digestive tract from the mouth to the anus. Previous studies have not reported that this "probiotic" colonizing the human body could cause severe pneumonia. This case report describes a 56-year-old healthy female worker with gum pain followed by fever. Despite prompt medical attention given by the use of empirical antibiotics and tooth and oral cleaning, the disease rapidly progressed to retropharyngeal abscess and severe pneumonia. Although the surgeon performed pharynx and cervical incisions and drainage, the patient's symptoms were not significantly relieved. After repeated blood culture and sputum culture, no positive findings were found. Fortunately, Prevotella oris was found in the peripheral blood of the patient by metagenomic next-generation sequencing (mNGS). The disease was controlled quickly by changing the targeted antibiotics according to the guidelines for the detection of pathogenic bacteria. Three months after discharge, the patient's symptoms did not resolve, and reexamination with computerized tomography (CT) showed that the neck and chest were normal. This case is unique in that it shows that normally colonized Prevotella oris could also cause fatal pneumonia as an opportunistic pathogen. Our goal is to highlight that serious infections that rapidly develop from common symptoms in an era of widespread antibiotic use not only increase patient misunderstanding but also lead to over detection and testing of such symptoms by clinicians. Expanding the pathogenic characteristics of special pathogens through the literature and using accurate mNGS may be the technical tool for resolving this contradiction.},
}
@article {pmid39776755,
year = {2025},
author = {Niu, X and Qiu, S and Zheng, Y and Li, L and Tian, E and Liu, J and Gai, W and Zhang, Q and Jin, H},
title = {A Rare Q-Fever Infection Diagnosed Using Metagenomic Next-Generation Sequencing in Liver Transplantation Patient: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {25-30},
pmid = {39776755},
issn = {1178-6973},
abstract = {Q fever is a zoonotic disease caused by the Gram-negative bacterium Coxiella burnetii, typically transmitted through exposure to infected animal secretions. As the clinical signs of Q-fever are largely non-specific in humans, a definitive diagnosis can often be overlooked, particularly when physicians fail to consider C. burnetii on the list of differentials. This case report describes Q-fever in a male patient who had previously undergone orthotopic liver transplantation. The patient had a sudden onset of fever and received the anti-infective moxifloxacin which proved ineffective. Despite the comprehensive laboratory tests and CT imaging that were performed, the etiology remained undetermined. The patient's blood was subjected to metagenomic next-generation sequencing (mNGS), which identified C. burnetii, after which the patient was treated with doxycycline and recovered well. Eight literature articles on Q fever infection in solid organ transplant recipients were reviewed. To our knowledge, this is the first case of Q fever identified by mNGS in an organ transplantation patient. The case underscores the potential of mNGS has in aiding the rapid detection of rare pathogens in immunocompromised patients.},
}
@article {pmid39776437,
year = {2024},
author = {Tang, J and Wang, K and Xu, H and Han, J},
title = {Metagenomic next-generation sequencing of cerebrospinal fluid: a diagnostic approach for varicella zoster virus-related encephalitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1509630},
pmid = {39776437},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; Aged ; Retrospective Studies ; Adult ; *Herpesvirus 3, Human/genetics/isolation &amp; purification ; *Encephalitis, Varicella Zoster/diagnosis/cerebrospinal fluid ; China ; Cerebrospinal Fluid/virology ; },
abstract = {PURPOSE: Varicella zoster virus-related encephalitis (VZV-RE) is a rare and often misdiagnosed condition caused by an infection with the VZV. It leads to meningitis or encephalitis, with patients frequently experiencing poor prognosis. In this study, we used metagenomic next-generation sequencing (mNGS) to rapidly and accurately detect and identify the VZV pathogen directly from cerebrospinal fluid (CSF) samples, aiming to achieve a definitive diagnosis for encephalitis patients.<br><br>METHODS: In this retrospective study, we analyzed the clinical characteristics and laboratory evaluations of 28 patients at the Harrison International Peace Hospital in Hebei, China, between 2018 and 2024. These patients were diagnosed with neurological disorders using mNGS techniques applied to CSF.<br><br>RESULTS: In this cohort of 28 patients, 11 were females and 17 males, with a median age of 65 (IQR: 42.3-70). VZV-RE presented with a range of clinical manifestations, the most common being headaches (81.2%), fever>38&#xb0;C (42.9%), and vomiting (42.9%). Less frequent symptoms include personality changes (10.7%), speech impairments (21.4%), cranial nerve involvement (21.4%), altered consciousness (17.9%) and convulsions (3.6%). Herpes zoster rash was observed in 35.7% of the cases. Neurological examination revealed nuchal rigidity in only 5 patients. CSF analysis indicated mild pressure and protein levels increase, with all patients having negative bacterial cultures. Abnormal electroencephalogram (EEG) findings were noted in 10.7% (N=3), and encephalorrhagia on Magnetic Resonance Imaging (MRI) was observed in 3.6%. VZV-RE was confirmed through mNGS analysis of CSF within three days of admission. All patients received empiric treatment with acyclovir or valacyclovir, with 21.4% receiving hormonotherapy, and 7.14% receiving immunoglobulin therapy. At the three-month follow-up, 10.7% of the patients had persistent neurologic sequelae, and the mortality rate was 3.6%.<br><br>CONCLUSIONS: Performing mNGS on CSF offers a rapidly and precisely diagnostic method for identifying causative pathogens in patients with VZV central nervous system (CNS) infections, especially when traditional CNS examination results are negative. Furthermore, the cases reported highlight the positive therapeutic effect of ganciclovir in treating VZV infections.},
}
@article {pmid39775567,
year = {2025},
author = {Kalaiselvi, P and Haripriya, RJ and Saravanan, VS and Davamani, V and Sebastian, SP and Parameswari, E and Poornima, R and Bharani, A and Maheswari, M},
title = {Formulation and evaluation of the effective microorganisms in sewage treatment.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {5},
pages = {2298-2323},
pmid = {39775567},
issn = {1614-7499},
mesh = {*Sewage ; *Waste Disposal, Fluid/methods ; Bacteria ; Water Purification/methods ; Wastewater/chemistry/microbiology ; },
abstract = {Effective microorganisms pose a great potential in wastewater treatment. In the present study, effective microorganisms' formulations were developed using different organic substrates that support the growth of more beneficial microorganisms for sewage treatment. Based on the metagenomic analysis and biochemical profile information, the fish waste-based effective microorganisms' formulation was identified as the effective formulation. Metagenomic analysis showed that fish-based effective microorganisms' formulation had the Lactobacillus and Acetobacter groups of bacteria. The dominant groups were Lactobacillus pontis (64.85%), Acetobacter aceti (8.92%), and Lactobacillus reuteri (8.98%). The developed fish waste-based effective microorganisms' formulation was used to treat the sewage water with different concentrations. Effective microorganisms' formulation at 3% showed appreciable results. It recorded a significant reduction in BOD from 389.2 to 117.9 mg L[-1] and COD from 820.5 to 257.1 mg L[-1] in 96 h. It also significantly decreased the concentration of ammoniacal and nitrate nitrogen, phosphorus, sulphate, and coliforms. Besides, the effective microorganisms' formulation ensured the reduced level of odour from sewage water. Therefore, we can effectively use the effective microorganisms' formulation for sewage water treatment and recycling.},
}
@article {pmid39775111,
year = {2025},
author = {Lee, J and Xiang, K and Au, E and Sarabi, S and Acosta, N and Bhatnagar, S and Van Doorn, J and Bertazzon, S and Conly, JM and Rennert-May, E and Pitout, JDD and Lee, BE and Pang, X and O'Grady, C and Frankowski, K and Hubert, CRJ and Parkins, MD},
title = {Longitudinal monitoring of sewershed resistomes in socioeconomically diverse urban neighborhoods.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {7},
pmid = {39775111},
issn = {2730-664X},
abstract = {BACKGROUND: Understanding factors associated with antimicrobial resistance (AMR) distribution across populations is a necessary step in planning mitigation measures. While associations between AMR and socioeconomic-status (SES), including employment and education have been increasingly recognized in low- and middle-income settings, connections are less clear in high-income countries where SES remains an important influence on other health outcomes.<br><br>METHODS: We explored the relationship between SES and AMR in Calgary, Canada using spatially-resolved wastewater-based surveillance of resistomes detected by metagenomics across eight socio-economically diverse urban neighborhoods. Resistomes were established by shotgun-sequencing of wastewater pellets, and qPCR of targeted-AMR genes. SES status was established using 2021 Canadian census data. Conducting this comparison during the height of COVID-related international travel restrictions (Dec. 2020-Oct. 2021) allowed the hypotheses linking SES and AMR to be assessed with limited confounding. These were compared with sewage metagenomes from 244 cities around the world, linked with Human Development Index (HDI).<br><br>RESULTS: Wastewater metagenomes from Calgary's socioeconomically diverse neighborhoods exhibit highly similar resistomes, with no quantitative differences (p&#x2009;>&#x2009;0.05), low Bray-Curtis dissimilarity, and no significant correlations with SES. By comparison, dissimilarity is observed between globally-sourced resistomes (p&#x2009;<&#x2009;0.05), underscoring the homogeneity of resistomes in Calgary's sub-populations. The analysis of globally-sourced resistomes alongside Calgary's resistome further reveals lower AMR burden in Calgary relative to other cities around the world. This is particularly pronounced for the most clinically-relevant AMR genes (e.g., beta-lactamases, macrolide-lincosamide-streptogramin).<br><br>CONCLUSIONS: This work showcases the effectiveness of inclusive and comprehensive wastewater-based surveillance for exploring the interplay between SES and AMR.},
}
@article {pmid39774647,
year = {2025},
author = {Yagita-Sakamaki, M and Ito, T and Sakaguchi, T and Shimma, S and Li, B and Okuzaki, D and Motooka, D and Nakamura, S and Hase, K and Fukusaki, E and Kikuchi, A and Nagasawa, T and Kumanogoh, A and Takeda, K and Kayama, H},
title = {Intestinal Foxl1+ cell-derived CXCL12 maintains epithelial homeostasis by modulating cellular metabolism.},
journal = {International immunology},
volume = {},
number = {},
pages = {},
doi = {10.1093/intimm/dxae068},
pmid = {39774647},
issn = {1460-2377},
abstract = {Several mesenchymal cell populations are known to regulate intestinal stem cell (ISC) self-renewal and differentiation. However, the influences of signaling mediators derived from mesenchymal cells other than ISC niche factors on epithelial homeostasis remain poorly understood. Here, we show that host and microbial metabolites, such as taurine and GABA, act on PDGFRαhigh Foxl1high sub-epithelial mesenchymal cells to regulate their transcription. In addition, we found that CXCL12 produced from Foxl1high sub-epithelial mesenchymal cells induces epithelial cell cycle arrest through modulation of the mevalonate-cholesterol synthesis pathway, which suppresses tumor progression in ApcMin/+ mice. We identified that Foxl1high sub-epithelial cells highly express CXCL12 among colonic mesenchymal cells. Foxl1-cre; Cxcl12f/f mice showed an increased number of Ki67+ colonic epithelial cells. CXCL12-induced Ca2+ mobilization facilitated phosphorylation of AMPK in intestinal epithelial cells, which inhibits the maturation of SREBPs that are responsible for mevalonate pathway activation. Furthermore, Cxcl12 deficiency in Foxl1-expressing cells promoted tumor development in the small and large intestines of ApcMin/+ mice. Collectively, these results demonstrate that CXCL12 secreted from Foxl1high mesenchymal cells manipulates intestinal epithelial cell metabolism, which links to the prevention of tumor progression in ApcMin/+ mice.},
}
@article {pmid39774426,
year = {2024},
author = {Segura, D and Sharma, D and Espin-Garcia, O},
title = {Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0315720},
pmid = {39774426},
issn = {1932-6203},
mesh = {Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Infant ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Metagenome/genetics ; },
abstract = {The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs). However, the microbiome field has progressed towards amplicon sequencing variants (ASVs), as they provide more precise microbe identification and sample diversity information. The aim of this work is to compare the subsampling strategies for two-phase metagenomic studies when using ASVs instead of OTUs, and to propose data driven strategies for subsample selection through dimension reduction techniques. We used 199 samples of infant-gut microbiome data from the DIABIMMUNE project to generate ASVs and OTUs, then generated subsamples based on five existing biologically driven subsampling methods and two data driven methods. Linear discriminant analysis Effect Size (LEfSe) was used to assess differential representation of taxa between the subsamples and the overall sample. The use of ASVs showed a 50-93% agreement in the subsample selection with the use of OTUs for the subsampling methods evaluated, and showed a similar bacterial representation across all methods. Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.},
}
@article {pmid39773989,
year = {2025},
author = {Bbosa, N and Ssemwanga, D and Weiss, SL and Kalungi, S and Mawanda, A and Ssentudde, R and Ssekyeru, E and Ssekagiri, A and Kiiza, R and Rwankindo, C and Buule, J and Namagembe, HS and Nabirye, S and Nassolo, JP and Downing, R and Lutwama, J and Lutalo, T and Kyobe Bosa, H and Berg, MG and Rodgers, MA and Averhoff, F and Cloherty, GA and Kaleebu, P},
title = {Identification of Anthrax as the Cause of a Cluster of Unexplained Deaths, Uganda, 2023: The Role of Metagenomic Next-Generation Sequencing and Postmortem Specimens.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0489},
pmid = {39773989},
issn = {1476-1645},
abstract = {Between April and November 2023, 27 unexplained human deaths that presented with swelling of the arms, skin sores with black centers, difficulty in breathing, obstructed swallowing, headaches, and other body aches were reported in Kyotera District, Uganda by the Public Health Emergency Operations Center. Subsequently, the death of cattle on farms and the consumption of carcass meat by some residents were also reported. Field response teams collected clinical/epidemiological data and autopsy samples to determine the cause of deaths. Metagenomic next-generation sequencing (mNGS) and target enrichment sequencing conducted on postmortem samples confirmed Bacillus anthracis, the etiological agent of anthrax disease, as the cause of the deaths. Applying mNGS to autopsy specimens is useful as a retrospective tool for identifying high-consequence pathogens during suspected outbreaks of unknown etiology.},
}
@article {pmid39773899,
year = {2025},
author = {Han, F and Ou, J and Huang, N},
title = {Invasive Eye Infection Caused by Trichoderma Harzianum.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0037},
pmid = {39773899},
issn = {1476-1645},
abstract = {Trichoderma is a widely distributed thermophilic fungus that grows on moist soil, fallen leaves, and rotten wood. It plays an important role in agricultural production, food processing, and soil. However, some forms of Trichoderma can infect humans. Aggressive infections are more common in immunocompromised patients, with manifestations ranging from focal to disseminated infections. Here, we report a case of an invasive eye infection in China. The patient, a healthy 64-year-old man, was inadvertently struck by a puncture vine, injuring his eye and resulting in reduced visual acuity, lacrimation, and redness in the right eye. Upon admission, he was diagnosed with right eye perforation injury, right eye iris damage, right eye vitreous opacity, and right eye infection. After completion of the relevant auxiliary examinations, the diagnosis was confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and metagenomic next-generation sequencing, and the patient responded to antifungal therapy.},
}
@article {pmid39773654,
year = {2025},
author = {Taylor, W and Bohm, K and Dyet, K and Weaver, L and Pattis, I},
title = {Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {5},
pmid = {39773654},
issn = {1756-0500},
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction/methods ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Humans ; },
abstract = {OBJECTIVE: The World Health Organization (WHO) has declared antimicrobial resistance (AMR) as one of the top threats to global public health. While AMR surveillance of human clinical isolates is well-established in many countries, the increasing threat of AMR has intensified efforts to detect antibiotic resistance genes (ARGs) accurately and sensitively in environmental samples, wastewater, animals, and food. Using five ARGs and the 16S rRNA gene, we compared quantitative PCR (qPCR) and metagenomic sequencing (MGS), two commonly used methods to uncover the wastewater resistome. We compared both methods by evaluating ARG detection through a municipal wastewater treatment chain.<br><br>RESULTS: Our results demonstrate that qPCR was more sensitive than MGS, particularly in diluted samples with low ARG concentrations such as oxidation pond water. However, MGS was potentially more specific and has less risk of off-target binding in concentrated samples such as raw sewage. MGS analysis revealed multiple subtypes of each gene which could not be distinguished by qPCR; these subtypes varied across different sample types. Our findings affect the conclusions that can be drawn when comparing different sample types, particularly in terms of inferring removal rates or origins of genes. We conclude that both methods appear suitable to profile the resistome of wastewater and other environmental samples, depending on the research question and type of sample.},
}
@article {pmid39773117,
year = {2025},
author = {Albert, E and Biksi, I and Laczkó, L and Miló, L and Cseri, K and Bőkényné Tóth, R and Papp, D and Halmay, D and Bódai, E and Bakos, Z},
title = {Streptococcus hillyeri isolated from septic pleuritis in a horse.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {10406387241306724},
pmid = {39773117},
issn = {1943-4936},
abstract = {Here we report the isolation of Streptococcus hillyeri from a thoracic sample from a horse. A 17-y-old Hungarian Sport Horse mare was referred to the equine clinic of the University of Veterinary Medicine Budapest, Hungary, with suspected pleuritis. Upon arrival, the horse was febrile and had tachycardia, severe inspiratory dyspnea, and tachypnea. Thoracic ultrasonography revealed severe bilateral pleural effusion, and a large area of lung consolidation. After sampling of both hemithoraces, 66 L of turbid exudate were drained. Based on these findings, a tentative diagnosis of septic pleuritis was made, and the horse was immediately started on a course of broad-spectrum antibiotics, a NSAID, an anticoagulant, and intravenous fluids. Despite intensive care, the clinical parameters deteriorated, and the horse was euthanized 6 d later. Cytology confirmed septic pleuritis, with short chains or groups of coccoid bacteria. Anaerobic culture yielded gram-positive cocci from both hemithoraces in almost pure culture, which we identified as S. hillyeri by 16S rDNA and whole-genome analysis. Additionally, we identified 4 previously unassigned Streptococcus sp. sequences as S. hillyeri. Of these, 3 were obtained from aborted equine fetuses and a fourth from a donkey mastitis case, supporting the pathogenic nature of S. hillyeri in these host species.},
}
@article {pmid39772992,
year = {2025},
author = {Zeng, Y and You, X and You, C},
title = {Rare Cause of Chest Wall Abscess: Salmonella Enterica Infection Based on Metagenomics Next-Generation Sequencing Diagnosis.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1089/sur.2024.316},
pmid = {39772992},
issn = {1557-8674},
}
@article {pmid39772877,
year = {2025},
author = {Ahmed, MA and Campbell, BJ},
title = {Genome-resolved adaptation strategies of Rhodobacterales to changing conditions in the Chesapeake and Delaware Bays.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0235724},
doi = {10.1128/aem.02357-24},
pmid = {39772877},
issn = {1098-5336},
abstract = {UNLABELLED: The abundant and metabolically versatile aquatic bacterial order, Rhodobacterales, influences marine biogeochemical cycles. We assessed Rhodobacterales metagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closed Rhodobacterales genomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. Rhodobacterales genera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity. Planktomarina genomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. These Rhodobacterales also differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarine Rhodobacterales within and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes.<br><br>IMPORTANCE: In the complex web of global biogeochemical nutrient cycling, the Rhodobacterales emerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range of Rhodobacterales genera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarine Rhodobacterales, revealing their various energy production pathways and diverse resource management, especially during phytoplankton or algal blooms. Whether adopting a free-living or particle-attached existence, these organisms demonstrate remarkable flexibility in their metabolic strategies, underscoring their pivotal role in driving ecosystem dynamics within estuarine ecosystems.},
}
@article {pmid39772868,
year = {2025},
author = {Hart, LN and Zepernick, BN and Natwora, KE and Brown, KM and Obuya, JA and Lomeo, D and Barnard, MA and Okech, EO and , and Kiledal, EA and Den Uyl, PA and Olokotum, M and Wilhelm, SW and McKay, RM and Drouillard, KG and Sherman, DH and Sitoki, L and Achiya, J and Getabu, A and Otiso, KM and Bullerjahn, GS and Dick, GJ},
title = {Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150724},
doi = {10.1128/aem.01507-24},
pmid = {39772868},
issn = {1098-5336},
support = {F31 ES036421/ES/NIEHS NIH HHS/United States ; },
abstract = {The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf's cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf's cyanobacterial composition, function, and biosynthetic potential. Dolichospermum was the dominant bloom-forming cyanobacterium, co-occurring with Microcystis at most sites. Microcystis and Planktothrix were more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) of Dolichospermum harbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation of Dolichospermum in the nitrogen-limited gulf. Over 300 biosynthetic gene clusters (BGCs) putatively encoding the synthesis of toxins and other secondary metabolites were identified across the gulf, even at sites where there were no visible cyanoHAB events. Almost all BGCs identified had no known synthesis product, indicating a diverse and novel biosynthetic repertoire capable of synthesizing harmful or potentially therapeutic metabolites. Microcystis MAGs contained mcy genes encoding the synthesis of hepatotoxic microcystins which are a concern for drinking water safety. These findings illustrate the spatial variation of bloom-forming cyanobacteria in the Winam Gulf and their available strategies to dominate different ecological niches. This study underscores the need for further use of genomic techniques to elucidate the dynamics and mitigate the potentially harmful effects of cyanoHABs and their associated toxins on human, environmental, and economic health.IMPORTANCEThe Winam Gulf (Kenya) is a vital resource that experiences prolific cyanobacterial harmful algal blooms (cyanoHABs). Bloom-forming cyanobacteria produce cyanotoxins, threatening human and environmental health, recreation, and fishing. However, cyanotoxin production in the gulf has not been linked to a specific type of cyanobacteria. We used DNA sequencing of whole microbial communities to track the species of cyanobacteria present across the gulf and investigate the genes responsible for synthesis of known and novel toxins. Our results reveal Dolichospermum as the main bloom-forming cyanobacteria in the gulf, often co-occurring with high abundance of toxigenic Microcystis. Over 300 unique gene clusters were found, with most predicted to encode the synthesis of uncharacterized molecules. These results provide initial insights into the diverse biosynthetic potential encoded by cyanobacteria in the Winam Gulf and underscore the need to further elucidate and investigate the effects of known and novel molecules produced in cyanoHABs in this region.},
}
@article {pmid39772804,
year = {2025},
author = {Cottingham, H and Judd, LM and Wisniewski, JA and Wick, RR and Stanton, TD and Vezina, B and Macesic, N and Peleg, AY and Okeke, IN and Holt, KE and Hawkey, J},
title = {Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0141324},
doi = {10.1128/msystems.01413-24},
pmid = {39772804},
issn = {2379-5077},
abstract = {UNLABELLED: Sequencing DNA directly from patient samples enables faster pathogen characterization compared to traditional culture-based approaches, but often yields insufficient sequence data for effective downstream analysis. CRISPR-Cas9 enrichment is designed to improve the yield of low abundance sequences but has not been thoroughly explored with Oxford Nanopore Technologies (ONT) for use in clinical bacterial epidemiology. We designed CRISPR-Cas9 guide RNAs to enrich the human pathogen Klebsiella pneumoniae, by targeting multi-locus sequence type (MLST) and transfer RNA (tRNA) genes, as well as common antimicrobial resistance (AMR) genes and the resistance-associated integron gene intI1. We validated enrichment performance in 20 K. pneumoniae isolates, finding that guides generated successful enrichment across all conserved sites except for one AMR gene in two isolates. Enrichment of MLST genes led to a correct allele call in all seven loci for 8 out of 10 isolates that had depth of 30× or more in these regions. We then compared enriched and unenriched sequencing of three human fecal samples spiked with K. pneumoniae at varying abundance. Enriched sequencing generated 56× and 11.3× the number of AMR and MLST reads, respectively, compared to unenriched sequencing, and required approximately one-third of the computational storage space. Targeting the intI1 gene often led to detection of 10-20 proximal resistance genes due to the long reads produced by ONT sequencing. We demonstrated that CRISPR-Cas9 enrichment combined with ONT sequencing enabled improved genomic characterization outcomes over unenriched sequencing of patient samples. This method could be used to inform infection control strategies by identifying patients colonized with high-risk strains.<br><br>IMPORTANCE: Understanding bacteria in complex samples can be challenging due to their low abundance, which often results in insufficient data for analysis. To improve the detection of harmful bacteria, we implemented a technique aimed at increasing the amount of data from target pathogens when combined with modern DNA sequencing technologies. Our technique uses CRISPR-Cas9 to target specific gene sequences in the bacterial pathogen Klebsiella pneumoniae and improve recovery from human stool samples. We found our enrichment method to significantly outperform traditional methods, generating far more data originating from our target genes. Additionally, we developed new computational techniques to further enhance the analysis, providing a thorough method for characterizing pathogens from complex biological samples.},
}
@article {pmid39772525,
year = {2025},
author = {Yum, SJ and Yu, SY and Kim, SM and Jeong, HG},
title = {Antibiotic Resistance Genes and Microbiota in Brassica oleracea var. acephala Cultivated in South Korea: Potential for Resistance Transmission.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {3},
pages = {2156-2166},
pmid = {39772525},
issn = {1520-5118},
mesh = {*Brassica/microbiology ; Republic of Korea ; *Microbiota/drug effects ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge. This study investigates the microbiome of Brassica oleracea var. acephala (kale) to evaluate the role of food production systems, particularly plant-derived foods, in AMR dissemination. Using 16S rRNA gene sequencing and metagenomic shotgun sequencing, we analyzed microbial diversity and antimicrobial resistance genes (ARGs) in kale samples. Results showed significant regional differences in microbiota composition and ARG distribution, with traditional fertilizer use linked to higher ARG prevalence in coliform bacteria compared to farms using other fertilization methods. Additionally, we confirmed ARG transfer potential by Klebsiella pneumoniae within coliform populations. Storage conditions notably affected microbial dynamics, with higher temperatures promoting K. pneumoniae growth in washed samples. These findings revealed the importance of AMR research in plant-derived foods and highlight the need for improved agricultural practices to mitigate the risks associated with high ARG abundance in coliform bacteria.},
}
@article {pmid39772193,
year = {2024},
author = {Buigues, J and Viñals, A and Martínez-Recio, R and Monrós, JS and Sanjuán, R and Cuevas, JM},
title = {Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain.},
journal = {Viruses},
volume = {16},
number = {12},
pages = {},
pmid = {39772193},
issn = {1999-4915},
support = {CIAICO/2022/110//Conselleria de Educaci&#xf3;n, Universidades y Empleo (Generalitat Valenciana)/ ; PID2020-118602RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n (MICINN)/ ; },
mesh = {Animals ; *Feces/virology ; *DNA Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Spain ; *Phylogeny ; *Mammals/virology ; },
abstract = {Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analyzed 160 fecal samples from 14 species of small terrestrial mammals, 9 of them belonging to the order Rodentia. This allowed us to identify a total of 25 complete or near-complete genomes belonging to the families Papillomaviridae, Polyomaviridae, Adenoviridae, Circoviridae, and Genomoviridae, 18 of which could be considered new species or types. Our results provide a significant increase in the number of complete genomes of DNA viruses of European origin with zoonotic potential in databases, which are at present under-represented compared to RNA viruses. In addition, the characterization of whole genomes is of relevance for the further study of the evolutionary forces governing virus adaptation, such as recombination, which may play an important role in cross-species transmission.},
}
@article {pmid39772171,
year = {2024},
author = {Silva, SLSD and Silva, SPD and Aragão, CF and Gorayeb, IS and Cruz, ACR and Dias, DD and Nascimento, BLSD and Chiang, JO and Casseb, LMN and Nunes Neto, JP and Martins, LC and Vasconcelos, PFDC},
title = {Investigation of RNA Viruses in Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) in a Mining Complex in the Southeastern Region of the Brazilian Amazon.},
journal = {Viruses},
volume = {16},
number = {12},
pages = {},
pmid = {39772171},
issn = {1999-4915},
mesh = {Animals ; *Ceratopogonidae/virology ; Brazil ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Phylogeny ; *Insect Vectors/virology ; Metagenomics ; Genome, Viral ; },
abstract = {The biting midges Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) is highly relevant to epidemiology and public health, as it includes species that are potential vectors of human and animal arboviruses. The aim of this study was to investigate the presence of RNA viruses in species of the genus Culicoides collected in the Carajás mining complex in the state of Pará. The biting midges were collected in the municipalities of Canaã dos Carajás, Curionópolis and Marabá and morphologically identified. A total of 1139 specimens of seven Culicoides species were grouped into eight pools and subjected to metagenomic analysis. Eight new insect-specific viruses (ISVs) were characterized and assigned to the order Tolivirales, the families Chuviridae, Nodaviridae, Iflaviridae, Mesoniviridae, and Flaviviridae, and the taxon Negevirus. All viruses identified were assigned to clades, families and taxa never reported in Culicoides in Brazil. This study demonstrated that biting midges harbor a significant diversity of RNA viruses, many of which are still unknown, highlighting the importance of studies aiming at virome of these insects.},
}
@article {pmid39771135,
year = {2024},
author = {Li, Z and Yuan, D},
title = {Metagenomic Analysis Reveals the Effects of Microplastics on Antibiotic Resistance Genes in Sludge Anaerobic Digestion.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
pmid = {39771135},
issn = {2305-6304},
support = {No. 52170097//the National Natural Science Foundation of China/ ; },
abstract = {Sewage sludge is recognized as both a source and a reservoir for antibiotic resistance genes (ARGs). Within an anaerobic digestion (AD) system, the presence of microplastics (MPs) has been observed to potentially facilitate the proliferation of these ARGs. Understanding the influence of MPs on microbial behavior and horizontal gene transfer (HGT) within the AD system is crucial for effectively managing the dissemination of ARGs in the environment. This study utilized metagenomic approaches to analyze the dynamics of various types of ARGs and potential microbial mechanisms under exposure to MPs during the AD process. The findings indicated that MPs in the AD process can enhance the proliferation of ARGs, with the extent of this enhancement increasing with the dosage of MPs: polyethylene (PE), polyethylene terephthalate (PET), and polylactic acid (PLA) MPs increased the abundance of ARGs in the anaerobic digestion system by up to 29.90%, 18.64%, and 14.15%, respectively. Additionally, the presence of MPs increased the relative abundance of mobile genetic elements (MGEs) during the AD process. Network correlation analysis further revealed that plasmids represent the predominant category of MGEs involved in the HGT of ARGs. Propionibacterium and Alicycliphilus were identified as the primary potential hosts for these ARGs. The results of gene function annotation indicated that exposure to MPs led to an increased the relative abundance of genes related to the production of reactive oxygen species (ROS), alterations in membrane permeability, ATP synthesis, and the secretion of extracellular polymeric substances (EPS). These genes play crucial roles in influencing the HGT of ARGs.},
}
@article {pmid39771131,
year = {2024},
author = {Wang, K and Shen, D and Guo, Z and Zhong, Q and Huang, K},
title = {Contamination Characteristics of Antibiotic Resistance Genes in Multi-Vector Environment in Typical Regional Fattening House.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
pmid = {39771131},
issn = {2305-6304},
support = {2023YFD1800400//National Key Research and Development Program of China/ ; SJCX19-0129//postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as significant environmental contaminants, posing potential health risks worldwide. Intensive livestock farming, particularly swine production, is a primary contributor to the escalation of ARG pollution. In this study, we employed metagenomic sequencing and quantitative polymerase chain reaction to analyze the composition of microorganisms and ARGs across four vectors in a typical swine fattening facility: dung, soil, airborne particulate matter (PM), and fodder. Surprisingly, soil and PM harbored a higher abundance of microorganisms and ARGs than dung. At the same time, fodder was more likely to carry eukaryotes. Proteobacteria exhibited the highest propensity for carrying ARGs, with proportions 9-20 times greater than other microorganisms. Furthermore, a strong interrelation among various ARGs was observed, suggesting the potential for cooperative transmission mechanisms. These findings underscore the importance of recognizing soil and PM as significant reservoirs of ARGs in swine facilities alongside dung. Consequently, targeted measures should be implemented to mitigate their proliferation, mainly focusing on airborne PM, which can rapidly disseminate via air currents. Proteobacteria, given their remarkable carrying capacity for ARGs with the primary resistance mechanism of efflux, represent a promising avenue for developing novel control strategies against antibiotic resistance.},
}
@article {pmid39770918,
year = {2024},
author = {Masedunskas, A and de Ciutiis, I and Hein, LK and Ge, A and Kong, YX and Qi, M and Mainali, D and Rogerson-Wood, L and Kroeger, CM and Aguirre Candia, YA and Cagigas, ML and Wang, T and Hutchinson, D and Sabag, A and Passam, FH and Piccio, L and Sargeant, TJ and Fontana, L},
title = {Investigating the Impact of Glycogen-Depleting Exercise Combined with Prolonged Fasting on Autophagy and Cellular Health in Humans: A Randomised Controlled Crossover Trial.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39770918},
issn = {2072-6643},
support = {APP1177797//National Health and Medical Research Council/ ; },
mesh = {Humans ; *Autophagy ; *Fasting ; *Cross-Over Studies ; *Glycogen/metabolism ; *Exercise/physiology ; Adult ; Middle Aged ; Male ; Young Adult ; Female ; Aged ; Leukocytes, Mononuclear/metabolism ; Adolescent ; },
abstract = {IMPORTANCE: Although prolonged fasting has become increasingly popular, the favourable biological adaptations and possible adverse effects in humans have yet to be fully elucidated.<br><br>OBJECTIVE: To investigate the effects of a three-day water-only fasting, with or without exercise-induced glycogen depletion, on autophagy activation and the molecular pathways involved in cellular damage accumulation and repair in healthy humans.<br><br>DESIGN: A randomised, single-centre, two-period, two-sequence crossover trial. The primary outcome is autophagic activity, assessed as flux in peripheral blood mononuclear cells (PBMCs) measured in the context of whole blood. Secondary outcomes include changes in body composition, heart rate variability, endothelial function, and genomic, epigenomic, metabolomic, proteomic, and metagenomic adaptations to fasting in plasma, platelets, urine, stools, and PBMCs. Detailed profiling of circulating immune cell populations and their functional states will be assessed by flow cytometry.<br><br>SETTING: All clinical investigations will be undertaken at the Charles Perkins Centre Royal Prince Alfred Hospital clinic, University of Sydney, Australia.<br><br>PARTICIPANTS: Twenty-four individuals aged 18 to 70 years, with a BMI of 20-40 kg/m[2], free of major health conditions other than obesity.<br><br>DISCUSSION: While autophagic flux induction through fasting has garnered interest, there is a notable lack of human studies on this topic. This trial aims to provide the most detailed and integrated analysis of how three days of prolonged water-only fasting, combined with glycogen-depleting exercise, affects autophagy activation and other crucial metabolic and molecular pathways linked to cellular, metabolic, and immune health. Insights from this study may pave the way for safe and effective strategies to induce autophagy, offering potential preventive interventions for a range of chronic conditions.},
}
@article {pmid39770890,
year = {2024},
author = {Wells, RK and Torres, A and Mau, MK and Maunakea, AK},
title = {Racial-Ethnic Disparities of Obesity Require Community Context-Specific Biomedical Research for Native Hawaiians and Other Pacific Islanders.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39770890},
issn = {2072-6643},
support = {P20GM139753//NIH-NIGMS/ ; R01MD016593//NIH-NIMHD/ ; R56MD014630//NIH-NIMHD/ ; UG03HL169657//NIH-NHLBI/ ; },
mesh = {Humans ; *Biomedical Research ; Gastrointestinal Microbiome ; Hawaii/epidemiology ; Health Status Disparities ; *Native Hawaiian or Pacific Islander ; *Obesity/ethnology ; Pacific Island People ; },
abstract = {Compared to the general population of Hawai'i, Native Hawaiians and Other Pacific Islanders (NHPI) shoulder a disproportionately high risk for obesity-related cardiometabolic disorders, such as type 2 diabetes and cardiovascular disease. The gut microbiome is an area of rapid research interest for its role in regulating adjacent metabolic pathways, offering novel opportunities to better understand the etiology of these health disparities. Obesity and the gut microbiome are influenced by regional, racial-ethnic, and community-specific factors, limiting the generalizability of current literature for understudied populations. Additionally, anthropometric and directly measured obesity indices are variably predictive of adiposity and metabolic health risk in this diverse population. Thus, further NHPI-inclusive research is required to adequately characterize community-specific factors in the context of obesity-related disease etiology. Culturally responsible research ethics and scientific communication are crucial to conducting such research, especially among indigenous and understudied populations. In this review, we explore these limitations in current literature, emphasizing the urgent need for NHPI-inclusive research to assess community-specific factors accurately. Such accuracy in Indigenous health research may ensure that findings relevant to individual or public health recommendations and/or policies are meaningful to the communities such research aims to serve.},
}
@article {pmid39770844,
year = {2024},
author = {Yang, F and Liu, M and Wang, X and Hong, Y and Yao, Q and Chang, X and Shi, G and Chen, W and Tian, B and Hegazy, A},
title = {Differences in the Microbial Composition and Function of the Arundo donax Rhizosphere Under Different Cultivation Conditions.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770844},
issn = {2076-2607},
support = {2024ZC035//Henan Academy of Agricultural Sciences/ ; CARS-24-G-15//National Characteristic Vegetable Industry Technology System/ ; 2211111110100//Key R &amp; D Projects in Henan Province/ ; 2024TD38, 2024TD43//Henan Academy of Agricultural Sciences Science and Technology Innovation Team/ ; 241100110200//Independent Innovation Project of Major Science and Technology Special Project of Henan Province/ ; },
abstract = {Rhizosphere microorganisms play an important role in the health and development of root systems. Investigating the microbial composition of the rhizosphere is central to understanding the inter-root microbial function of Arundo donax under various cultivation conditions. To complement the metagenomic study of the Arundo donax rhizosphere, here, an amplicon-based metagenomic survey of bacteria and fungi was selected as a practical approach to analyzing the abundance, diversity index, and community structure of rhizosphere bacteria and fungi, as well as to study the effects of different cultivation methods on rhizosphere microbial diversity. Next-generation sequencing and QIIME2 analysis were used. The results indicated that microbial community richness, diversity, and evenness of the hydroponic samples were lower than those of soil samples when examining the α diversity indices of bacteria and fungi using Chao1, ACE, and Shannon metrics. In particular, the relative abundances of Proteobacteria, Rhizobiales, and Incertae sedis in hydroponic materials were higher, while Basidiomycota, Ascomycota, and Actinobacteriota dominated the flora in soil materials when comparing the numbers of OTUs and the ACE community richness estimator. Furthermore, the rhizosphere of hydroponic A. donax contained a higher abundance of nitrogen-fixing bacteria and photosynthetic bacteria, which contribute to root formation. Additionally, there was a significant presence of Basidiomycota, Ascomycota, and Actinobacteriota in soil A. donax, which can form hyphae. This reveals that the microbial community composition of the A. donax rhizosphere is significantly different under various cultivation conditions, suggesting that employing two distinct culturing techniques for Arundo donax may alter the microbiome. Furthermore, it provides technical support for the synergistic interaction between Arundo donax and rhizosphere microorganisms so as to better use the relationship between Arundo donax and basic microorganisms to solve the problems of Arundo donax growth and ecological restoration.},
}
@article {pmid39770834,
year = {2024},
author = {Brunner-Mendoza, C and Calderón-Ezquerro, MDC and Guerrero-Guerra, C and Sanchez-Flores, A and Salinas-Peralta, I and Toriello, C},
title = {Diversity and Composition of the Airborne Fungal Community in Mexico City with a Metagenomic Approach.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770834},
issn = {2076-2607},
abstract = {Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly in individuals with weakened immune systems. An aerobiological study was conducted to detect airborne fungi using metagenomics in three areas of Mexico City, each representing different degrees of urbanization, during the dry and rainy seasons of 2017. Seasonality showed a significant role in the composition of airborne fungi. Ascomycota predominated in the three areas sampled during dry an