@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.

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.

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.

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.},
}

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

@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.},
}

*RNA, Double-Stranded/genetics
RNA Interference
Animals
*Software
*Crop Protection/methods
*Crops, Agricultural/genetics/parasitology

@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.},
}

*Sewage/microbiology/chemistry
*Methane/metabolism/biosynthesis
*Drug Resistance, Microbial/genetics
Anaerobiosis
*Microplastics
*Waste Disposal, Fluid/methods
Bioreactors/microbiology
Bacteria/genetics

@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 & 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.},
}

Humans
Diagnosis, Differential
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
*Mycobacterium avium Complex/genetics/isolation & purification
*Mycobacterium avium-intracellulare Infection/diagnosis
Neoplasm Metastasis/diagnosis

@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 & 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.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Archaea/metabolism/classification/genetics/isolation & purification
*Lakes/microbiology
Phylogeny
Biodiversity
Tibet
RNA, Ribosomal, 16S/genetics

@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.

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.

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.

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.},
}

Humans
*Metagenomics/methods
*Diarrhea/diagnosis/microbiology/virology
Feces/microbiology/virology
*Transcriptome
Metagenome
Gene Expression Profiling
Female
Male

@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.

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.

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.},
}

*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

@article {pmid40390074,
year = {2025},
author = {Kazmi, FA and Mander, Ü 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&D Program of China/ ; 2024YFC2707800//National Key R&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.

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 < 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 = 0.001, M[2] = 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.

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.},
}

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

@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.},
}

*Endophytes/physiology
*Plant Diseases/microbiology
*Amorphophallus/microbiology
*Microbiota
*Disease Resistance
*Adaptation, Physiological
Stress, Physiological
*Bacteria

@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 & Human Services | National Institutes of Health (NIH)/ ; D43TW010540//U.S. Department of Health & 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 & 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.},
}

Humans
Female
Male
Sex Factors
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gastrointestinal Microbiome/genetics
Adult
*Drug Resistance, Bacterial/genetics
Metagenome
Global Health
Middle Aged

@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 & 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 & 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.

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.

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.

INTERVENTIONS: After discharge, the patient regularly took trimethoprim-sulfamethoxazole for anti-infective treatment.

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.

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.},
}

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 & purification
Lung/diagnostic imaging/pathology
*Lung Diseases/diagnosis

@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.},
}

*Anti-Bacterial Agents/pharmacology/chemistry
*Drug Resistance, Bacterial/genetics
Metagenomics/methods
Metagenome
Bacteria/drug effects/genetics

@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.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Benchmarking
Computer Simulation
Humans
*Metagenomics/methods
Computational Biology/methods

@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.

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.

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.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Feces/microbiology
*Gastrointestinal Microbiome
Female
*Peripartum Period/metabolism
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Pregnancy

@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, Innovación 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 & 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.},
}

Animals
Phylogeny
*Sea Cucumbers/parasitology
*Apicomplexa/genetics/classification/isolation & purification
Host Specificity
Female
Host-Parasite Interactions
Genome, Mitochondrial

@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.

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&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.

METHODS: This longitudinal cohort study observed patients with NORSE (n = 15), SE (n = 17), and chronic epilepsy who were not in SE (n = 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.

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.

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 & 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&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.

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.

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.

DISCUSSION: This study elucidates AD's pathophysiological progression and highlights the potential of machine learning-assisted multimodal strategies for early detection and staging.

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.},
}

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

@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 & 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.

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.

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.

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.},
}

Humans
*Computational Biology/methods
*Metagenomics/methods
*Software
Animals
*Communicable Diseases/diagnosis/microbiology

@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.

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.

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.

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.

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.

METHODS: Population: Patients with invasive infection with Extended-spectrum Beta-Lactamase (ESBL-) or Carbapenem-resistant Enterobacterales (CRE) and persistent GIT carriage.

INTERVENTION: Three doses of encapsulated lyophilised FMT.

COMPARATOR: Matched placebo capsules.

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.

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.

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 & 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.

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.

CONCLUSIONS: When clinicians encounter patients with atypical pneumonia with the RHS and a history of contact with poultry, psittacosis should be considered.},
}

Humans
Male
Adult
*Psittacosis/diagnostic imaging/drug therapy/diagnosis/microbiology
*Chlamydophila psittaci/isolation & purification/genetics
Tomography, X-Ray Computed
Animals
Lung/diagnostic imaging/microbiology
Columbidae/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Lung Diseases/diagnosis

@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 & purification ; Archaea/classification/genetics/isolation & purification ; Ecosystem ; Fungi/classification/genetics/isolation & 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.},
}

*Porifera/microbiology
Animals
Antarctic Regions
*Microbiota
Symbiosis
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Ecosystem
Fungi/classification/genetics/isolation & purification

@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.},
}

Animals
Greenland
*Virome/genetics
*Metagenomics/methods
*Aedes/virology/genetics
*Mosquito Vectors/virology
Metagenome
Phylogeny
*Culicidae/virology
Climate Change

@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.},
}

Color
*Taste
*Food Microbiology
*Hot Temperature
Odorants/analysis
Humans
*Bacteria/classification/genetics
*Microbiota
China

@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 & 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.

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 𝛃-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.

RESULTS: Gut microbiota underwent significant alterations after chemotherapy, transitioning from a diverse and balanced enterotype to enterotypes exhibiting a reduced α-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.

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.

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.

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.

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 & 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.

RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77 ± 1.21 μM. 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.

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.},
}

Animals
*Sulfinic Acids/pharmacology/chemistry
*Urease/antagonists & 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

@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 & 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.},
}

Animals
Humans
*Reverse Genetics/methods
*Henipavirus/genetics/pathogenicity/isolation & purification
Genome, Viral
*Henipavirus Infections/virology/transmission
*Containment of Biohazards/methods
Zoonoses/virology

@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.},
}

Humans
*DNA, Mitochondrial/genetics
*Metagenome
*Metagenomics/ethics
Privacy
Microbiota
*Genetic Privacy/ethics

@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.

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.

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 = 0.048), organ transplantation (HR = 4.93, 95% CI = 1.48-16.4, P = 0.009), and immunosuppression (HR = 8.83, 95% CI = 1.13-69.14, P = 0.038).

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.},
}

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

@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.

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.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Stress, Physiological
Metagenome
*Bacteria/metabolism/genetics/classification

@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.

METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4×10[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.

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.

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 & purification/classification ; Adult ; Viruses/genetics/isolation & purification/classification ; Fungi/genetics/isolation & 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.

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.

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.

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.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Middle Aged
Aged
*Bacteria/genetics/isolation & purification/classification
Adult
Viruses/genetics/isolation & purification/classification
Fungi/genetics/isolation & purification/classification
Sensitivity and Specificity
*Respiratory Tract Infections/microbiology/diagnosis
Aged, 80 and over
*Lung Diseases/microbiology/diagnosis

@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.

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.

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.

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.},
}

Animals
China
Phylogeny
*Ixodidae/virology/classification
Genome, Viral
Genetic Variation
Metagenomics
Recombination, Genetic
Sequence Analysis, DNA

@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.

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.

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 & 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&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.

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.

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.},
}

*Deep Learning
*Metagenomics/methods
*Bacteriophages/genetics
Genome, Viral
*DNA, Viral/genetics
Metagenome
*Computational Biology/methods
*Sequence Analysis, DNA/methods
Humans
*Software

@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.

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-1β, IL-6, and TNF-α, 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.

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 & 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.},
}

Humans
*Fecal Microbiota Transplantation
*Colitis, Ulcerative/therapy/virology/microbiology
*Virome
Male
Female
Feces/virology
Adult
Gastrointestinal Microbiome
Middle Aged
*Bacteriophages/genetics/isolation & purification/classification
Young Adult

@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.

AIM: The aim of the present study was to assess whether Menthacarin affects the composition and metabolic activity of human fecal microbiota.

METHODS: Fecal slurry samples from 10 healthy volunteers were cultivated for 36 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.

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 ± 8.6%) and Actinobacteria (+54.9 ± 47.6%) significantly increased, whereas that of Bacteroidetes (-27.7% ± 21.9%) and Proteobacteria (-25.7% ± 12.3%) significantly decreased in the presence of Menthacarin. At the genus level, the most notable changes were significant increases in Bifidobacterium (+105.1 ± 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.

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.

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.

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.},
}

*Metagenomics/methods
Humans
*Metagenome
*Computational Biology/methods
Algorithms

@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&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 & 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.

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.

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.},
}

Particle Size
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seawater/microbiology/chemistry
*Microbiota/genetics
Metagenomics/methods
Carbon/metabolism
Metagenome

@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.

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 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.

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.},
}

*Nitrogen/metabolism
*Lolium/metabolism
*Soil/chemistry
Soil Microbiology
Nitrogen Fixation
Nitrification
*Nutrients/metabolism
Denitrification
Nitrogen Cycle
Microbiota
Nitrates/metabolism

@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.},
}

*Biodiversity
*Metagenomics/methods
North Sea
Animals
*Wind
Seawater
*DNA, Environmental/genetics/analysis
Ecosystem
*Metagenome
Denmark

@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).

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.

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.

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.

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.},
}