@article {pmid41161821,
year = {2025},
author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L},
title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {10},
pages = {},
doi = {10.1136/jitc-2025-012444},
pmid = {41161821},
issn = {2051-1426},
mesh = {Humans ; Male ; Female ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; Middle Aged ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Aged ; *Lung/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.

METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.

RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).

CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.},
}

Humans
Male
Female
Prospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Immune Checkpoint Inhibitors/adverse effects/pharmacology
Middle Aged
*Metagenomics/methods
*Microbiota
*Pneumonia/chemically induced/microbiology/diagnosis
Aged
*Lung/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid41161652,
year = {2025},
author = {Li, R and Qiu, C and Chen, X and Liu, N and Zhang, Y and Qi, L and Wang, S},
title = {Effects of thermal alkaline hydrolysis and biochar addition on anaerobic digestion of sewage sludge and fate of antibiotic resistance genes.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133569},
doi = {10.1016/j.biortech.2025.133569},
pmid = {41161652},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) has gained wide attention as a potential method to reduce the spread of antibiotic resistance genes (ARGs). This study systematically evaluated the impacts of thermal alkaline hydrolysis (TA), biochar addition (BA), and the combination of these two methods (TA-BA) on the efficiency of AD and the removal of ARGs in the sewage sludge AD process. Metagenomic sequencing and quantitative PCR were used to systematically analyze the dissemination of ARGs in different sludge samples. The results indicated that both TA and TA-BA could enhance the efficiency of sludge AD, and the cumulative biogas production was increased by 68.35 %-258.57 % compared to the control group. In addition, the absolute abundance of ARGs was significantly reduced by 59.31 %-74.67 % in the TA- and BA-treated groups compared to the control group. The combination of TA-BA exhibited a synergistic effect, achieving the most significant reduction in ARGs absolute abundance (up to 74.67 % removal), outperforming individual treatments. Both TA and BA could promote the generation of Anaerolinea and Longilinea. Meanwhile, TA significantly increased the relative abundance of Methanobacteriaceae, while BA enhanced the relative abundance of Methanothrix. The correlation analysis demonstrated a significant negative correlation between TOC and sul1 (P < 0.01), and revealing a significant positive correlation between intI1 and sul1 (P < 0.05). Moreover, a significant correlation was observed between the fate of ARGs and the succession of microbial community structure.},
}

@article {pmid41161648,
year = {2025},
author = {Kadam, R and Jo, S and Park, J},
title = {Importance of substrate mixture ratio optimization on efficient anaerobic co-digestion of organic wastes generated in livestock sector: Insights into process performances and metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133561},
doi = {10.1016/j.biortech.2025.133561},
pmid = {41161648},
issn = {1873-2976},
abstract = {Improving the efficiency of anaerobic co-digestion of livestock wastes, particularly through optimizing mixture ratios, is a key research focus. This study identifies an optimal substrate mixture ratio of 23 % cow manure, 22 % pig manure, and 55 % carcass waste, which significantly enhances the degradation of lignocellulose, protein, and lipids compared to equal ratios. In the optimal mixture, the methane (CH4) yield remained stable at 310-360 mL-CH4/g-VS (volatile solids) as the organic loading rate increased to 5 kg-VS/m[3]/d. In contrast, the equal substrate mixture ratio showed lower CH4 yield and less stability under increasing organic loads. Key bacterial genera in the optimal mixture included Cloacamonas, Pseudomonas, Geofilum, and Clostridium, with methanogenic archaea such as Methanosaeta and Methanosarcina. Metagenomic analysis showed enriched pathways for cellulose, hemicellulose, and lipid degradation, alongside enhanced metabolism of volatile fatty acids and ammonia. This study highlights the importance of optimizing substrate ratios for efficient CH4 yield and stability.},
}

@article {pmid41161351,
year = {2025},
author = {Rao, H and Gao, L and Zheng, X and Wei, J and Yue, M and Li, B and Wang, Z and Yang, M and Ren, X},
title = {Reducing environmental contamination during reprocessing of highly contaminated flexible bronchoscopes from the intensive care unit.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.10.006},
pmid = {41161351},
issn = {1532-2939},
abstract = {BACKGROUND: Flexible bronchoscopes (FBs) used in intensive care units (ICUs) frequently harbour pathogenic micro-organisms, creating early reprocessing risks for environmental contamination and staff exposure.

METHODS: In a six-month evaluation of 832 ICU FBs sampled immediately post-use with metagenomic next-generation sequencing, 55.4% carried one or more pathogens, including multi-drug-resistant bacteria, fungi and airborne agents. We instituted an enhanced reprocessing protocol centred on sealed transfer using double biohazard bags, a two-person dedicated handling method that separates contaminated-scope contact from support tasks, segregation of sinks and a dedicated automated endoscope reprocessor (AER) for ICU FBs, and rigorous terminal disinfection of equipment and work surfaces.

FINDINGS: Quality checks showed unchanged cleaning efficacy of FBs, whereas the environmental microbial burden on work surfaces after reprocessing was significantly reduced under the new protocol.

CONCLUSIONS: These findings identify ICU FBs as a high-load reservoir at the point of receipt and demonstrate that targeted, standardized controls during the earliest reprocessing steps can mitigate environmental contamination and enhance sterile-processing worker protection without compromising device reprocessing outcomes.},
}

@article {pmid41161274,
year = {2025},
author = {Cai, X and Yuan, X and Singh, AK and Chen, C and Zhu, X and Liu, W},
title = {Tradeoffs between microbial life-history strategies drive soil carbon cycling during revegetation in karst ecosystems: A metagenomic perspective.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127802},
doi = {10.1016/j.jenvman.2025.127802},
pmid = {41161274},
issn = {1095-8630},
abstract = {Revegetation strongly influences the dynamics of soil organic carbon (SOC) and microbial communities. While microbial communities are known to drive carbon (C) cycling, the specific traits responsible for C stabilization and mineralization during the revegetation of degraded karst ecosystems are not well understood. This study used a combination of metagenomic and instrumental methods to investigate variations in soil physicochemical properties, organic C fractions, C-cycle microbial community traits (diversity, life strategies, and co-occurrence patterns), and C-cycling (fixation and degradation) genes across four karst ecosystems representing a revegetation chronosequence encompassing cropland, grassland, shrubland, and primary forest. Our findings demonstrated that revegetation increased total SOC and recalcitrant OC (ROC) contents, while it decreased dissolved inorganic nitrogen (DIN) and reduced the ratio of labile OC (LOC) to SOC. This indicates enhanced C pool stabilization and storage, alongside reduced soil nutrient availability. These shifts favored the development of C-cycle microbial communities with low diversity and high proportions of K-strategists, which efficiently utilize recalcitrant C under oligotrophic conditions. Consequently, the increased dominance of K-strategists redirected microbial resource acquisition, manifested in a 29 % decrease in C-fixation gene abundances (rTCA, WL, and DC/4-HB pathways) and a 27 % decrease in genes degrading labile C compounds (starch, hemicellulose, cellulose, and chitin). Conversely, genes involved in degrading recalcitrant C compounds (pectin and lignin) increased by 19 %. Furthermore, the elevated proportion of K-strategists enhanced the complexity and stability of microbial taxonomic and functional networks, potentially strengthening community resilience and nutrient cycling efficiency. These results reveal a causal link between shifts in the soil C pool and nutrient availability during revegetation and the subsequent reshaping of C-cycling microbial communities. Such restructured communities, in turn, drive the expression of genes associated with C stabilization and mineralization, thereby impacting the soil C pool. This study provides mechanistic insights into microbial-mediated biochemical processes governing soil C decomposition and stabilization in karst ecosystems, offering critical guidance for ecological restoration in these degraded and fragile regions.},
}

@article {pmid41161238,
year = {2025},
author = {Chi, T and Liu, Z and Zhang, B and Zhu, L and Hu, B},
title = {Risk assessment of the spread of antibiotic resistance genes from hospitals to the receiving environment via wastewater treatment plants.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119264},
doi = {10.1016/j.ecoenv.2025.119264},
pmid = {41161238},
issn = {1090-2414},
abstract = {Antibiotics and antibiotic resistance genes (ARGs) enter the receiving environment from hospitals through wastewater treatment plants (WWTPs), increasing the presence of exogenous ARGs and conditional pathogens in the receiving environment, thereby elevating the risk of drug resistance. This study, based on metagenomics, investigated changes in risk across each node in the ARG transmission chain, from hospitals through WWTPs to downstream receiving water and sediments. The results showed that the total concentration of antibiotics decreased from 1467.80 ± 215.30 µg/L in hospital wastewater to 111.52 ± 18.70 µg/L in downstream receiving water, achieving a 92.40 % removal rate. However, the types of high ecological risk antibiotics in hospital wastewater were only reduced by 38.46 % after treatment by hospitals and sewage treatment plants. The abundance of Rank I ARGs was reduced by 37.03 % in hospital sewage treatment stations and 28.57 % in WWTPs, but these ARGs accounted for 81.8 % of the Rank I ARGs in receiving water. The potential host bacteria for these ARGs were mainly Proteobacteria, which carried bacitracin and multidrug resistance genes. While WWTPs removed 66.67 % of the conditional pathogens, bacteria such as Acinetobacter and Streptococcus still entered the receiving water. MetaCompare revealed that the potential transmission risk of ARGs decreased by 24.31 % after hospital wastewater treatment and by 20.71 % after WWTPs, with the risk of the receiving water being 7.01 times that in sediments. The potential risk assessment framework developed in this study for antibiotics and ARGs in the environment provides a theoretical guidance for antibiotic treatment and ARGs environmental risk control.},
}

@article {pmid41161021,
year = {2025},
author = {Sun, J and Tong, X and Liu, S and Zhang, S and Wang, L and Wang, D and Jia, Q and He, X and Lv, W and Abdo Qasem, MAA and Xiao, Y and Fan, H},
title = {Clinical characteristics and mortality risk factors of Streptococcus constellatus infection: A retrospective cohort study of 390 patients.},
journal = {Journal of infection and public health},
volume = {19},
number = {1},
pages = {103023},
doi = {10.1016/j.jiph.2025.103023},
pmid = {41161021},
issn = {1876-035X},
abstract = {BACKGROUND: Few studies have investigated the clinical characteristics and mortality associated with Streptococcus constellatus (S.constellatus) infection. To identify the clinical features and mortality of patients with S. constellatus infection.

METHODS: This retrospective cohort study analyzed hospitalized patients with confirmed S.constellatus infection at West China Hospital of Sichuan University from January 2016 to April 2024. S. constellatus was identified using sterile body fluid culture or metagenomic next-generation sequencing (mNGS). Patients were categorized as monomicrobial or polymicrobial infection. Kaplan-Meier curve analysis was performed to compare the 30-day survival rates based on infection type and infection site, while multivariate Cox regression was conducted to identify independent risk factors for 30-day mortality.

RESULTS: Of the 390 patients, 301 (77.2 %) were classified as monomicrobial S. constellatus infection. S. constellatus isolates were highly susceptible to penicillin (98.08 %) and levofloxacin (98.90 %).Overall 30- and 90-day mortality were 13.08 % and 15.13 %, higher in polymicrobial than monomicrobial infections (24.72 % vs 8.97 % at 30 days; 29.21 % vs 10.96 % at 90 days). Polymicrobial infection (adjusted hazard ratio [aHR] = 2.426, p = 0.007) and brain abscess (aHR = 16.689, p < 0.001) were identified as independent risk factors for 30-day mortality in patients with S. constellatus infection. In the subgroup of monomicrobial infection, mediastinal abscess (aHR = 6.738, p = 0.002) and brain abscess (aHR = 13.933, p < 0.001) were significantly associated with an increased risk of 30-day mortality.

CONCLUSIONS: Although S. constellatus was highly susceptible to antibiotics, short-term mortality remained substantial. Infection site and polymicrobial infection were key prognostic factors in patients with S. constellatus infection.},
}

@article {pmid41161015,
year = {2025},
author = {Ekman, M and Mahani, AN and Aralaguppe, SG and Normark, T and Stamouli, S and Andersson-Li, L and Sun, D and Broddesson, S and Wirta, V and Björkström, NK and Albert, J and Allander, T},
title = {Evaluation of a diagnostic metagenomic sequencing assay: Virus detection sensitivity and background nucleic acids in three different sample materials.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {181},
number = {},
pages = {105882},
doi = {10.1016/j.jcv.2025.105882},
pmid = {41161015},
issn = {1873-5967},
abstract = {BACKGROUND: Metagenomic sequencing has emerged as an attractive, general, and agnostic diagnostic method, in particular for detection of viruses. However, its application faces limitations, including reduced sensitivity due to background nucleic acid content of samples, and the search for an optimized protocol is still ongoing.

METHODS: We report the development of a metagenomic sequencing protocol for diagnostic use and its performance in detecting DNA and RNA viruses in three different sample materials: serum, cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS).

RESULTS: Sensitivity was higher for RNA viruses than for DNA viruses, and also higher in CSF than in serum and lowest in NPS. We characterized the background nucleic acids and found higher DNA than RNA levels in CSF and serum and overall highest nucleic acid levels in NPS, intermediate in serum and lowest in CSF. These differences largely explained the observed variability in sensitivity between sample preparations and sample materials.

CONCLUSIONS: Our results highlight the need to consider sample-type specific characteristics in efforts to improve the sensitivity of metagenomic assays e.g. via host depletion protocols.},
}

@article {pmid41160250,
year = {2025},
author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y},
title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.},
journal = {Clinical oral investigations},
volume = {29},
number = {11},
pages = {543},
pmid = {41160250},
issn = {1436-3771},
support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; },
mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; },
abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.

MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.

RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.

CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.

CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.

TRIAL REGISTRATION: ITMCTR2024000616.},
}

Humans
Pilot Projects
*Tongue/microbiology
*Microbiota
Adult
Male
Female
*Specimen Handling/methods
Reproducibility of Results
Biofilms

@article {pmid41160143,
year = {2025},
author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM},
title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {183},
pmid = {41160143},
issn = {1572-9699},
mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.},
}

*Anti-Bacterial Agents/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Metagenomics/methods
*Bacteria/classification/genetics/drug effects/isolation & purification
Phylogeny
Aquaculture
*Catfishes/microbiology
RNA, Ribosomal, 16S/genetics
Microbial Sensitivity Tests

@article {pmid41160089,
year = {2025},
author = {Abuzahrah, SS},
title = {The microbiome of marine sponges located on the Saudi Arabia coast of the Red sea using high-throughput 16S amplicon sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {160},
pmid = {41160089},
issn = {2191-0855},
support = {PROJECT NO.: CRP/SAU24-02//International Centre for Genetic Engineering and Biotechnology (ICGEB)/ ; },
abstract = {Marine sponges (Porifera) from the Red Sea host diverse microbial communities that are integral to sponge health, nutrient cycling, and ecological resilience. Using high-throughput 16S rRNA amplicon sequencing, we characterized the bacterial diversity and functional potential across several Red Sea sponge species. Our findings revealed that these microbiomes are dominated by Alphaproteobacteria, Gammaproteobacteria, and Roseobacteraceae, with notable contributions from bacterial taxa involved in nitrogen fixation, organic matter degradation, and antimicrobial compound production. Functional predictions indicate that these symbionts support sponge nutrition, defense, and adaptation to the extreme Red Sea environment, including high salinity and temperature. Compared to sponge microbiomes from other marine regions, the Red Sea communities display unique taxonomic compositions and enhanced metabolic and defensive capacities. This highlights the essential ecological roles and potential biotechnological applications of these symbiotic assemblages. Our study underscores the significance of exploring sponge-associated microbiomes in understudied and extreme marine ecosystems. These results provide a foundation for future bioprospecting and work on adaptive mechanisms, emphasizing the value of Red Sea sponges and their microbiota for marine biotechnology and ecosystem resilience.},
}

@article {pmid41159973,
year = {2025},
author = {Anani, H and Destras, G and Regue, H and Bulteau, S and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Metagenome-assembled complete genome of Bohxovirus, a virulent bacteriophage involved in the prediction of hospital-acquired pneumonia in intubated critically ill patients.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059225},
doi = {10.1128/mra.00592-25},
pmid = {41159973},
issn = {2576-098X},
abstract = {We present the complete genome of a Bohxovirus species, a virulent phage targeting Prevotella jejuni, reconstructed from viral metagenomes in respiratory endotracheal aspirates of intubated critically ill patients. The 98-kbp bacteriophage, belonging to the Suoliviridae family, does not contain genes associated with antibiotic resistance or bacterial virulence.CLINICAL TRIALSClinicalTrials.gov numbers: NCT02003196 and NCT04793568.},
}

@article {pmid41159804,
year = {2025},
author = {Spottiswoode, N and Neyton, LPA and Calfee, CS and Langelier, CR},
title = {Reply to Liu et al. and Chen et al.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202509-2218LE},
pmid = {41159804},
issn = {1535-4970},
}

@article {pmid41159664,
year = {2025},
author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E},
title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70289},
doi = {10.1002/mnfr.70289},
pmid = {41159664},
issn = {1613-4133},
support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; },
abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.},
}

@article {pmid41159034,
year = {2025},
author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN},
title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655428},
pmid = {41159034},
issn = {1664-3224},
mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.

METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.

RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.

DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.},
}

Animals
*Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Autoimmunity
Mice
Mice, Inbred C57BL
*Central Nervous System/immunology/microbiology
*Multiple Sclerosis/immunology/microbiology
Female
Akkermansia
*Verrucomicrobia/immunology
Disease Models, Animal

@article {pmid41158777,
year = {2025},
author = {Skoog, EJ and Cutts, E and Bosak, T},
title = {Linking microbial ecology to the cycling of neutral and acidic polysaccharides in pustular mats from Shark Bay, Western Australia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684648},
pmid = {41158777},
issn = {1664-302X},
abstract = {Cyanobacteria and other microbes in peritidal microbial mats have produced extracellular polymeric substances (EPS) for more than two billion years. The production and degradation of EPS contributes to the biogeochemical cycling of carbon and carbonate precipitation within modern microbial mats, but key microbes involved in the cycling of EPS remain unidentified. Here, we investigate the cycling of EPS in the peritidal pustular mats of Shark Bay, Western Australia. We characterize the chemical composition of EPS produced by cyanobacterial enrichment cultures under natural and UV-stress conditions and link these findings to the metabolic potential for EPS production and degradation encoded in 84 metagenome-assembled genomes (MAGs) from the mat community. We further identify the key microbial degraders of specific acidic and neutral polysaccharides in this community by cultivating enrichment cultures on seven commercially available polysaccharides representative of those present in the mats and assessing the dominant taxa. All sequenced Cyanobacteria MAGs have the potential to synthesize mannose, fucose, glucose, arabinose, rhamnose, galactose, xylose, N-acetylglucosamine, galacturonic acid and glucuronic acid. Biochemical analyses confirm the presence of nearly all these monosaccharides in the hydrolysates of EPS extracted from UV- and non-UV exposed cyanobacterial enrichments. Ultraviolet radiation influences the structure and composition of EPS by reducing the hydration, potentially due to cross-linking among polymers in EPS and increasing the relative abundances of uronic acids and xylose in polysaccharides. Analyses of carbohydrate-active enzymes (CAZymes) in the MAGs and of 16S rRNA sequences from experimental polysaccharide enrichments point to major roles for Bacteroidetes, Planctomycetes, and Verrucomicrobia in the cycling of acidic EPS. These experiments reveal a complex interplay among microbial community composition, CAZyme diversity, environmental stressors, and EPS cycling, which together shape carbon flow and biomineralization in pustular mats in Shark Bay.},
}

@article {pmid41158770,
year = {2025},
author = {Peng, Y and Huang, D and Li, J and Sun, X and Zhang, Q and Zhang, R and Yang, R and Li, B and Kong, T and Xiong, Z and Huang, Y and Chang, Z and Su, Y and Shang, Y and Ghani, MU and Wang, Y and Sun, W},
title = {Investigation of the role of sulfide oxidation in the gill-associated microbiota of freshwater mussel Limnoperna fortunei.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671425},
pmid = {41158770},
issn = {1664-302X},
abstract = {INTRODUCTION: Limnoperna fortunei is a notable invasive freshwater species, altering structure and function of natural and engineered aquatic ecosystems. The host-associated microbiomes play a critical role in the survival and thriving of L. fortunei, with the gill-associated microbiomes being particularly significant due to their involvement in filter feeding, nutrient metabolism, and symbiosis. However, research on microbiomes associated with L. fortunei remains limited, and studies specifically focusing on gill-associated microbiota are scarce, leaving a significant gap in our understanding of their ecological roles.

METHODS: In this study, gill-associated bacterial communities of the L. fortunei were compared with their surrounding water microbial populations in the largest water diversion projects (the Middle Route of the South-to-North Water Diversion Project) to elucidate their environmental adaptations and potential contribution to their hosts. Analyses included assessing bacterial diversity and composition, conducting Neutral Community Model (NCM) analysis to explore community assembly processes, constructing an environmental-microbial co-occurrence network to identify key environmental factors, and performing metagenomic analysis of gill samples to investigate functional genes.

RESULTS: Significant variations were observed in bacterial diversity and composition between gills and surrounding water. Sulfur oxidizing bacteria Pirellula, SM1A02, and Roseomonas were significantly enriched in gill-associated microbiota. Neutral community model (NCM) analysis unveiled that the assembly of gill microbial communities was primarily governed by stochastic processes, constrained by determined processes. Moreover, environmental-microbial co-occurrence network identified reduced sulfur as the key factor shaping the composition of bacterial communities. Metagenomic binning of gill samples further revealed that metagenome assembled genomes associated with Pirellula within the phylum Planctomycetota contained functional genes related to sulfide oxidation and resistant to oxidative stress.

DISCUSSION: This study provides systematic insights into the microbial community diversity, assembly patterns, and functional characteristics of L. fortunei gill-asscociated microbiota, contributing to a mechanistic understanding of their ecological roles.},
}

@article {pmid41158352,
year = {2025},
author = {Liu, J and Qian, H and Jin, J and Du, M and Wang, C and Yu, J and Pang, P and Shen, M and Mei, Z and Shi, Y and Wang, Z and Jiang, G and Guo, L and Zhong, C and Tang, P and Wang, Y and Shi, C and Ji, C},
title = {Use of metagenomic next-generation sequencing for accurate diagnosis of tuberculous pleurisy: a retrospective cohort study.},
journal = {Journal of thoracic disease},
volume = {17},
number = {9},
pages = {6771-6778},
pmid = {41158352},
issn = {2072-1439},
abstract = {BACKGROUND: Tuberculous pleurisy (TP) presents persistent diagnostic challenges owing to the suboptimal sensitivity of conventional microbiological assays. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) in diagnosing TP using formalin-fixed paraffin-embedded (FFPE) pleural biopsy tissues.

METHODS: This retrospective study evaluated the diagnostic efficacy of mNGS in FFPE pleural samples of suspected TP patients at The First Affiliated Hospital of Soochow University between April 1, 2018 and February 1, 2023. Those patients with inadequate pleural specimens for mNGS analysis were excluded. Diagnosis of TP was established according to the WS 288-2017 Health Industry Standard of the People's Republic of China.

RESULTS: A total of 73 patients were enrolled in this study and divided into the TP group and non-tuberculous pleurisy (NTP) group. The TP group comprised 51 patients with a median age of 52 years, including 33 (64.7%) males. The NTP group consisted of 22 patients with a median age of 64 years, including 13 (59.1%) males. Our results showed that mNGS assay on FFPE in pleural biopsies had a sensitivity of 78.43% [95% confidence interval (CI): 0.667-0.901] and a specificity of 100% (95% CI: 1.000-1.000) in diagnosing TP. In the 51 TP cases, mNGS detected Mycobacterium tuberculosis complex (MTBC) in 40 (78.43%) cases and non-tuberculous mycobacteria (NTM) in 31 (60.78%) cases. Of these, 16 cases were MTBC infections alone and 7 cases were NTM infections alone, while 24 were mixed MTBC and NTM infections.

CONCLUSIONS: mNGS of FFPE of pleural biopsy tissues not only improves the diagnostic efficiency of TP, but also potential accurately distinguishes between MTBC and NTM, providing molecular and microbial basis for the diagnosis of TP, which is helpful for the rapid diagnosis and precise treatment of TP.},
}

@article {pmid41158324,
year = {2025},
author = {Fatemi, S and Kriefall, NG and Yogi, D and Weber, D and Hynson, NA and Medeiros, MCI and Sadowski, P and Amend, AS},
title = {Microbial composition and function are nested and shaped by food web topologies.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf175},
pmid = {41158324},
issn = {2730-6151},
abstract = {Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.},
}

@article {pmid41157632,
year = {2025},
author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K},
title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101362},
pmid = {41157632},
issn = {1999-4915},
support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; },
mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation & purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; },
abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.},
}

*Ixodes/virology
Animals
Phylogeny
*Genome, Viral
Siberia
*Virome/genetics
Encephalitis Viruses, Tick-Borne/genetics/isolation & purification/classification
Metagenomics
Genomics
Humans
Encephalitis, Tick-Borne/virology

@article {pmid41157620,
year = {2025},
author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ},
title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101349},
pmid = {41157620},
issn = {1999-4915},
support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation & purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; },
abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.},
}

Animals
*Chiroptera/virology
*Feces/virology
*Adenoviridae/genetics/classification/isolation & purification
*Virome
New Mexico/epidemiology
Phylogeny
Dogs
COVID-19/epidemiology/virology
Adenoviridae Infections/veterinary/virology/epidemiology
Metagenomics
SARS-CoV-2
Humans

@article {pmid41157605,
year = {2025},
author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J},
title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101334},
pmid = {41157605},
issn = {1999-4915},
support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; },
mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation & purification ; Genotype ; Genetic Variation ; },
abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.},
}

*Solanum lycopersicum/virology
*Virome/genetics
*Metagenomics
Phylogeny
*Plant Diseases/virology
Genome, Viral
*Plant Viruses/genetics/classification/isolation & purification
Genotype
Genetic Variation

@article {pmid41157584,
year = {2025},
author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS},
title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101312},
pmid = {41157584},
issn = {1999-4915},
support = {202271250010//Parliamentary Amendment from the São Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; },
mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; },
abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.},
}

Animals
*Weevils/virology
Brazil
*Genome, Viral
Saccharum/parasitology
*Virome
Metagenomics
Phylogeny

@article {pmid41157271,
year = {2025},
author = {Al-Khalaifah, H and Rahman, MH and Al-Surrayai, T and Al-Dhumair, A and Al-Hasan, M},
title = {A One-Health Perspective of Antimicrobial Resistance (AMR): Human, Animals and Environmental Health.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/life15101598},
pmid = {41157271},
issn = {2075-1729},
abstract = {Antibiotics are essential for treating bacterial and fungal infections in plants, animals, and humans. Their widespread use in agriculture and the food industry has significantly enhanced animal health and productivity. However, extensive and often inappropriate antibiotic use has driven the emergence and spread of antimicrobial resistance (AMR), a global health crisis marked by the reduced efficacy of antimicrobial treatments. Recognized by the World Health Organization (WHO) as one of the top ten global public health threats, AMR arises when certain bacteria harbor antimicrobial resistance genes (ARGs) that confer resistance that can be horizontally transferred to other bacteria, accelerating resistance spread in the environment. AMR poses a significant global health challenge, affecting humans, animals, and the environment alike. A One-Health perspective highlights the interconnected nature of these domains, emphasizing that resistant microorganisms spread across healthcare, agriculture, and the environment. Recent scientific advances such as metagenomic sequencing for resistance surveillance, innovative wastewater treatment technologies (e.g., ozonation, UV, membrane filtration), and the development of vaccines and probiotics as alternatives to antibiotics in livestock are helping to mitigate resistance. At the policy level, global initiatives including the WHO Global Action Plan on AMR, coordinated efforts by (Food and Agriculture Organization) FAO and World Organisation for Animal Health (WOAH), and recommendations from the O'Neill Report underscore the urgent need for international collaboration and sustainable interventions. By integrating these scientific and policy responses within the One-Health framework, stakeholders can improve antibiotic stewardship, reduce environmental contamination, and safeguard effective treatments for the future.},
}

@article {pmid41156846,
year = {2025},
author = {Liu, Y and Shang, Y and Wang, X and Li, X and Yu, Z and Zeng, Z and Chen, Z and Wang, L and Xiang, T and Huang, X},
title = {Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102387},
pmid = {41156846},
issn = {2076-2607},
support = {31872181//National Natural Science Foundation of China/ ; 2021QDL062//Research Start-up Funds from the Hangzhou Normal University/ ; 2025JCXK01//Interdisciplinary Research Project of Hangzhou Normal University/ ; },
abstract = {In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis.},
}

@article {pmid41156834,
year = {2025},
author = {Kakumyan, P and Yang, L and Liu, S and Saninjuk, K and Dong, Q and Pan, X and Yu, C and Zhao, Y},
title = {Sustainable Recycling of Mushroom Residue as an Effective Substitute for Cotton Hull Waste in Volvariella volvacea Cultivation: Evidence from Physicochemical and Microbiome Analyses.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102372},
pmid = {41156834},
issn = {2076-2607},
support = {2024YFD1200204//National Key R&D Program of China/ ; 19390743000//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; },
abstract = {Mushroom residue (MR) is extensively produced during the industrialized cultivation of mushrooms, and its utilization is environmentally sustainable. Cotton hull waste (CW) serves as a common raw material for the cultivation of Volvariella volvacea in China. This study compared MR- and CW-based cultivation formulas with respect to their physicochemical characteristics, bacterial communities, and functional dynamics during substrate fermentation (composting). Xylanase production was greater in the MR formula than in the CW formula. Conversely, cellulase (CMCase) was generated at higher levels in the CW formula compared to the MR formula. Interestingly, the biological efficiency of MR was found to be comparable to that of CW, but the cost of MR was much lower. The dynamics of bacterial communities and their associated metabolic functions during substrate fermentation were monitored using 16S rRNA metagenomics techniques. Significant alterations in bacterial community structure were observed within both formulas throughout the preparation phase. Indicator species analysis revealed distinct patterns of bacterial diversity development between MR- and CW-based composts during fermentation. Metabolic function analysis indicated that carbohydrate and amino acid metabolism remained relatively active throughout this process. These results suggest that the MR formula is equally effective as conventional CW compost for supporting V. volvacea cultivation, while also offering a lower raw material cost.},
}

@article {pmid41156833,
year = {2025},
author = {Xing, L and Niu, S and Wu, D and Zhang, Z and Xu, M},
title = {Sodium Butyrate Supplementation in Whole Milk Modulates the Gastrointestinal Microbiota Without Altering the Resistome and Virulome in Preweaned Calves.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102375},
pmid = {41156833},
issn = {2076-2607},
support = {BR221506//Universitiy Basic Research Fund Project of Inner Mongolia Autonomous Region/ ; 2023LHMS03048//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; },
abstract = {This study investigated the effects of supplementing whole milk (WM) with sodium butyrate (SB) on the gastrointestinal microbiota of preweaned calves. Twelve newborn Holstein calves (4 days old, 39.21 ± 1.45 kg) were randomly assigned into one of two dietary treatments: (1) WM without SB (CON) and (2) WM supplemented with SB (8.8 g/d; SB). At 74 days of age, all calves were slaughtered to collect ruminal and cecal digesta. Metagenomic analysis was used to characterize the microbial composition, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs). SB supplementation altered the ruminal microbial composition and increased the abundance of beneficial bacteria, including Actinobacteria, Bifidobacterium, and Olsenella (p < 0.05). Although SB did not significantly affect the overall microbial composition or diversity in the cecum (p > 0.05), it promoted the growth of beneficial genera such as Flavonifractor and Subdoligranulum (p < 0.05). Furthermore, SB supplementation did not significantly alter the composition of VFGs or ARGs in either the rumen or the cecum (p > 0.05). However, significant differences in VFGs and ARGs were observed between the rumen and the cecum, with a greater diversity of both VFGs and ARGs detected in the cecum compared to that in the rumen (p < 0.05). In summary, supplementing whole milk with sodium butyrate modulates gastrointestinal health in preweaned calves by favorably shaping the microbial community without significantly altering the antibiotic resistome or virulome.},
}

@article {pmid41156832,
year = {2025},
author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P},
title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102373},
pmid = {41156832},
issn = {2076-2607},
support = {1671/22-03-2023//Green Fund/ ; },
abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.},
}

@article {pmid41156828,
year = {2025},
author = {Stock, EK and Rota, K and Dunn, B and Vasquez, M and Hernandez-Velazquez, D and Lespes, A and Bosmans, S and Smith, JC and Kyndt, JA},
title = {Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102369},
pmid = {41156828},
issn = {2076-2607},
support = {NSF OIA-2044049//EPSCoR NE/ ; },
abstract = {The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of Vibrio cholerae, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment.},
}

@article {pmid41156825,
year = {2025},
author = {Lorenzin, G and Carlin, M},
title = {Comparative Meta-Analysis of Long-Read and Short-Read Sequencing for Metagenomic Profiling of the Lower Respiratory Tract Infections.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102366},
pmid = {41156825},
issn = {2076-2607},
abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly employed for the diagnosis of lower respiratory tract infections (LRTIs). However, the relative diagnostic performance of long-read versus short-read sequencing platforms remains incompletely defined. For this systematic review, a search was conducted in PubMed, Embase, Scopus, Web of Science, and Google Scholar to identify studies directly comparing long-read (e.g., Oxford Nanopore, PacBio) and short-read (e.g., Illumina, Ion Torrent, BGISEQ) metagenomic sequencing for the diagnosis of LRTI. Eligible studies reported diagnostic accuracy or comparative performance between platforms. Risk of bias was evaluated using the QUADAS-2 tool. Thirteen studies met inclusion criteria. Reported platforms included Illumina, Oxford Nanopore, PacBio, Ion Torrent, and BGISEQ-500. A total of 13 studies met inclusion criteria. Across studies reporting sensitivity, average sensitivity was similar for Illumina (71.8%) and Nanopore (71.9%). Specificity varied substantially, ranging from 42.9 to 95% for Illumina and 28.6 to 100% for Nanopore. Concordance between platforms ranged from 56 to 100%. Illumina consistently produced superior genome coverage (approaching 100% in most reports) and higher per-base accuracy, whereas Nanopore demonstrated faster turnaround times (<24 h), greater flexibility in pathogen detection, and superior sensitivity for Mycobacterium species. Risk of bias was frequently high or unclear, particularly in patient selection (6 studies), index test interpretation (5), and flow and timing (4), limiting the robustness of pooled estimates. Long-read and short-read mNGS platforms exhibit comparable strengths in the diagnosis of LRTIs. Illumina remains optimal for applications requiring maximal accuracy and genome coverage, whereas Nanopore offers rapid, versatile pathogen detection, particularly for difficult-to-detect organisms such as Mycobacterium. However, there are certain limitations of the review, including a lack of comparable outcomes reported in all studies; therefore, further research is warranted to address this.},
}

@article {pmid41156813,
year = {2025},
author = {Mollova, D and Baev, V and Iliev, I},
title = {In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102352},
pmid = {41156813},
issn = {2076-2607},
support = {KP-06-M81/6//Bulgarian Science Fund/ ; },
abstract = {Establishing the relative stability of the gastrointestinal microbiome after birth is a long and complex process, and it occurs under various influences. The human gut microbiome plays a crucial role in influencing an individual's health and well-being across all stages of life. Breastfeeding, the introduction of solid food at a certain stage after birth, and the type of food largely determine the composition of the developing microbiome. The influence of probiotics on the early development of the microbiome is gaining increasing interest. The method of in vitro co-cultivation with probiotic strains provides a clearer picture of the influence of these microorganisms on the community and the functional changes that the infant's microbiome undergoes. We used fecal samples to study this influence by conducting metagenomic sequencing to determine the composition of the microbiome and a series of cultivations to determine the absorption of various fibers and prebiotic sugars from breast milk. We found statistically significant differences in the absorption of prebiotic sugars isolated from breast milk, as well as better absorption of several substrates in the presence of a probiotic strain.},
}

@article {pmid41156808,
year = {2025},
author = {Mqambalala, A and Maleke, M and Deysel, LM and Osman, JR and Gomez-Arias, A and Valverde, A and Hernandez, JC},
title = {First Insight into the Natural Attenuation of Emerging Contaminants Using a Metagenomics Approach from Drinking Water Sources in the Free State.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102349},
pmid = {41156808},
issn = {2076-2607},
support = {PMDS230718136664//National Research Foundation/ ; },
abstract = {Emerging contaminants have gained interest over the years due to their adverse effects on the aquatic environment. Therefore, it is essential to improve the current strategies for their removal. Biodegradation has emerged as an efficient strategy driven by microorganisms through metabolism and co-metabolism pathways. Enzymes encoded by specific genes facilitate these processes. This study aimed to identify and quantify the genes involved in these pathways. The research identified bacterial species belonging to the genera Pseudomonas, Nitrosomonas, Nitrosospira, and Methylotenera, which are associated with the degradation of emerging contaminants. Additionally, it successfully identified genes linked to metabolism and co-metabolism processes within the indigenous bacteria (MAGs). The findings suggest that the native bacteria in the samples may have the natural potential to mitigate emerging contaminants in aquatic environments through the combined actions of metabolism and co-metabolism.},
}

@article {pmid41156764,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Jiang, F and Song, P and Liu, Y and Fan, Q and Xu, Y and Zhang, R},
title = {Insights into Cold-Season Adaptation of Mongolian Wild Asses Revealed by Gut Microbiome Metagenomics.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102304},
pmid = {41156764},
issn = {2076-2607},
support = {32360139//National Natural Science Foundation of China/ ; 2023LHMS03067//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; LHZX-2023-02//Joint Grant from Chinese Academy of Sciences -People's Government of Qinghai Province on San-jiangyuan National Park/ ; },
abstract = {The Mongolian wild ass (Equus hemionus hemionus) is a flagship species of the desert-steppe ecosystem in Asia, and understanding its strategies for coping with cold environments is vital for both revealing its survival mechanisms and informing conservation efforts. In this study, we employed metagenomic sequencing to characterize the composition and functional potential of the gut microbiota, and applied DNA metabarcoding of the chloroplast trnL (UAA) g-h fragment to analyze dietary composition, aiming to reveal seasonal variations and the interplay between dietary plant composition and gut microbial communities. In the cold season, Bacteroidota and Euryarchaeota were significantly enriched, suggesting enhanced fiber degradation and energy extraction from low-quality forage. Moreover, genera such as Bacteroides and Alistipes were also significantly enriched and associated with short-chain fatty acid (SCFA) metabolism, bile acid tolerance, and immune modulation. In the cold season, higher Simpson index values and tighter principal coordinates analysis (PCoA) clustering indicated a more diverse and stable microbiota under harsh environmental conditions, which may represent an important microecological strategy for the host to cope with extreme environments. Functional predictions based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) further indicated upregulation of metabolic and signaling pathways, including ABC transporters, two-component systems, and quorum sensing, suggesting multi-level microbial responses to low temperatures and nutritional stress. trnL-based plant composition analysis indicated seasonal shifts, with Tamaricaceae detected more in the warm season and Poaceae, Chenopodiaceae, and Amaryllidaceae detected more in the cold season. Correlation analyses revealed that dominant microbial phyla were associated with the degradation of fiber, polysaccharides, and plant secondary metabolites, which may help maintain host energy and metabolic homeostasis. Despite the limited sample size and cross-sectional design, our findings highlight that gut microbial composition and structure may be important for host adaptation to cold environments and may also serve as a useful reference for future studies on the adaptive mechanisms and conservation strategies of endangered herbivores, including the Mongolian wild ass.},
}

@article {pmid41156729,
year = {2025},
author = {Carnaggio, AA and Barthet, MM},
title = {It's a Question at the 'Root' of the Problem: Fungal Associations of Dionaea muscipula (Venus' Flytrap) Roots in Its Native Habitat.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102269},
pmid = {41156729},
issn = {2076-2607},
support = {//US Fish & Wildlife Services; Coastal Carolina University Coastal Marine and Wetlands Science Master's program; the Coastal Carolina University Graduate Student Research Incentive Grant; Savannah Presbytery's M.K. Pentecost Ecology Fund Grant/ ; },
abstract = {Carnivorous plants survive in harsh habitats with limited nutrients and a low pH. Much focus has been placed on carnivorous trap evolution as the primary mechanism to increase nutrient acquisition through insect digestion. Soil microbiome, however, may also play a pertinent role in nutrient acquisition influencing plant vigor and overall success. Dionaea muscipula, commonly known as the Venus' flytrap, is endemic to rims of the Carolina Bays located in southeast North Carolina and northeast South Carolina, where D. muscipula survives in nutrient poor soils with a vestigial root system. We utilized a combination of microscopy, plating, and metagenomics, to investigate the presence/absence of fungal partners that may contribute to success and vigor of D. muscipula in its native habitat in order to further conservation of this carnivorous plant. Results support that D. muscipula forms both mycorrhizal and fungal endophytic associations, most likely to aid nutrient uptake from otherwise nutrient-poor soils, as well as aid in stress defense. Several ectomycorrhizal, endophytic, and saprophytic fungal species were identified from the surrounding rhizosphere of D. muscipula roots presenting a first glimpse into fungal communities that may influence D. muscipula physiology and compose the microbiome of the Carolina Bays ecosystem.},
}

@article {pmid41156696,
year = {2025},
author = {Wang, Y and Shi, F and Lang, F and Wang, G and Mao, Y and Xiao, Y and Yin, L and He, G and Liao, Y},
title = {Ecological Imprint of Rare Earth Mining on Microbial Communities and Water Quality Across Depth and Distance Gradients in Ganzhou, China.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102236},
pmid = {41156696},
issn = {2076-2607},
support = {42167014//National Natural Science Foundation of China/ ; GJJ2401516//Jiangxi Provincial Department of Education Science and Technology research-youth project/ ; S202510419008//Innovation and Entrepreneurship Project for College Students in Jiangxi Province/ ; JZB1915//the Research Project of Jinggangshan University (Natural Sciences)/ ; },
abstract = {Rare earth element (REE) mining exerts profound impacts on aquatic ecosystems, yet the microbial community responses and water quality under such stress remain underexplored. In this study, the surface (0.2 m) and subsurface (1.0 m) water along a spatial transect from proximal to distal points was investigated in a REE-mining area of Ganzhou, China. Physicochemical analyses revealed pronounced gradients of nitrogen (e.g., NH4[+]-N, NO3[-]-N), heavy metals (e.g., Mn, Zn, Pb), and REEs (e.g., La, Nd, Ce), with higher accumulation near mining sources and partial attenuation downstream. Dissolved oxygen and redox potential indicated mildly reducing conditions at contaminated points, potentially promoting denitrification and altering nitrogen cycling. Metagenomic sequencing showed significant shifts in microbial community composition, with enrichment of metal- and nitrogen-tolerant taxa, and key denitrifiers (e.g., Acidovorax, Bradyrhizobium, Rhodanobacter), particularly at upstream polluted points. KEGG-based gene annotation highlighted dynamic nitrogen transformations mediated by multiple pathways, including nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and nitrogen fixation. Notably, genes associated with nitrite and nitrate reduction (e.g., nir, nar, nrf) were enriched near mining sources, indicating enhanced nitrogen conversion potential, while downstream activation of nitrogen-fixing genes suggested partial ecosystem recovery. Meanwhile, some microbial such as Variovorax carried metal tolerant genes (e.g., ars, chr, cnr). These findings demonstrate that REE and heavy metal contamination restructure microbial networks, modulate nitrogen cycling, and create localized ecological stress gradients. This study provides a comprehensive assessment of mining-related water pollution, microbial responses, and ecological risks, offering valuable insights for monitoring, restoration, and sustainable management of REE-impacted aquatic environments.},
}

@article {pmid41156619,
year = {2025},
author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB},
title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14101008},
pmid = {41156619},
issn = {2076-0817},
mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; },
abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.},
}

Animals
Kazakhstan
*Metagenomics/methods
*Ixodidae/microbiology
Male
Female
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Cattle
*Microbiota
*Metagenome
DNA, Bacterial/genetics

@article {pmid41156596,
year = {2025},
author = {Dao, TK and Pham, TTN and Nguyen, HD and Dam, QT and Phung, TBT and Nguyen, TVH and Nguyen, TQ and Hoang, KC and Do, TH},
title = {Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14100985},
pmid = {41156596},
issn = {2076-0817},
support = {ĐTĐLCN.63/22//Ministry of Science and Technology, Vietnam/ ; },
mesh = {Humans ; *Diarrhea/microbiology/virology ; *Dysbiosis/microbiology/virology ; Metagenomics/methods ; Infant ; *Bacteriophages/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Male ; Female ; Vietnam ; Child, Preschool ; *Metagenome ; Bacteria/classification/genetics/virology ; *Virome ; Feces/microbiology/virology ; },
abstract = {Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.},
}

Humans
*Diarrhea/microbiology/virology
*Dysbiosis/microbiology/virology
Metagenomics/methods
Infant
*Bacteriophages/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Male
Female
Vietnam
Child, Preschool
*Metagenome
Bacteria/classification/genetics/virology
*Virome
Feces/microbiology/virology

@article {pmid41156563,
year = {2025},
author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M},
title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/nu17203312},
pmid = {41156563},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
*Dairy Products/adverse effects
Animals
Milk
Probiotics
*Immunity
Cardiometabolic Risk Factors

@article {pmid41155945,
year = {2025},
author = {Bodnár, K and Fehér, P and Ujhelyi, Z and Haimhoffer, Á and Papp, B and Sinka, D and Freytag, C and Fidrus, E and Szarka, K and Kardos, G and Nacsa, F and Bácskay, I and Józsa, L},
title = {Formulation and Testing of Alginate Microbeads Containing Salvia officinalis Extract and Prebiotics.},
journal = {Pharmaceutics},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/pharmaceutics17101308},
pmid = {41155945},
issn = {1999-4923},
support = {eköp-24-3-I//university research scholarship program of the ministry for culture and innovation from the source of the national research, development and innovation fund/ ; TKP2021-EGA-18//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; 2022-1.2.2-TÉT-IPARI-UZ-2022-00006//National Research, Development and Innovation Fund/ ; },
abstract = {Background/Objectives: This study aimed to develop an advanced oral delivery platform for Salvia officinalis (S. officinalis) extract by co-encapsulating it with inulin and pectin in alginate-based microbeads, formulated via ionic gelation. Methods: The microbeads were comprehensively characterized, including the assessment of morphology, particle size, encapsulation efficiency, swelling behavior, in vitro dissolution, and enzymatic stability, and Caco-2 cell-based assays for cytocompatibility, permeability, and transepithelial electrical resistance. Antioxidant capacity and anti-inflammatory effects were also evaluated. Results: The resulting microbeads (~275 µm) achieved > 90% encapsulation efficiency and exhibited pronounced swelling (~90%). The release of S. officinalis constituents displayed pH sensitivity, with sustained release in simulated intestinal fluid, alongside significant enhancement of enzymatic stability. Encapsulation led to markedly improved permeability of bioactive compounds across Caco-2 monolayers, attributable to reversible modulation of tight junctions. Encapsulated extract retained potent antioxidant activity and significantly reduced pro-inflammatory cytokines. The formulation, across various concentrations, further promoted the growth and viability of Lactobacillus strains. Conclusions: Collectively, these findings demonstrate that alginate-inulin-pectin microbeads provide a multifunctional system for stabilizing S. officinalis extract, enabling controlled release, enhanced intestinal absorption, and maintained bioefficacy. Importantly, the formulation also promoted Lactobacillus viability, indicating a prebiotic effect and offering considerable potential for improved oral therapeutic applications.},
}

@article {pmid41155696,
year = {2025},
author = {Ji, M and Ma, B and Dong, J and Liu, S and Shi, Y and Bu, M and Wang, L and Liu, L},
title = {Mining Microbial Dark Matter: Advanced Cultivation Techniques for Bioactive Compound Discovery.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/ph18101583},
pmid = {41155696},
issn = {1424-8247},
support = {2022YFC2303100, 32472320, 32022002 and 32270083//National Key Research and Development Program of China, National Natural Science Foundation of China/ ; },
abstract = {The vast majority of microorganisms in the environment remain uncultured using conventional laboratory techniques, representing an immense untapped reservoir of genetic and chemical diversity. Recent innovations in cultivation strategies, combined with advances in metagenomics, single-cell genomics, and synthetic biology, have opened new avenues for accessing and harnessing bioactive natural products from these previously inaccessible microorganisms. This review highlights recent methodological and technological advancements in the cultivation and identification of novel microorganisms, and showcases the resulting discoveries of new natural products, demonstrating their potential for drug development.},
}

@article {pmid41155464,
year = {2025},
author = {Usui, M and Miyagi, S and Yamanaka, R and Oka, Y and Kobayashi, K and Sato, T and Sano, K and Onizuka, S and Inoue, M and Fujii, W and Iwasaki, M and Ariyoshi, W and Nakashima, K and Nishihara, T},
title = {Measuring the Invisible: Microbial Diagnostics for Periodontitis-A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010172},
pmid = {41155464},
issn = {1422-0067},
mesh = {Humans ; *Periodontitis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; Porphyromonas gingivalis/isolation & purification/genetics ; },
abstract = {Periodontitis is a biofilm-driven inflammatory disease in which conventional indices (probing depth, clinical attachment level, and radiographs) quantify tissue destruction without capturing the biology of infection. In this review, we synthesized microbiological diagnostics, from chairside tools to omics. We outline sampling strategies and emphasize the quantitative monitoring of bacterial load. Enzymatic assays (e.g., N-benzoyl-DL-arginine-2-naphthylamide hydrolysis assay test) measure functional activity at the point of care. Immunological methods include rapid immunochromatography for Porphyromonas gingivalis and enzyme-linked immunosorbent assay for the high-throughput measurement of bacterial antigens. Molecular platforms encompass quantitative polymerase chain reaction (qPCR) (TaqMan, SYBR, multiplex panels; propidium monoazide quantitative-qPCR for viable cells), checkerboard DNA-DNA hybridization for semi-quantitative community profiling, loop-mediated isothermal amplification (LAMP)/molecular beacon-LAMP for portable isothermal detection, and microarrays. Complementary modalities such as fluorescent in situ hybridization, next-generation sequencing, and Fourier transform infrared spectroscopy provide spatial, ecological, and biochemical resolutions. We discuss the limitations of current approaches, including sampling bias, presence-activity discordance, semi-quantitation, method biases, limited strain/function resolution, low-biomass artifacts, and lack of validated cutoffs. To address these challenges, we propose a pragmatic hybrid strategy: site-specific quantitative panels combined with activity and host-response markers interpreted alongside clinical metrics under standardized quality assurance/quality control. Priorities include outcome-linked thresholds, strain-aware/functional panels, robust point-of-care chemistry, and harmonized protocols to enable personalized periodontal care.},
}

Humans
*Periodontitis/diagnosis/microbiology
*Molecular Diagnostic Techniques/methods
Nucleic Acid Amplification Techniques/methods
Porphyromonas gingivalis/isolation & purification/genetics

@article {pmid41155136,
year = {2025},
author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T},
title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms26209841},
pmid = {41155136},
issn = {1422-0067},
support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; },
mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation & purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; },
abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.},
}

Humans
*Microbiota/genetics
*High-Throughput Nucleotide Sequencing/methods
RNA, Ribosomal, 16S/genetics
Middle Aged
Male
Female
*Bronchoalveolar Lavage Fluid/microbiology
Aged
Germany
*Bacteria/genetics/isolation & purification/classification
Hospitals, University
Bronchoalveolar Lavage
Nanopore Sequencing/methods
Adult
*Respiratory Tract Infections/microbiology/diagnosis
Aged, 80 and over

@article {pmid41154862,
year = {2025},
author = {Yin, R and Chen, B and He, X and Cai, C and Zhai, T and Shi, H and Li, N and Ma, X},
title = {Enhanced Phosphorus Removal by Iron-Carbon in Constructed Wetlands Across Salinity Gradients: Mechanisms and Microbial Insights for Aquaculture Tailwater Treatment.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101459},
pmid = {41154862},
issn = {2079-7737},
support = {No. BK20220682//Natural Science Foundation of Jiangsu Province/ ; LYG20230005//Postdoctoral Science Foundation of Lianyungang/ ; KYCX24-3671//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 2025SNJF008//Zhejiang Province 'San Nong Jiu Fang' Science and Technology Collaboration Project/ ; },
abstract = {Saline aquaculture tailwater challenges conventional constructed wetlands (CWs) with their limited phosphorus (P) removal capacity. To address this, iron-carbon constructed wetlands (IC-CWs) were developed and operated under four salinity gradients (0, 10, 20, and 30) for 155 days to investigate the effects of salinity on P removal and associated microbial mechanisms. The results showed that salinity critically influenced long-term P removal, with the system at salinity 20 (S20) achieving the highest total phosphorus (TP) removal efficiency (78.80 ± 6.01%). Enhanced P removal was primarily attributed to the upregulation of phosphate transport genes (pstS, 14.25-fold increase) and elevated activity of key enzymes (AKP and ACP) in phosphorus-accumulating organisms (PAOs). However, high salinity (30) suppressed microbial metabolic functions. Metagenomic analysis revealed that salinity stress reshaped microbial community structure, with Bacteroidota abundance increasing 10-fold in S20 compared to S0 (control). This phylum harbored the phnE gene, significantly promoting organic phosphorus mineralization. Additionally, iron release increased with rising salinity, and the relative abundance of the phnE gene in Bacteroidota was highest in the S20 group, indicating a close association between iron release and PAOs as well as organic P mineralization genes. The quadratic polynomial model revealed that iron release under high salinity followed nonlinear kinetics, with passivation layer rupture promoting iron-phosphorus precipitate desorption in later stages. These findings provide a theoretical basis for optimizing salinity parameters to enhance chemical-biological P removal synergy, offering a promising strategy for saline aquaculture wastewater treatment.},
}

@article {pmid41154799,
year = {2025},
author = {Promariya, A and Treenarat, S and Akrimajirachoote, N and Sricharern, W and Raksajit, W},
title = {Cultivation of Arthrospira platensis in Veterinary Hospital Wastewater Enhances Pigment Production and Reduces Antibiotic Resistance Genes.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101396},
pmid = {41154799},
issn = {2079-7737},
support = {FF(KU)18.66 and FF(KU)50.67//Kasetsart University Research and Development (KURDI)/ ; The 80th Anniversary of Kasetsart University's Establishment//Graduate School, Kasetsart University/ ; High Quality Research Graduate Development Cooperation Project//Kasetsart University and the National Science and Technology Development Agency (NSTDA)/ ; },
abstract = {Veterinary hospital wastewater (VHW) is a significant environmental concern due to its high nutrient content, organic pollutants, and antibiotic resistance genes (ARGs). This study evaluated the physicochemical properties of VHW, its potential to support Arthrospira platensis cultivation, and its effects on microbial and resistome profiles. VHW contained high levels of ammonia nitrogen, total Kjeldahl nitrogen, biological oxygen demand (BOD), and chemical oxygen demand (COD), indicating substantial contamination. A. platensis was cultivated for 8 days in Zarrouk medium supplemented with 0-100% VHW. Biomass production peaked in 25% VHW (0.78 ± 0.05 g/L), while growth was strongly suppressed at concentrations ≥75%. Pigment levels in 25% VHW increased significantly compared to the control: 1.3-fold for chlorophyll-a (12.0 μg/mL), 1.5-fold for carotenoids (4.4 μg/mL), 1.7-fold for phycocyanin (120 μg/mL), and 2.3-fold for allophycocyanin (54 μg/mL). Shotgun metagenomic analysis revealed that A. platensis cultivation markedly altered the microbial community and reduced the prevalence of ARGs. In 25% VHW, Proteobacteria dominated the community (97.0%), but their abundance declined to 11.6% when co-cultivated with A. platensis. Likewise, Acinetobacter sp. carrying high levels of the aph gene, along with Methylophaga sp. and Pseudomonas_E sp. harboring oqxB, decreased substantially, suggesting that A. platensis effectively suppressed ARG-rich genera. These findings highlight the dual potential of A. platensis for sustainable pigment-rich biomass production and efficient wastewater treatment.},
}

@article {pmid41154019,
year = {2025},
author = {Zhang, S and Wang, Q and Gong, S and Li, M and Zhang, Y and Sun, L and Sun, L},
title = {The Effect of Cucumaria frondosa Tentacles Hydrolysates on Dextran Sulfate Sodium-Induced Colitis: Integrated Metagenomics and Metabolomics Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/foods14203483},
pmid = {41154019},
issn = {2304-8158},
support = {42106111//National Natural Science Foundation of China/ ; 2023JCYJ088//The Yantai Science and Technology Innovation Development Program/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; QSCDP202304//Fund of Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food/ ; },
abstract = {Inflammatory bowel disease continues to pose substantial therapeutic challenges in modern gastroenterology. This study systematically evaluated the anti-colitis efficacy of Cucumaria frondosa tentacles hydrolysates (CFTHs) using a dextran sulfate sodium (DSS)-induced murine colitis model. Characterized by enhanced stability and solubility with molecular weights below 1000 Da, administration of CFTHs demonstrated a significant mitigation in colitis pathology. Therapeutic outcomes included an improved splenic index, attenuated colonic mucosal damage, and substantial decreases in serum pro-inflammatory cytokines. Relative to the DSS group, the MPO value in the CFTHs-H group decreased by 27.6%, and the IL-6 value exhibited a reduction of 33%. Metagenomic profiling revealed that CFTHs mediated gut microbiota modulation, particularly the enrichment of beneficial Bacteroidetes and suppression of pro-inflammatory Proteobacteria. Metabolomic analysis identified elevated colonic concentrations of anti-inflammatory metabolites such as gamma-linolenic acid and prostaglandin I2, suggesting a microbiome-metabolome crosstalk in the therapeutic mechanism. These multi-omics findings in a murine model suggest that CFTHs may represent a promising candidate for future studies as a nutraceutical intervention for inflammatory bowel disorder. This intervention may operate through mechanisms that include simultaneous immunomodulation, microbiota restoration, and metabolic reprogramming.},
}

@article {pmid41153961,
year = {2025},
author = {Xiang, R and Chen, J and Wang, J and Song, H and Jiang, J and Wu, F and Luo, J and Duan, M and Zhu, G},
title = {Characteristics of the Gut Microbiota in Different Segments of the Gastrointestinal Tract of Big-Eyed Bamboo Snake (Pseudoxenodon macrops).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {20},
pages = {},
doi = {10.3390/ani15203035},
pmid = {41153961},
issn = {2076-2615},
abstract = {Snakes are model animals to study energy balance, but studies on the gut microbiota of the animals are rather scarce. To fill the gap, we used metagenome sequencing to investigate the microbial community composition and adaptability in the stomach, small intestine, and large intestine of Big-eyed Bamboo Snake. The results showed that there was no significant differences in α-diversity among different gastrointestinal segments. Pseudomonadota, Bacteroidota, and Bacillota were the most abundant phyla. The dominant genera in the stomach and small intestine were similar, while those in the large intestine were distinct. The abundance of Bacteroides, Citrobacter and Clostridium was significantly higher in the large intestine than in the small intestine. The LEfSe analysis revealed that the small intestine had the most characteristic bacteria, with a total of 20 species, while the stomach and large intestine each had two species. Additionally, in the current study, we also focused on the impact of the microbial community structure on functions through functional annotations in the KEGG and CAZy. There were significant differences in the KEGG level 2 between the stomach and the small intestine. The LEfSe analysis revealed the differences in the CAZy level 2 between the large intestine and the small intestine. Overall, our study provided a comparative and contrastive analysis of the gut microbiota in different gastrointestinal segments of Big-eyed Bamboo Snake, offering valuable insights for the co-evolution mechanism of the host and the gut microbiota.},
}

@article {pmid41153865,
year = {2025},
author = {Wei, J and Wei, L and Ullah, A and Geng, M and Zhang, X and Wang, C and Khan, MZ and Wang, C and Zhang, Z},
title = {Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {20},
pages = {},
doi = {10.3390/ani15202938},
pmid = {41153865},
issn = {2076-2615},
support = {2022YFD1600103; 2023YFD1302004//the National Key R&D Program of China/ ; },
abstract = {Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host-microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants like cattle, sheep, and goats host microbiota enriched with fibrolytic and methanogenic microbes that facilitate fiber degradation and volatile fatty acid production, contributing significantly to energy balance. In contrast, non-ruminants such as horses and rabbits rely on hindgut fermentation, with distinct microbial taxa contributing to carbohydrate and protein breakdown. The review further explores how specific microbial taxa, including Prevotella, Fibrobacter, and Ruminococcus, correlate with improved feed efficiency and growth performance, particularly in ruminants. Additionally, the roles of probiotics, prebiotics, and symbiotics in modulating gut microbial composition and enhancing productivity are discussed. Despite significant advances, challenges remain in microbial sampling, functional annotation, and understanding the integration of microbiota with host physiology. The review emphasizes the potential of metagenomic insights in optimizing herbivore gut microbiota to improve feed efficiency, health, and sustainable livestock production.},
}

@article {pmid41153262,
year = {2025},
author = {Feng, Y and Feng, H and Yu, X and Zhao, J and Zhou, H and Li, J and Chen, P and Feng, L},
title = {Next-Generation Sequencing for Diagnosis of Fatal Balamuthia Amoebic Encephalitis: A Case Report.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {20},
pages = {},
doi = {10.3390/diagnostics15202590},
pmid = {41153262},
issn = {2075-4418},
support = {Z20200307//The scientific research project of Guangxi Health Commission/ ; },
abstract = {Background:Balamuthia mandrillaris is a free-living amoebic parasite that primarily causes rare opportunistic infections in immunocompromised hosts. Balamuthia amoebic encephalitis (BAE) is a rare yet severe parasitic infection affecting the central nervous system. It has an extremely low incidence in China but can have a mortality rate as high as 98%. The clinical manifestations of amebic infections are similar to those of bacterial and tuberculous meningitis, lacking specificity, which makes accurate diagnosis challenging in the clinical setting. Case Presentation: A 61-year-old immunocompetent woman experienced worsening headache and a moderate fever over the course of five days, initially treated as a common cold. On 25 February 2025, she exhibited behavioral abnormalities, dysphagia, and a high fever of 40.2 °C, which progressed to a coma. On 26 February, her cranial CT scan revealed multifocal hemorrhagic lesions in the right frontotemporoparietal lobes. The MRI revealed similar lesions with slight enhancement and herniation. She underwent an emergency decompressive craniectomy, yet her condition continued to deteriorate following the surgery. On 27 February, serum targeted next-generation sequencing (tNGS) detected B. mandrillaris. Additionally, metagenomic NGS (mNGS) of the cerebrospinal fluid (CSF) sample confirmed the presence on 28 February. Finally, B. mandrillaris was identified through a brain tissue biopsy on 3 March. However, due to the delayed diagnosis and lack of effective drugs, her condition rapidly deteriorated and became irreversible. Her family ultimately chose to withdraw treatment. Conclusions: This study highlights the application of NGS for early diagnosis of patients with severe CNS infection. Both tNGS and mNGS can be considered for the rapid detection of rare or novel pathogens and for facilitating diagnosis.},
}

@article {pmid41152730,
year = {2025},
author = {Su, Y and Xiao, Q and Ye, S and Qiu, F and Guo, Q and Chen, Q and Chen, P and You, Y and Huang, S and Wu, Z},
title = {Metagenomic next-generation sequencing (mNGS) guides targeted antibiotic therapy and reduces mortality in sepsis: a propensity-matched retrospective cohort study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1430},
pmid = {41152730},
issn = {1471-2334},
support = {A2024130//Guangdong Medical Research Foundation/ ; A2023198//Guangdong Medical Research Foundation/ ; 82374216//National Natural Science Foundation of China/ ; 20251363//Traditional Chinese Medicine Bureau of Guangdong Province/ ; 2320001006680//Foshan Science and Technology Bureau/ ; 2320001006896//Foshan Science and Technology Bureau/ ; 2220001005576//Foshan Science and Technology Bureau/ ; YN2022QN01//Guangdong Hospital of Traditional Chinese Medicine Special Research Project on Traditional Chinese Medicine Science and Technology/ ; SL2025A04J4201//Planned Science Technology Project of Guangzhou/ ; 20210001//Foshan Medical Research Project/ ; },
}

@article {pmid41152727,
year = {2025},
author = {Chen, L and Wang, C and Zhang, H and Wu, Y and Li, F and Shi, H and Ren, Z and Chen, Y and Huang, J and Zhao, D and Pan, J and Lu, H and Zheng, S},
title = {Characterization of microbiota dysbiosis in papillary thyroid carcinoma and benign thyroid nodules: low abundance of intestinal butyrate-producing bacteria.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {691},
pmid = {41152727},
issn = {1471-2180},
support = {2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//the National Natural Science Foundation of China/ ; JNL-2022001A//the Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; *Thyroid Cancer, Papillary/microbiology ; *Butyrates/metabolism ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Feces/microbiology ; *Thyroid Nodule/microbiology ; Adult ; *Thyroid Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: The thyroid-gut axis refers to the intricate relationships among the gut, intestinal microbiota, and thyroid gland, and it is speculated to play an important role in the development of thyroid diseases. The aim of this study was to identify the differentiated bacteria in the intestinal microbiota associated with papillary thyroid carcinoma (PTC) and benign thyroid nodules (BTNs) to offer potential avenues for further exploration and therapeutic interventions.

METHODS: Faecal microbiotas of 197 subjects (73 from subjects with BTNs, 62 from subjects with PTC, and 62 from sex- and age-matched controls) were characterized by sequencing the V3-V4 region of 16 S rDNA using the Illumina NovaSeq 6000 platform. Microbiomics and machine learning-assisted approaches were used to identify the PTC-/BTN-associated intestinal microbial indicators.

RESULTS: Compared with the abundance of coabundant groups (CAGs) in the PTC, BTN, and control groups, the abundance of two Genus-CAGs consisting of butyrate producers, such as Blautia, Lachnoclostridium, Lachnospiraceae_unclassified, Eisenbergiella, Flavonifractor and Hungatella, was lower in the PTC group than in the control group. In particular, both ANCOM-BC2 and Wilcoxon rank-sum test results consistently demonstrated significant enrichment of the butyrate-producing genera Oscillibacter, Coprobacter, and Colidextribacter in both BTN patients and healthy controls. The majority of discriminatory amplicon sequence variants (ASVs) that could discriminate PTCs from controls, as well as from BTNs, were from Prevotella, Streptococcus, Bacteroides, and butyrate-producing groups, such as the Oscillibacter, Lachnospiraceae, and Christensenellaceae (R7) groups. ASV indicators from Prevotella and Streptococcus were most abundant in the PTC group, and those from Bacteroides and the butyrate-producing/-promoting group were least abundant in the PTC group. Additionally, the ASVs that could discriminate the BTN group from the control group, as well as PTC group included other butyrate-producing groups, the Clostridium_sensu_stricto group, and the Eubacterium_siraeum group.

CONCLUSIONS: This study demonstrates that dysbiosis linked to thyroid nodules is marked by a substantial decline in intestinal butyrate-producing and butyrate-promoting taxa. Future work to confirm these results should include shotgun metagenomic sequencing paired with quantitative analyses of gene abundance and expression to fully ascertain the functional implications.},
}

Humans
*Dysbiosis/microbiology
Female
Male
*Gastrointestinal Microbiome
*Thyroid Cancer, Papillary/microbiology
*Butyrates/metabolism
Middle Aged
*Bacteria/classification/metabolism/genetics/isolation & purification
Feces/microbiology
*Thyroid Nodule/microbiology
Adult
*Thyroid Neoplasms/microbiology
RNA, Ribosomal, 16S/genetics
Aged
DNA, Bacterial/genetics

@article {pmid41152726,
year = {2025},
author = {Zou, Y and Zou, Q and Wang, Y and Han, C},
title = {Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {693},
pmid = {41152726},
issn = {1471-2180},
support = {62402344//Youth Found of the National Natural Science Foundation of China/ ; 62373080//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; *Seasons ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; China ; Feces/microbiology ; },
abstract = {BACKGROUND: Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of Eospalax rothschildi, a subterranean zokor endemic to China.

RESULTS: Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of α-galactosidase and β-galactosidase genes from enriched microbial populations, particularly Bacteroides, unclassified_f_Lachnospiraceae, Roseburia, and Faecalibacterium. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in E. rothschildi during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.

CONCLUSIONS: Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of E. rothschildi.},
}

*Gastrointestinal Microbiome/genetics
*Seasons
*Metagenomics/methods
Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
China
Feces/microbiology

@article {pmid41152332,
year = {2025},
author = {Ciuchcinski, K and Bluszcz, A and Dziewit, L},
title = {Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1702},
pmid = {41152332},
issn = {2052-4463},
support = {BOB-IDUB-622-105/2024//Uniwersytet Warszawski (University of Warsaw)/ ; },
mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Poland ; Salinity ; *Plasmids ; *Microbiota ; Metagenomics ; },
abstract = {Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.},
}

*Soil Microbiology
RNA, Ribosomal, 16S/genetics
Poland
Salinity
*Plasmids
*Microbiota
Metagenomics

@article {pmid41152293,
year = {2025},
author = {Pold, G and Saghaï, A and Jones, CM and Hallin, S},
title = {Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9495},
pmid = {41152293},
issn = {2041-1723},
support = {2016-03551//Vetenskapsrådet (Swedish Research Council)/ ; 2023-03627//Vetenskapsrådet (Swedish Research Council)/ ; Senior Career Grant 2019//Sveriges Lantbruksuniversitet (Swedish University of Agricultural Sciences)/ ; },
mesh = {*Denitrification/genetics ; *Bacteria/genetics/metabolism/classification ; Nitrates/metabolism ; *Genome, Bacterial ; *Genome, Microbial ; Metagenome ; Nitrites/metabolism ; Metabolic Networks and Pathways/genetics ; },
abstract = {Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.},
}

*Denitrification/genetics
*Bacteria/genetics/metabolism/classification
Nitrates/metabolism
*Genome, Bacterial
*Genome, Microbial
Metagenome
Nitrites/metabolism
Metabolic Networks and Pathways/genetics

@article {pmid41152000,
year = {2025},
author = {Saguti, F and Wang, H and Churqui, MP and Tunovic, T and Holmer, L and Pettersson, Ä and Schleich, C and Pott, BM and Bergstedt, O and Nyström, K and Norder, H},
title = {Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70222},
doi = {10.1111/1758-2229.70222},
pmid = {41152000},
issn = {1758-2229},
support = {2020-02710//Svenska Forskningsrådet Formas/ ; 20-102//Svenskt Vatten/ ; },
mesh = {*Drinking Water/virology ; *Virome ; *Water Purification/methods ; *Viruses/genetics/classification/isolation & purification ; Sweden ; Metagenomics ; *Water Microbiology ; Genome, Viral ; Bacteriophages/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.},
}

*Drinking Water/virology
*Virome
*Water Purification/methods
*Viruses/genetics/classification/isolation & purification
Sweden
Metagenomics
*Water Microbiology
Genome, Viral
Bacteriophages/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing

@article {pmid41151807,
year = {2025},
author = {Bontemps, Z and Abrouk, D and Moënne-Loccoz, Y and Hugoni, M},
title = {Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70112},
doi = {10.1111/1758-2229.70112},
pmid = {41151807},
issn = {1758-2229},
support = {//DRAC Nouvelle Aquitaine (Bordeaux, France)/ ; },
mesh = {*Caves/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota/genetics ; *Fungi/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Melanins/biosynthesis/genetics ; Carotenoids/metabolism ; Phylogeny ; },
abstract = {Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.},
}

*Caves/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota/genetics
*Fungi/genetics/metabolism/classification/isolation & purification
Metagenomics
Melanins/biosynthesis/genetics
Carotenoids/metabolism
Phylogeny

@article {pmid41151605,
year = {2025},
author = {Burillo, A and Serrano-Lobo, J and Bouza, E and Muñoz, P},
title = {Is it possible to identify genotypes underlying resistant phenotypes in Gram-negative pathogens?.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001158},
pmid = {41151605},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review explores the relationship between genotypes and resistant phenotypes in Gram-negative pathogens. We analyse to what extent conventional phenotypic methods predict genetic mechanisms of resistance, the reliability of genotypic approaches, and how integrated strategies may improve diagnostic accuracy and clinical utility.

RECENT FINDINGS: Traditional AST remains the clinical reference standard due to its correlation with therapeutic outcomes, yet it often fails to identify the molecular basis of resistance. Molecular methods such as PCR, microarrays, and targeted sequencing allow rapid detection of known genes but cannot reliably predict expression or functionality. Whole-genome sequencing provides the most comprehensive overview, capturing both known and novel resistance determinants as well as mobile genetic elements. Nevertheless, genotype-phenotype discordance persists, driven by regulatory mutations, inducible expression, or synergistic mechanisms. Emerging technologies - including real-time sequencing, metagenomics, and machine learning-based predictive models - are enhancing our ability to infer phenotypes from genomic data. Still, these approaches face challenges of standardization, validation, and integration into clinical workflows.

SUMMARY: Linking genotypes to resistant phenotypes in Gram-negative pathogens remains complex. While phenotypic AST ensures reliability for therapy, genotypic methods provide unprecedented insight into resistance mechanisms and epidemiology. Discrepancies between the two highlight the need for integrated diagnostic platforms that combine functional and genomic perspectives. Artificial intelligence-driven predictive models and curated resistance databases hold promise for improving accuracy, but widespread adoption requires robust datasets, clinical validation, and harmonized interpretative frameworks. Ultimately, integrating phenotypic and genotypic data represents the most effective strategy to provide mechanism-informed, clinically actionable diagnostics for antimicrobial resistance management.},
}

@article {pmid41151513,
year = {2025},
author = {Qin, C and Xie, X and Wang, H and Ma, L and Lu, X},
title = {Metagenomic investigation of antibiotic resistance genes and assessment of their health risk in antimony-mining area.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140278},
doi = {10.1016/j.jhazmat.2025.140278},
pmid = {41151513},
issn = {1873-3336},
abstract = {Here, we conducted a metagenomic investigation of antibiotic resistance genes (ARGs) from soil, surface water, and groundwater samples collected in Xikuangshan antimony (Sb)-mine area in China. Overall, 1737 subtypes of ARGs were detected which collectively conferred resistance to 27 classes of antibiotics. The health risk of the ARGs to humans were quantitatively evaluated by integrating human accessibility, mobility, pathogenicity, and clinical availability. A total of 6706 ARGs were identified within metagenome-assembled genomes (MAGs), with 44 of these ARGs posing a health risk, particularly those that confer multidrug resistance. Soil served as a potential reservoir of ARGs, harboring a greater variety of ARGs. In contrast, aquatic environments were hotspots for high-risk ARGs, with groundwater containing the most numerous risk-associated ARGs but surface waters posing the greatest health risks. Remediated soils showed significantly reduced ARG abundance and health risk, indicating that ecological restoration effectively mitigates ARG-related health risks. Pseudomonadota persisted as the dominant functional phylum in Sb mining area, exhibiting significant positive correlations with ARGs abundance. Acinetobacter, Achromobacter, and Stenotrophomonas, were identified as opportunistic pathogens carrying high-risk ARGs. Our analysis suggested that mining activities may amplify public health risks of ARGs, highlighting the importance for ecological remediation of mining areas.},
}

@article {pmid41151484,
year = {2025},
author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J},
title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.},
journal = {International immunopharmacology},
volume = {167},
number = {},
pages = {115730},
doi = {10.1016/j.intimp.2025.115730},
pmid = {41151484},
issn = {1878-1705},
abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).

METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-κB signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.

RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-κB pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-κB pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-κB activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-κB and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.

CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-κB pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.},
}

@article {pmid41151425,
year = {2025},
author = {Lv, J and Zhao, Q and Jiang, J and Ding, J and Wei, L and Liang, J},
title = {Electron transfer performance and mechanism in twin microbial fuel cell powered electro-Fenton system with waste activated sludge as substrate.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {168},
number = {},
pages = {109154},
doi = {10.1016/j.bioelechem.2025.109154},
pmid = {41151425},
issn = {1878-562X},
abstract = {The twin microbial fuel cell powered electro-Fenton system (twin-MFCⓅEFs), combining active oxygen component and microbial metabolism, was constructed to improve the treatment process of waste activated sludge (WAS). Nevertheless, the performance and mechanism of electron transfer underlying this enhancement remain poorly understood. This study investigated the performance and mechanism of electron generation and utilization in twin-MFCⓅEFs with WAS as substrate. The higher electron generation and recovery efficiency (8.25 % of coulombic efficiency) was attributed to the higher content of amino acids (such as tryptophan), humic substances and their aromatic groups and unsaturated conjugated double bonds in the soluble organic matter, which facilitated biodegradation and electron transfer. The higher electron utilization performance (52.76 % of faraday efficiency) relied on the superior electron supply system that exhibited greater free radical oxidation. Metagenomic analysis indicated that an increased secretory capacity of glycosyltransferases (including glucosyltransferases and β-glucosidases) and a reduced activity of acetate kinase and methyl-coenzyme M reductase alpha subunit in cellular metabolic processes favored signaling and electricity production. The study focused on electron flow in twin-MFCⓅEFs and offered a promising strategy for improving the sludge treatment process.},
}

@article {pmid41151197,
year = {2025},
author = {Ortiz-López, G and Sánchez-Reyes, A and Téllez-Galván, A and Bustamante, VH and Breton-Deval, L},
title = {Influence of anthropogenic inputs on microbial risks and resistance genes in a riverine environment.},
journal = {International journal of hygiene and environmental health},
volume = {271},
number = {},
pages = {114699},
doi = {10.1016/j.ijheh.2025.114699},
pmid = {41151197},
issn = {1618-131X},
abstract = {Rivers face significant anthropogenic pressures due to diverse water discharges, which alter microbial community structures and may facilitate the dissemination of potentially pathogenic microorganisms and antibiotic-resistance genes (ARGs). This study used metagenomic analysis to characterize microbial and viral communities, determine antibiotic resistance profiles, and evaluate potential public health risks associated with different discharges sources. Water samples were collected from agricultural, hospital, untreated domestic wastewater, treated wastewater, and environmental inputs. Results revealed that hospital wastewater (HW) had microbial genera associated with the wastewater treatment plant; however, we were able to isolate a multidrug-resistant Klebsiella aerogenes, Enterobacter spp. and Staphylococcus spp. Untreated domestic wastewater (UW) was dominated by species such as Arcobacter cryaerophilus, Acinetobacter johnsonii, Escherichia coli, and Acinetobacter lwoffii, while treated wastewater (TW) showed the presence of Arcobacter cryaerophilus, Aeromonas caviae, Prevotella copri, Arcobacter butzleri, Acinetobacter johnsonii, Escherichia coli, and Pseudomonas stutzeri. Regarding ARGs, HW contributed significantly to ARGs diversity, particularly genes conferring resistance to critical antibiotics such as meropenem and vancomycin. TW exhibits the highest ARG diversity, including genes for broad-spectrum resistance to aminoglycosides, penicillins, and cephalosporins, suggesting cumulative contamination from multiple sources. These findings emphasize the importance of advancing efforts to tackle this challenge in wastewater treatment practices and stricter regulations to mitigate the spread of antibiotic resistance and pathogenic microorganisms in aquatic environments.},
}

@article {pmid41150814,
year = {2025},
author = {Jiang, L and Qing, Y and Huang, K and Huang, H and Li, C and Mei, Q and Wu, Q},
title = {Comparison of Gut Microbial Structure and Function Changes in Sichuan-Tibetan Black Pigs at Different Growth Stages Based on Metagenomic Analysis.},
journal = {Current issues in molecular biology},
volume = {47},
number = {10},
pages = {},
doi = {10.3390/cimb47100866},
pmid = {41150814},
issn = {1467-3045},
support = {2023NSFSC0206//the Natural Science Foundation Project of Science and Technology Department of Sichuan Province/ ; },
abstract = {The gut microbiota plays a crucial role in maintaining swine health and understanding its stage-specific variations provides a scientific basis for health assessment. This study investigated the structural changes in intestinal microbiota during the development of Sichuan-Tibetan black pigs (n = 15) by collecting fecal samples at three growth stages: the nursery period (1 month), growing period (3 months), and finishing period (10 months). Microbial profiling was performed using 16S rRNA sequencing. Results showed no significant difference in the Shannon index between the nursery and growing periods, while the finishing period exhibited distinct ACE and Chao 1 indices compared to other stages. PCoA and NMDS analyses revealed significant structural divergence in the finishing period microbiota, with greater intra-group variability observed in the nursery and growing periods. At the phylum level, Firmicutes abundance increased progressively with growth, becoming the absolute dominant phylum, whereas Bacteroidota showed a declining trend. These characteristics are particularly prominent during the finishing period. At the family level, Lactobacillaceae abundance increased continuously. Oscillospiraceae remained stable during the early stages but decreased significantly in the finishing period. Genus-level analysis shows that Lactobacillus, especially L. amylovorus and L. reuteri, become dominant bacterial species during the finishing period. A total of 84 differentially abundant core microbiota were identified, with the finishing period containing the highest number. Functional annotation revealed 19 significantly different metabolic pathways across the three stages. The most significant is the enhanced activity of microorganisms during the finishing period in pathogen-related metabolism and exogenous degradation, reflecting their adaptability to complex feed. These findings demonstrate stage-dependent variations in the gut microbiota of Sichuan-Tibetan black pigs, providing valuable references for nutritional regulation and feeding management practices.},
}

@article {pmid41150726,
year = {2025},
author = {Ma, M and Li, Q and Wu, F and Zhu, B and Lu, H and Zhang, D and Łukasik, P and Hu, Y},
title = {Symbiotic solutions for colony nutrition: Conserved nitrogen recycling within the bacterial pouch of Tetraponera ants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2514882122},
doi = {10.1073/pnas.2514882122},
pmid = {41150726},
issn = {1091-6490},
support = {32370448//MOST | National Natural Science Foundation of China (NSFC)/ ; 2243200009//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
mesh = {*Ants/microbiology/physiology/metabolism ; Animals ; *Symbiosis/physiology ; *Nitrogen/metabolism ; Microbiota/physiology ; Larva/microbiology/growth & development ; Amino Acids/metabolism ; *Bacteria/metabolism/genetics ; Urea/metabolism ; },
abstract = {While microbial symbioses are fundamental to the nutrition of many animal groups, current paradigms focus on symbiont functions at the host individual level. It remains unclear whether microbial symbioses can sustain colony-level fitness in social insects, whose ecological success depends on nutrient coordination across castes. Here, we investigate the specialized bacterial pouch, a symbiont-containing organ present exclusively in adult workers of Tetraponera nigra-group ants, revealing its crucial role in colony-wide nutrient provisioning. Using a combination of microscopy, amplicon and metagenomic sequencing, and [15]N-urea feeding experiments on four species in the group, we show that its adult-specific pouch-associated microbiota, primarily Tokpelaia, recycle nitrogen from urea and convert it into amino acids which are provisioned to adult workers and developing larvae. Disruption of this nitrogen-recycling symbiosis severely impairs larval growth and overall colony fitness. Our results show how caste-restricted microbial organs can centralize metabolic functions at the colony level, challenging individual-centric paradigms of host-microbe mutualism and providing insights into the pivotal role of microbial symbionts in superorganismal adaptation to nutritional constraints.},
}

*Ants/microbiology/physiology/metabolism
Animals
*Symbiosis/physiology
*Nitrogen/metabolism
Microbiota/physiology
Larva/microbiology/growth & development
Amino Acids/metabolism
*Bacteria/metabolism/genetics
Urea/metabolism

@article {pmid41150505,
year = {2025},
author = {Zong, C and Gao, S and Wei, Q and Yin, Y and Shi, Y},
title = {Impact of Chromium Exposure on Potato Farming Systems and Plant Responses.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09289},
pmid = {41150505},
issn = {1520-5118},
abstract = {Chromium (Cr) is a major source of heavy metal pollution, posing a significant threat to agricultural production. This study investigated the impact of chromium on potato farmland and explored integrated control strategies using the potato cultivar Dongnong 310 as the research subject. Transcriptomic and rhizosphere microbial metagenomic sequencing methods were employed. The main findings were as follows: (1) chromium stress downregulated genes encoding photosystem II, thereby inhibiting photosynthesis in potatoes. (2) Chromium stress altered the diversity of rhizosphere soil microorganisms, reduced the abundance of nitrous oxide reductase, and increased emissions of the greenhouse gas N2O. (3) The rhizosphere microorganism Bacillus strain C5 and potato gene LOC102599109 exhibited chromium resistance. This study provides theoretical guidance for the integrated management of chromium pollution in potato farmland.},
}

@article {pmid41149776,
year = {2025},
author = {Tana, C and Moffa, S and Tana, M and Ucciferri, C and Moffa, L},
title = {Gut Microbiota, Mild Cognitive Impairment and Dementia: A Systematic Review.},
journal = {Neurology international},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/neurolint17100155},
pmid = {41149776},
issn = {2035-8385},
abstract = {BACKGROUND: Alterations of the gut microbiota have been increasingly implicated in the pathogenesis of dementia through mechanisms involving systemic inflammation, immune dysregulation, and gut-brain axis disruption. Clinical evidence, however, remains fragmented.

OBJECTIVES: This systematic review aimed to characterize gut microbiota profiles in individuals with mild cognitive impairment (MCI) or Alzheimer's dementia (AD), explore mechanistic associations with neurodegeneration, and evaluate the impact of microbiota-targeted interventions on cognitive outcomes.

METHODS: Following PRISMA 2020 guidelines and a registered protocol (PROSPERO CRD420251074832), PubMed/Medline was searched through May 2025. Eligible studies included randomized controlled trials (RCTs) and cohort and case-control studies assessing microbiota composition or interventions in participants with MCI or AD.

RESULTS: Twenty-one studies were included (1 RCT, 20 observational; sample size 22-302). Most used 16S rRNA sequencing; one used shotgun metagenomics. Across cohorts, MCI and AD patients consistently showed reduced short-chain fatty acid-producing bacteria (Faecalibacterium, Ruminococcaceae, Lachnospiraceae) and increased pro-inflammatory taxa (Escherichia/Shigella, Enterobacteriaceae, Bacteroides). Several studies reported reduced microbial diversity. Specific taxa, including Akkermansia muciniphila and Faecalibacterium, were associated with amyloid burden, hippocampal atrophy, and cognitive decline. Environmental and dietary factors influenced microbial composition and cognition. The RCT reported that probiotic supplementation improved inflammatory markers and BDNF levels, although changes in microbiota composition were inconsistent.

CONCLUSIONS: Gut dysbiosis is strongly associated with cognitive impairment and markers of neurodegeneration. Modulation of the microbiota through diet and probiotics emerges as a promising avenue for dementia prevention and management, though robust longitudinal and interventional studies are needed to confirm causality and therapeutic efficacy.},
}

@article {pmid41149107,
year = {2025},
author = {Matsumoto, R and Takahashi, M and Hosomichi, K and Okuwaki, S and Koizumi, S and Hikita, Y and Hatanaka, R and Yamaguchi, T},
title = {Comparison of Long-Term Oral Bacterial Flora Before and After Orthognathic Surgery in Surgical Orthodontic Treatment.},
journal = {Dentistry journal},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/dj13100458},
pmid = {41149107},
issn = {2304-6767},
support = {24K20091//Yu Hikita/ ; 24K13185//Tetsutaro Yamaguchi/ ; },
abstract = {Background/Objectives: Multi-bracket appliances are essential in surgical orthodontic treatment, and perioperative oral management during orthognathic surgery is critical. Thorough plaque control, appropriate use of antibiotics, and shortening of operative time have been reported to be effective in preventing postoperative infections and ensuring surgical success. As highly invasive orthognathic surgery involving osteotomy may influence the postoperative oral microbiota, this study aimed to investigate the characteristics of and clarify the changes occurring in the salivary oral microbiota after orthognathic surgery. Methods: The study included 14 patients (Group S; mean age 29.3 ± 9.8 years) who underwent surgical orthodontic treatment and 15 control patients (Group C; mean age 27.1 ± 8.7 years) who received orthodontic treatment alone. Salivary samples were analyzed via 16S rRNA gene sequencing, and the relative abundances of bacteria were evaluated using the Linear Discriminant Analysis Effect Size. Results: The prevalence of Neisseria, which is associated with early biofilm formation, decreased over time in both groups. In contrast, Streptococcus exhibited an increase in prevalence. In Group S, members of Pseudomonas, the family Saccharimonadaceae, and the order Rhizobiales showed increases at 5-8 months post-surgery. Conclusions: Surgical orthodontic treatment may influence the oral microbiota and promote colonization by opportunistic pathogens. Instructions regarding oral hygiene and appropriately timed professional cleaning interventions are critical in preventing such colonization. Longitudinal monitoring of the microbiota using metagenomic analysis may be useful for future perioperative management and guidance of oral hygiene.},
}

@article {pmid41149072,
year = {2025},
author = {Amorim Filho, AG and Martins, RCR and Franco, LAM and Marinelli, JVC and Peres, SV and Francisco, RPV and Carvalho, MHB},
title = {Vaginal Microbiota in Short Cervix Pregnancy: Secondary Analysis of Pessary vs. Progesterone Trial.},
journal = {Diseases (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/diseases13100338},
pmid = {41149072},
issn = {2079-9721},
abstract = {BACKGROUND/OBJECTIVES: Preterm birth (PTB) is a leading cause of neonatal mortality, particularly in women with a short cervix. Vaginal dysbiosis has been associated with increased PTB risk. Progesterone (PR) and Arabin pessary (PE) are commonly used for PTB prevention, but their impact on vaginal microbiome composition is unclear. This study aimed to compare the effects of these interventions on the vaginal microbiome in women at risk of PTB.

METHODS: In a secondary analysis of a randomized trial at Hospital das Clínicas, Universidade de São Paulo, 203 women with singleton pregnancies and cervical length ≤ 25 mm at the second trimester were assigned to daily vaginal PR (200 mg) or PE. Vaginal swabs from 44 participants (n = 22 per group) were collected at baseline and 4 weeks post-treatment and analyzed via 16S rRNA gene sequencing.

RESULTS: From 88 samples analyzed, 80 showed a low-diversity, Lactobacillus-dominated microbiota, 42 classified into Lactobacillus iners-dominated community state type (CST-III), and 38 presented other Lactobacillus species dominance (termed CST-I/II/V). The remaining eight samples presented non-Lactobacillus dominance (CST-IV). Comparing the two groups, no significant changes in CST were observed between sampling timepoints (PE group, p = 0.368; PR group, p = 0.223). Similarly, Shannon alpha diversity did not change (PE group, p = 0.62; PR group, p = 0.30), and Bray-Curtis dissimilarity also did not change after treatment (p = 0.96, before; p = 0.87, after treatment).

CONCLUSIONS: Arabin pessary and vaginal progesterone maintain vaginal microbiome stability in women at high PTB risk, supporting the microbiological safety of both interventions.},
}

@article {pmid41148745,
year = {2025},
author = {Tewolde, R and Thombre, R and Farley, C and Nadarajah, S and Khan, I and Sewell, M and Spiller, OB and Afshar, B},
title = {Comparison of Phenotypic and Whole-Genome Sequencing-Derived Antimicrobial Resistance Profiles of Legionella pneumophila Isolated in England and Wales from 2020 to 2023.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101053},
pmid = {41148745},
issn = {2079-6382},
abstract = {Background: Antimicrobial resistance (AMR) in Legionella pneumophila is emerging as a concern, particularly with resistance to macrolides and fluoroquinolones. Although clinically significant resistance in Legionella pneumophila remains uncommon, systematic genomic surveillance using whole-genome sequencing (WGS) is needed to anticipate treatment failure as metagenomic diagnostics move toward routine use. Objectives: We assessed the UK Health Security Agency AMR pipeline for predicting resistance in L. pneumophila by analysing 522 L. pneumophila isolates from England and Wales (2020-2023) together with nine database sequences that carry confirmed 23S rRNA mutations conferring high-level azithromycin resistance. The objective of the present study was to examine the presence of antimicrobial resistance genes (ARGs) in L. pneumophila isolates and to determine whether they exhibited phenotypic resistance through minimum inhibitory concentration (MIC) testing. Methods: Serogroups (sgs) were determined using an in-house qPCR assay, and L. pneumophila non-sg1 isolates were serogrouped using the Dresden monoclonal antibody (mAb) typing method. Sequence types were determined using the standard sequence-based typing method by Sanger sequencing. WGS reads were screened against standard AMR databases to identify resistance genes and resistance-mediating mutations. Agar dilution measured MICs for azithromycin, erythromycin, ampicillin, levofloxacin, tetracycline and spectinomycin in isolates possessing the blaOXA-29, lpeAB or aph(9)-Ia gene. Results: AMR screening detected lpeAB, two allelic β-lactamase variants (blaOXA-29 and blaLoxA) and aph(9)-Ia in 165 of the 522 L. pneumophila isolates, while all high-azithromycin MIC reference sequences contained the expected 23S mutation. Only lpeAB was associated with a significant twofold elevation in macrolide MICs. Neither β-lactamase variant increased ampicillin MICs, and aph(9)-Ia carriage did not correlate with higher spectinomycin MICs. Conclusions: Advanced genomic analytics can now deliver timely therapeutic guidance, yet database-flagged genes may not translate into phenotypic resistance. Continuous pairing of curated mutation catalogues with confirmatory testing remains essential for distinguishing clinically actionable determinants such as 23S mutations and lpeAB from silent markers like blaOXA-29 and aph (9)-Ia.},
}

@article {pmid41148714,
year = {2025},
author = {Lertcanawanichakul, M and Bhoopong, P and Horpet, P},
title = {Mangrove Ecosystems as Reservoirs of Antibiotic Resistance Genes: A Narrative Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101022},
pmid = {41148714},
issn = {2079-6382},
support = {The official grant number has not yet been assigned.//Plant Genetic Conservation Project Undeพ the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn - RSPG/ ; },
abstract = {Background: Mangrove ecosystems are critical coastal environments providing ecological services and acting as buffers between terrestrial and marine systems. Rising antibiotic use in aquaculture and coastal agriculture has led to the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in these habitats. Aim: This narrative review aims to synthesize current knowledge on the prevalence, diversity, and environmental drivers of ARGs in mangrove ecosystems, highlighting their role as reservoirs and the potential for horizontal gene transfer. Methods: Studies published up to September 2024 were identified through PubMed, Scopus, Web of Science, and Google Scholar. Inclusion criteria focused on ARGs and ARB in mangrove sediments, water, and associated biota. Data on ARG prevalence, microbial community composition, detection methods, and environmental factors were extracted and narratively synthesized. Results: Seventeen studies from Asia, South America, and Africa were included. ARGs conferring resistance to tetracyclines, sulfonamides, β-lactams, and multidrug resistance were found to be widespread, particularly near aquaculture and urban-influenced areas. Metagenomic analyses revealed diverse resistomes with frequent mobile genetic elements, indicating high potential for horizontal gene transfer. Environmental factors, including sediment type, organic matter, and salinity, influenced ARG abundance and distribution. Conclusions: Mangrove ecosystems act as both reservoirs and natural buffers for ARGs. Sustainable aquaculture practices, continuous environmental monitoring, and integrated One Health approaches are essential to mitigate ARG dissemination in these sensitive coastal habitats.},
}

@article {pmid41148708,
year = {2025},
author = {Lynch, S and Thomson, P and Santibañez, R and Avendaño-Herrera, R},
title = {Influence of Florfenicol Treatments on Marine-Sediment Microbiomes: A Metagenomic Study of Bacterial Communities in Proximity to Salmon Aquaculture in Southern Chile.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101016},
pmid = {41148708},
issn = {2079-6382},
support = {FONDAP No. 1523A0007//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {Background/Objectives: Metagenomic analyses are an important tool for understanding ecological effects, particularly in sites exposed to antimicrobial treatments. Marine sediments host diverse microbial communities and may serve as reservoirs for microbial resistance. Although it is known that antimicrobials can alter microbial composition, specific impacts on sediments surrounding salmon farms remain poorly understood. This study analyzed bacterial community structure in marine sediments subjected to florfenicol treatment from salmon farms in the Los Lagos Region of southern Chile. Methods: Sediment samples were collected and examined through DNA extraction and PCR amplification of the 16S rRNA gene (V3-V4 region). Sequences were analyzed using a bioinformatics pipeline, and amplicon sequence variants (ASVs) were taxonomically classified with a Naïve Bayesian classifier. The resulting ASV abundance were then used to predict metabolic functions and pathways via PICRUSt2, referencing the MetaCyc database. Results: Significant differences in bacterial phyla were observed between the control farm and two farms treated with florfenicol (17 mg kg[-1] body weight per day) for 33 and 20 days, respectively. Farm 1 showed notable differences in phyla such as Bacteroidota, Bdellovibrionota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fibrobacterota, Firmicutes, and Fusobacteriota, while Farm 2 exhibited differences in the phyla Bdellovibrionota, Calditrichota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fusobacteriota, Nanoarchaeota, and Nitrospirota. Shannon Index analysis revealed a reduction in alpha diversity in the treated farms. Comparative analysis between the control and the treated farms showed pronounced shifts in the relative abundance of several bacterial phyla, including statistically significant differences in Chloroflexi and Firmicutes. Predicted functional pathways revealed a notable enrichment of L-methionine biosynthesis III in Farm 2, suggesting a shift in sulfur metabolism potentially driven by antimicrobial treatment. Additionally, increased activity in fatty acid oxidation pathways indicates a higher microbial potential for lipid degradation at this site. Conclusions: These findings highlight the considerable influence of florfenicol on sediment microbial communities and reinforce the need for sustainable management strategies to minimize ecological disruption and the spread of antimicrobial resistance.},
}

@article {pmid41148701,
year = {2025},
author = {Ramsay, DE and McDonald, W and Gow, SP and McLeod, L and Otto, SJG and Osgood, ND and Waldner, CL},
title = {The Potential for Sample Testing at the Pen Level to Inform Prudent Antimicrobial Selection for Bovine Respiratory Disease Treatment: Investigations Using a Feedlot Simulation Tool.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101009},
pmid = {41148701},
issn = {2079-6382},
support = {N/A//Genome Canada/ ; N/A//Saskatchewan Agriculture Development Fund/ ; N/A//Beef Cattle Research Council (BCRC)/ ; N/A//National Sciences and Engineering Research Council (NSERC)/ ; N/A//University of Saskatchewan/ ; N/A//University of Alberta/ ; },
abstract = {Background: Antimicrobial drugs are used to treat bacterial diseases in livestock production systems, including bovine respiratory disease (BRD) in feedlot cattle. It is recommended that therapeutic antimicrobial use (AMU) in food animals be informed by diagnostic tests to limit the emergence of antimicrobial resistance (AMR) and preserve the effectiveness of available drugs. Recent evidence demonstrates preliminary support for the pen as a prospective target for AMR testing-based interventions in higher-risk cattle. Methods: A previously reported agent-based model (ABM) was modified and then used in this study to investigate the potential for different pen-level sampling and laboratory testing-informed BRD treatment strategies to favorably impact selected antimicrobial stewardship and management outcomes in the western Canadian context. The incorporation of sample testing to guide treatment choice was hypothesized to reduce BRD relapses, subsequent AMU treatments and resultant AMR in sentinel pathogen Mannheimia haemolytica. The ABM was extended to include a discrete event simulation (DES) workflow that models the testing process, including the time at sample collection (0 or 13 days on feed) and the type of AMR diagnostic test (antimicrobial susceptibility testing or long-read metagenomic sequencing). Candidate testing scenarios were simulated for both a test-only control and testing-informed treatment (TI) setting (n = 52 total experiments). Key model outputs were generated for both the pen and feedlot levels and extracted to data repositories. Results: There was no effect of the TI strategy on the stewardship or economic outcomes of interest under baseline ecological and treatment conditions. Changes in the type and number of uses by antimicrobial class were observed when baseline AMR in M. haemolytica was assumed to be higher at feedlot arrival, but there was no corresponding impact on subsequent resistance or morbidity measures. The impacts of sample timing and diagnostic test accuracy on AMR test positivity and other outputs were subsequently explored with a theoretical "extreme" BRD treatment protocol that maximized selection pressure for AMR. Conclusions: The successful implementation of a pen-level sampling and diagnostic strategy would be critically dependent on many interrelated factors, including the BRD treatment protocol, the prevalences of resistance to the treatment classes, the accuracy of available AMR diagnostic tests, and the selected "treatment change" thresholds. This study demonstrates how the hybrid ABM-DES model can be used for future experimentation with interventions proposed to limit AMR risk in the context of BRD management.},
}

@article {pmid41148456,
year = {2025},
author = {Loera, MY and de Figueras, CG and Sánchez-Costa, M and Martínez-Rodríguez, P and Mirete, S and Lamprecht-Grandío, M and Díaz, S and González-Pastor, JE and Díaz-Rullo, J},
title = {Co-expression of environmental extremophilic genes strongly enhances Escherichia coli cross-protection to abiotic stress.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {3},
pages = {39},
pmid = {41148456},
issn = {1433-4909},
support = {PID2021-126114NB-C43//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Escherichia coli/genetics/physiology/metabolism/radiation effects ; *Extremophiles/genetics ; *Stress, Physiological ; Oxidative Stress ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Nature is home to a wide range of species that thrive in extreme conditions. Despite the identification and study of many extremophilic organisms, significant questions remain regarding the limits of life and the potential for enhancing, combining, or transferring extreme characteristics to other organisms. In previous works of our group, several genes retrieved from environmental extremophiles using functional metagenomics were shown to increase the tolerance of the model bacterium Escherichia coli towards different stress conditions. Here, we proposed to evaluate whether the rational combination of those resistance genes isolated from environmental extremophiles and involved in different molecular mechanisms enhanced the cross-protection of E. coli to extreme conditions. Data revealed that the simultaneous introduction in E. coli of environmental extremophilic resistance genes involved in protein degradation, biofilm formation, oxidative stress, and DNA protection resulted in strongly enhanced, non-additive effects, significantly increasing survival rate under perchlorate exposure, UV radiation, and low pH compared to the individual introduction of these genes. Our findings supports that the introduction of multiple resistance genes isolated from environmental extremophiles that belong to diverse biological processes of stress adaptation may be crucial for engineering of multi-resistant species of interest in biomanufacturing and astrobiology.},
}

*Escherichia coli/genetics/physiology/metabolism/radiation effects
*Extremophiles/genetics
*Stress, Physiological
Oxidative Stress
Escherichia coli Proteins/genetics/metabolism

@article {pmid41148396,
year = {2025},
author = {Xie, X and Ren, W and Zhou, W and Wang, Y and Zhu, H and Wu, Y and Lu, Q},
title = {Genetic prediction of the effect of gut microbiota on retinal vein occlusion via blood metabolites.},
journal = {International ophthalmology},
volume = {45},
number = {1},
pages = {447},
pmid = {41148396},
issn = {1573-2630},
support = {2024KY376//Medical Science and Technology Program of Zhejiang Province/ ; 2022L003//Ningbo Clinical Research Center for Ophthalmology/ ; 2016-370 S05//Ningbo Clinical Research Center for Ophthalmology and the Project of NINGBO Leading Medical & Health Disipline/ ; 2021Z054//Technology Innovation 2025 Major Project of Ningbo/ ; 2024Z233//Ningbo"Innovation Yongjiang 2035" Key Technology Breakthrough program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Retinal Vein Occlusion/genetics/blood/microbiology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; *Polymorphism, Single Nucleotide ; Biomarkers/blood ; },
abstract = {PURPOSE: Given the unclear causal relationship between gut microbiota (GM) and retinal vein occlusion (RVO) and the potential mediating role of blood metabolites, this study aims to investigate this causal link and the mediating effects of blood metabolites.

METHODS: Our Mendelian randomization (MR) study used data from genome-wide association studies pooled data, including 473 microbiota taxa (n = 5959), 233 blood metabolites (n = 136,016), and RVO cases and controls from the FinnGen consortium (cases, n = 775; controls, n = 308,633). We used bidirectional two-sample MR, multivariate MR, and mediation analysis to assess the causal association between GM and RVO.

RESULTS: By analyzing gut microbial metagenomic data with adjustment for confounding factors, we identified 1 taxon with significant causal association and 14 taxa with potential causal links to RVO, where Halomonadaceae remained after Bonferroni correction. Parallel analysis of blood metabolites revealed 18 causal associations (2 significant, 16 potential), with apolipoprotein A-I and creatinine retaining significance post-correction. Three GM taxa affected RVO through three blood metabolites. Caloranaerobacteraceae, Rhodococcus, and Citrobacter A affected RVO through Total cholesterol in HDL2, Apolipoprotein A-I, and phenylalanine, respectively. Apolipoprotein A-1 possessed the greatest mediated effect (5.6%) between Rhodococcus and RVO.

CONCLUSION: These findings provide new insights into the pathogenesis of RVO and may contribute to the development of new strategies for preventing the onset of RVO.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Retinal Vein Occlusion/genetics/blood/microbiology
Mendelian Randomization Analysis
Genome-Wide Association Study
Male
Female
*Polymorphism, Single Nucleotide
Biomarkers/blood

@article {pmid41148302,
year = {2025},
author = {Hirayama, M and Maeda, T and Kashihara, K and Tsuboi, Y and Ito, M and Nishiwaki, H and Ohno, K and Ueyama, J},
title = {Linking diet, gut microbiota, and metabolites to Parkinson's disease risk: a shotgun metagenomic comparison of Japanese and Taiwanese cohorts.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {},
number = {},
pages = {},
pmid = {41148302},
issn = {1435-1463},
support = {24K10657//Japan Society for the Promotion of Science/ ; 23H02794//Japan Society for the Promotion of Science/ ; 2022G025//Smoking Research Foundation/ ; },
abstract = {Emerging evidence suggests that gut microbiota and its metabolites play pivotal roles in the pathogenesis of Parkinson's disease (PD). However, cross-national differences in diet and microbial composition may account for the striking variability in PD prevalence worldwide. To address this, we performed a comparative shotgun metagenomic analysis between Japanese and Taiwanese individuals, two genetically similar East Asian populations with distinct dietary habits and differing PD incidence rates. Our analysis revealed marked differences in dietary intake: Taiwanese individuals consumed higher amounts of animal fats and tropical fruits, whereas the Japanese diet was characterized by greater intake of seafood, root vegetables, and traditional fermented foods such as natto. These dietary patterns were reflected in gut microbiota profiles. Japanese individuals exhibited a higher abundance of Blautia, Faecalibacterium, and Bifidobacterium, while Taiwanese samples were enriched in Bacteroides and Alistipes. Functionally, genes involved in short-chain fatty acid (SCFA), vitamin, and polyamine biosynthesis were significantly reduced in PD patients and in the Taiwanese cohort. Metabolomic analyses corroborated these findings, showing decreased levels of SCFAs, polyamines, and key vitamins such as nicotinate and pantothenate in PD patients. Notably, Blautia abundance correlated positively with a broad range of beneficial metabolites, highlighting its potential role as a central modulator of host-microbe metabolic interactions. Our findings suggest that traditional Japanese dietary practices may shape a gut microbial environment that confers resistance to PD, underscoring the need for future interventional studies targeting diet-microbiota interactions in PD prevention and treatment.},
}

@article {pmid41148242,
year = {2025},
author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R},
title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02725},
pmid = {41148242},
issn = {1588-2640},
abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.},
}

@article {pmid41147939,
year = {2025},
author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Ai, L and Zhang, Z and Xie, F},
title = {Docynia delavayi (Franch.) Schneid polyphenols alleviate dextran sulfate sodium-induced colitis by regulating the gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03604f},
pmid = {41147939},
issn = {2042-650X},
abstract = {Docynia delavayi (Franch.) Schneid is rich in polyphenols; however, its functions remain unclear. In this study, we identified and characterized the key constituents of D. delavayi fruit polyphenols (DDP), validated their anti-inflammatory effects, and provided insights into their underlying mechanisms of action. UPLC-MS/MS was used to quantify the major phenolic compounds in DDP, including glycitin, procyanidin B2, vitexin, myricitrin, astilbin, chlorogenic acid, phlorizin, (-)-epicatechin, naringenin-7-O-glucoside, taxifolin-7-O-rhamnoside, rhoifolin, methylnissolin-3-O-glucoside, and scutellarein. In the dextran sulfate sodium-induced colitis mouse model, DDP significantly improved colon length and the disease activity index. It also reduced the expression of inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α. Metagenomic analysis revealed that DDP increased gut microbiota diversity, particularly enriching species capable of producing short-chain fatty acids (SCFAs), such as Lawsonibacter and Ruminiclostridium. Metabolomic data further demonstrated the upregulation of SCFA-associated pathways, such as glycolysis and pyruvate metabolism, with elevated colonic acetate, propionate, and butyrate levels corroborating these findings. Multi-omics analysis linked SCFAs to reduced inflammation. Collectively, these findings suggest that SCFAs play a pivotal role in the anti-inflammatory effects of DDP by modulating the gut microbiota to enhance SCFA biosynthesis. These findings demonstrate that SCFAs serve as critical mediators of the anti-inflammatory properties of DDP, highlighting their considerable potential as natural therapeutic agents for intestinal inflammation.},
}

@article {pmid41147782,
year = {2025},
author = {Zhang, L and Yang, G and Zhang, C and Ji, B and Wu, D},
title = {Symbiotic nitrogen fixation and recycling in xylophagous insects: insights from gut microbiota of Apriona swainsoni larvae.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70323},
pmid = {41147782},
issn = {1526-4998},
support = {81503115//National Natural Science Foundation of China/ ; JNFX2025192//Domestic Visiting Program for Young Key Teachers of Anhui Province/ ; BK2012816//Natural Science Foundation of Jiangsu Province/ ; 201409/WT_/Wellcome Trust/United Kingdom ; CX (16)1005//Jiangsu Agricultural Science and Technology Independent Innovation Project/ ; 2023AH050727//Natural Science Foundation (Key project) of the University in Anhui Province/ ; 2024AH050921//Natural Science Foundation (Key project) of the University in Anhui Province/ ; HZR2436//Hefei Municipal Natural Science Foundation/ ; 2024A755//Anhui Postdoctoral Scientific Research Program Foundation/ ; },
abstract = {BACKGROUND: Xylophagous insects, as nitrogen-limited organisms, face severe nutritional constraints due to the inherently low nitrogen content of lignocellulosic substrates-insufficient for growth. To alleviate this limitation, they rely on gut microbiota-mediated symbiotic nitrogen fixation and nitrogenous waste recycling. Apriona swainsoni, a model wood-boring cerambycid, exemplifies this adaptation: under extreme nitrogen scarcity in its xylem diet. While gut symbionts are hypothesized to overcome nitrogen limitation, the underlying mechanisms remain unclear.

RESULTS: First, metagenomic sequencing and functional gene analysis revealed enrichment of nitrogenase and urease genes in the posterior hindgut (PHG). Metaproteomics detected the nitrogenase gene nifU but no urease proteins, identifying nitrogen fixation as the primary nitrogen limitation mitigation strategy in A. swainsoni larvae. Subsequently, in vivo/in vitro [15]N isotope tracing showed peak [15]N in the PHG (105.02% higher than the natural environment) and ~ 25-fold greater [15]N incorporation in cultured Klebsiella oxytoca versus controls. Targeted amino acid profiling further demonstrated [15]N enrichment in both essential and non-essential amino acids, with a spatial gradient (intestinal tissues > extra-intestinal tissues > frass)-indicating efficient microbial conversion of nitrogen into host-utilizable amino acids. Importantly, we identified that intestinal microbiota primarily mediate ammonia-to-amino acid conversion via the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway in the PHG. This is the first reported GS/GOGAT-mediated nitrogen fixation pathway in cerambycids.

CONCLUSIONS: Our comprehensive analysis of gut microbial nitrogen metabolism might elucidate a set of mechanisms by which some xylophagous insects may overcome nutritional constraints in nitrogen-deficient niches, via evolutionarily optimized host-microbe metabolic interactions. © 2025 Society of Chemical Industry.},
}

@article {pmid41147731,
year = {2025},
author = {Jones, JA and Moczek, AP and Newton, ILG},
title = {The dung beetle microbiome complements host metabolism and nutrition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117225},
doi = {10.1128/msystems.01172-25},
pmid = {41147731},
issn = {2379-5077},
abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.},
}

@article {pmid41147494,
year = {2025},
author = {Naureckas Li, C and Jhaveri, R and Huston, S},
title = {Results of a local modified Delphi consensus on use of plasma metagenomic next-generation sequencing.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1017/ice.2025.10334},
pmid = {41147494},
issn = {1559-6834},
abstract = {Molecular tests without well-defined test performance characteristics are increasingly available for diagnosis of infectious diseases. These tests present a diagnostic stewardship challenge for institutions. We share the results of a local modified Delphi consensus undertaken to define appropriate scenarios for use of plasma metagenomic next-generation sequencing.},
}

@article {pmid41147490,
year = {2025},
author = {Qin, X and Liu, P and Lu, D and Lu, T and Li, C and Deng, Z and Liu, Z},
title = {The clinical value of metagenomic next-generation sequencing for diagnosing pulmonary infections in kidney transplant recipients.},
journal = {Laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/labmed/lmaf035},
pmid = {41147490},
issn = {1943-7730},
abstract = {INTRODUCTION: Rapid and accurate identification of pathogens is essential for managing lung infections in patients following kidney transplantation. This study aimed to compare the diagnostic performance and clinical utility of conventional detection methods and metagenomic next-generation sequencing (NGS) in kidney transplant recipients with respiratory infections.

METHODS: We conducted a retrospective analysis of metagenomic NGS and conventional detection method results in 71 patients, examining the spectrum of pathogen detection characteristics between the 2 methods.

RESULTS: The overall positivity rate of conventional detection methods was statistically significantly lower than that of metagenomic NGS (61.97% vs 84.51%, P = .004). Among the 38 participants who tested positive by both methods, metagenomic NGS identified a greater number of pathogens than conventional detection methods. Following metagenomic NGS results, antibiotic therapy was modified in 71.83% of participants, leading to improved prognoses in 33.33% of patients. In additionally, metagenomic NGS demonstrated a shorter turnaround time than conventional detection methods. The most prevalent bacteria identified in pulmonary infections among kidney transplant recipients were Klebsiella pneumoniae, while cytomegalovirus was the most common virus and Pneumocystis jirovecii was the predominant fungus.

DISCUSSION: This study offers preliminary insights into the spectrum of pathogens responsible for pulmonary infections following kidney transplantation, laying the foundation for better understanding their clinical characteristics. In patients with post-transplant pulmonary infections, metagenomic NGS outperforms conventional detection methods in terms of pathogen detection, speed, positivity rate, sensitivity, and ability to diagnose mixed infections.},
}

@article {pmid41147138,
year = {2025},
author = {Lee, YL and Hsueh, PR},
title = {An update on antimicrobial selection and duration for intra-abdominal infections.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2025.2580451},
pmid = {41147138},
issn = {1744-8336},
abstract = {INTRODUCTION: Intra-abdominal infections (IAIs) pose significant challenges to clinicians. The increasing prevalence of multidrug-resistant (MDR) organisms with evolving resistance patterns adds to the difficulty in managing IAIs.

AREAS COVERED: This review synthesizes the latest evidence and recommendations from major global guidelines. Key topics include novel antimicrobial agents, empirical and targeted therapy strategies, and the role of antimicrobial stewardship in optimizing antibiotic use. Furthermore, advances in diagnostic tools, such as metagenomic next-generation sequencing and rapid resistance detection assays, are highlighted. Updates in therapy duration, emphasizing shorter courses guided by biomarkers and source control, are critically analyzed.

EXPERT OPINION: The management of IAIs has advanced significantly, with updated guidelines highlighting the importance of early and appropriate antimicrobial therapy tailored to the infection's severity and resistance patterns, along with effective source control. Novel antibiotics such as ceftolozane-tazobactam, ceftazidime-avibactam, imipenem-relebactam, eravacycline, and cefiderocol have broadened treatment options for MDR pathogens. Shorter antibiotic courses, guided by source control and biomarkers, have shown to be as effective as traditional longer regimens. Future research should focus on understanding of global resistance patterns, expanding real-world evidence for novel antibiotics, refining biomarker-guided strategies, enhancing rapid diagnostics, and applying artificial intelligence for more personalized and precise management of IAIs.},
}

@article {pmid41146816,
year = {2025},
author = {Wang, N and Wu, J and Xiang, X and Zhao, Q and Yao, L},
title = {Endogenous Fungal Endophthalmitis Following Eyebrow Tattooing: A Case Report.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e93246},
pmid = {41146816},
issn = {2168-8184},
abstract = {This case report describes a rare instance of bilateral endogenous fungal endophthalmitis in a 50-year-old healthy female patient, following a facial tattooing procedure. Initially misdiagnosed as iritis in the right eye due to presenting symptoms of blurred vision and ocular pain, the patient's condition worsened following treatment with corticosteroids. Ophthalmic examination revealed severe vitreous opacity in the right eye and a yellowish-white lesion in the inferonasal retina of the left eye. Metagenomic sequencing of the vitreous fluid confirmed infection with Aspergillus fumigatus. The patient underwent pars plana vitrectomy with silicone oil tamponade, retinal laser photocoagulation, and intravitreal voriconazole injection in the right eye. Both eyes received multiple intravitreal voriconazole injections, supplemented with systemic antifungal therapy. Postoperatively, the visual acuity in the right eye improved, and the left eye gradually recovered to 20/35. Serial optical coherence tomography follow-up of the left eye documented the progressive detachment of the fungal embolus from the retinal lesion into the vitreous cavity. This case highlights that traumatic cosmetic procedures, such as eyebrow tattooing, can be a potential risk factor for endogenous fungal infection. In cases of atypical uveitis, early etiological investigation is crucial to avoid misdiagnosis and inappropriate treatment. Dynamic imaging provides valuable evidence for assessing the efficacy of antifungal therapy and determining prognosis.},
}

@article {pmid41146290,
year = {2025},
author = {Kraft, L and Söding, J and Steinegger, M and Jochheim, A and Wad Sackett, P and Fernandez-Guerra, A and Renaud, G},
title = {CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {372},
pmid = {41146290},
issn = {1474-760X},
support = {NNF20OC0062491//Novo Nordisk Fonden/ ; NNF20OC0062491//Novo Nordisk Fonden/ ; 031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B//German Network for Bioinformatics Infrastructure (de.NBI)/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Software ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Humans ; },
abstract = {De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, CarpeDeam demonstrates improved recovery of longer continuous sequences and protein sequences in many simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, CarpeDeam opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.},
}

*Metagenome
*Metagenomics/methods
*Software
*DNA, Ancient/analysis
Sequence Analysis, DNA/methods
Humans

@article {pmid41145643,
year = {2025},
author = {Karpęcka-Gałka, E and Zielińska, K and Frączek, B and Łabaj, PP and Kościółek, T and Humińska-Lisowska, K},
title = {High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37529},
pmid = {41145643},
issn = {2045-2322},
support = {39/PB/RID/2022//Ministerstwo Edukacji i Nauki/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Altitude ; Adult ; *Mountaineering/physiology ; Biomarkers/blood ; *Diet ; Young Adult ; },
abstract = {This study examined how high-altitude exposure and expedition-specific dietary changes influence gut microbiome composition, functional pathways, and their relationships with performance and health markers in alpinists. Seventeen male mountaineers (age 30.29 ± 5.8 years) participating in multi-week expeditions (> 3,000 MASL) were assessed before and after their climbs. Assessments included dietary intake analysis, blood and urine biomarkers, aerobic and anaerobic performance tests, and metagenomic sequencing of the gut microbiome. Bioinformatic and statistical analyses evaluated changes in microbiome composition and function and their correlations with physiological and dietary parameters. High-altitude exposure was associated with significant shifts in gut microbial composition and functional capacity. While the total number of bacterial species and functions remained stable, the glucose degradation pathway increased post-expedition. Participants with greater microbiome shifts showed improved performance and had richer baseline microbiomes. Pre-expedition, certain microbial functions were associated with vitamin B6 and C intake, while post-expedition correlations involved specific macronutrients and micronutrients. Additionally, some microbiome changes correlated with blood markers, indicating links to nutrient metabolism and electrolyte balance. The gut microbiome of alpinists adapts to extreme environmental stress and dietary changes, influencing metabolic, immune, and performance-related processes. Optimizing dietary strategies to support a beneficial microbiome profile may enhance resilience and performance in challenging high-altitude environments.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
*Altitude
Adult
*Mountaineering/physiology
Biomarkers/blood
*Diet
Young Adult

@article {pmid41145216,
year = {2025},
author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM},
title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280550.125},
pmid = {41145216},
issn = {1549-5469},
abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.},
}

@article {pmid41145088,
year = {2025},
author = {Dan Guan, and Chen, C and Zheng, Y and Shen, W and Huang, Y and Ge, M and Jiang, T and Zhang, J and Liu, R and Xiong, L},
title = {Chlorination-driven selection of resistant pathogens and mobile genetic elements exacerbates antibiotic resistance risks in drinking water treatment.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119281},
doi = {10.1016/j.ecoenv.2025.119281},
pmid = {41145088},
issn = {1090-2414},
abstract = {The dissemination of Antibiotic resistance genes (ARGs) in drinking water systems poses public health risks; treatment impacts on pathogen dynamics remain unclear. In this study, two treatment trains-PK (sand filtration, ozonation-activated carbon, 5 % NaClO)and CX(ozonation-activated carbon, ultrafiltration, and 10 % NaClO) were compared through metagenomics analysis. Chlorination reduced microbial α-diversity but selected for divergent pathogens: CX-Treated Water (TW) was enriched with Salmonella enterica, Escherichia coli, and Erwinia amylovora, while PK retained Xanthomonas oryzae and Mycobacterium tuberculosis. Virulence gene tufA persisted, with 43 human-associated virulence factors being differentially expressed after disinfection. ARG analysis revealed high abundances of bacitracin and multidrug resistance gene (MRG) in early treatment stages for both lines. Chlorination paradoxically enriched these ARGs in TW, particularly MRG, which increased by 5.99 and 126.12 times in PK and CX, respectively. Mobile genetic elements (MGEs), particularly IS91, rebounded after disinfection and strongly correlated with the dissemination of ARGs (R > 0.9, p < 0.05). Higher concentrations of hypochlorite doses in CX-DWTP amplified plasmid associated Rep7/IS91 abundances, increasing ARG transmission risks. These findings revealed that aggressive disinfection selected resistant pathogens, enriches virulence determinants, and facilitated the dissemination of ARGs via MGEs, highlighting the need for optimized disinfection strategies to safeguard water biosafety.},
}

@article {pmid41145028,
year = {2025},
author = {Zhu, F and Penha, FM and Cetecioglu, Z},
title = {Functional microbial enrichment and chelation-enhanced phosphorus release from marine sediments: Toward sustainable phosphorus management.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124842},
doi = {10.1016/j.watres.2025.124842},
pmid = {41145028},
issn = {1879-2448},
abstract = {To improve the efficiency of phosphorus (P) release from marine sediments and contribute to P loop closure, this study proposed a novel strategy combining bio-inoculation with polyphosphate-accumulating organisms (PAOs) and chemical enhancement via chelating agents. Based on prior findings, two-stage experiments were conducted. In Stage 1, anaerobic batch tests assessed the effect of different chelating agents for P release. While citrate showed no promoting effect, the addition of ethylenediaminetetraacetic acid (EDTA) significantly enhanced total P release, reaching 48.5 % within 15 days. In Stage 2, PAO-acclimated sediments were introduced into the system, followed by alternating anaerobic-aerobic fed-batch operation for 7 days, and subsequent EDTA addition with anaerobic incubation for another 6 days. This combined approach achieved a total P release efficiency 83.4 %, with final soluble P concentrations reaching 145.9 mg/L. During this process, PAOs were rapidly enriched, with their relative abundance increasing from 12.9 % to 65.0 %. Metagenomic analysis revealed that EDTA promoted environmental filtering, selectively enriching PAOs (Candidatus Accumulibacter) and thereby reinforcing their specific contributions to P functional genes. The resulting P-rich supernatant was then subjected to precipitation. PHREEQC simulations guided the prediction of optimal precipitation conditions, and laboratory experiments confirmed that most soluble P, especially Fe-bound forms, could be efficiently recovered, with maximum precipitation efficiencies of 98.8 %.},
}

@article {pmid41144667,
year = {2025},
author = {Xu, JY and Yu, YT and Du, S and Shen, LQ and Zhang, Q and Qian, H and Cai, TG and Wang, YF and Zhao, J and Li, HZ and Zhang, C and Zhu, D},
title = {Discarded cigarette butts as overlooked reservoirs and amplifiers of antibiotic resistance genes and pathogens in urban green spaces.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2525377122},
doi = {10.1073/pnas.2525377122},
pmid = {41144667},
issn = {1091-6490},
support = {42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22125601//MOST | NSFC | National Science Fund for Distinguished Young Scholars (NSF for Distinguished Young Scholars)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; China ; *Tobacco Products/microbiology ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Biofilms/growth & development ; },
abstract = {Cigarette butts are widely discarded in urban green spaces, yet their microbial health risks remain poorly understood. In a nationwide survey across China, we investigated the presence, sources, health risks, and drivers of antibiotic resistance genes (ARGs) and potential pathogens in discarded cigarette butts. Shotgun metagenomic and full-length 16S ribosomal rRNA (rRNA) sequencing revealed that cigarette butts harbored significantly higher abundances of ARGs and bacterial pathogens than plant litter or soil. Health risk assessment further showed that cigarette butts carried ARGs with greater mobility, clinical relevance, and pathogenic potential. Genomic analyses highlighted enrichment of ARG-carrying pathogens, particularly Enterobacteriaceae and Pseudomonas, with mobile genetic elements and oxidative stress responses as key contributors. Functional assays, including plasmid transfer, transcriptomic profiling, and single-cell Raman spectroscopy, demonstrated that cigarette butts promoted horizontal gene transfer and upregulated key ARGs (e.g., mexE, mexF, cfrC) under stress conditions. Scanning electron microscopy confirmed biofilm formation on cigarette fibers, supporting enhanced bacterial persistence. Source-tracking analyses identified both human oral and environmental sources of the enriched ARGs and pathogens in cigarette butts. Finally, socioeconomic factors such as lower gross domestic product (GDP), reduced education, and poor sanitation were strongly associated with elevated ARG and pathogen risks. Collectively, our findings identify cigarette butts as overlooked yet potent vectors of ARG and pathogen dissemination in urban green spaces, underscoring the need for targeted interventions within a One Health framework.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Drug Resistance, Microbial/genetics
China
*Tobacco Products/microbiology
Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Biofilms/growth & development

@article {pmid41144656,
year = {2025},
author = {Myburgh, DA and da Silva, NA and Haller-Caskie, M and Colominas, L and Castanyer, P and Frigola, J and Tremoleda, J and Hölzel, C and Unterweger, D and Nebel, A and Krause-Kyora, B},
title = {Detection of Clostridium sporogenes in a Roman-era cattle mass grave at Vilauba.},
journal = {Virulence},
volume = {},
number = {},
pages = {2580731},
doi = {10.1080/21505594.2025.2580731},
pmid = {41144656},
issn = {2150-5608},
abstract = {In the ancient Roman world, cattle played an integral role in daily agricultural tasks, providing the means necessary to plow fields, mill grains, and transport goods. The research presented here deals with the remains of 14 cattle discovered in a mass grave at the Roman villa of Vilauba in Catalonia, Spain. According to the archeological record, it can be ruled out that the animals were slaughtered for consumption, banqueting, or sacrificial purposes. By investigating the metagenomic sequences generated from the bovine remains, we identified in three individuals a group I Clostridium strain, phylogenetically related to known producers of botulinum neurotoxins - suggesting that the Vilauba strain may have had toxigenic potential. Moreover, we discovered a Mycolicibacterium species phylogenetically related to known opportunistic pathogens. While no definitive conclusions can be drawn about disease, the phylogenetic placement of these taxa and the detection of Clostridium virulence-associated genes suggest a possible role beyond postmortem contamination. Collectively, these findings draw attention to atypical bacterial species, such as C. sporogenes, which are often overlooked in palaeogenomic studies due to their ambiguous status as environmental microbes, commensals, or potential pathogens. Their detection in animal remains highlights that they may represent a blind spot in our current understanding of livestock health. More broadly, this study underscores the current complexity of investigating such taxa and emphasizes the need for novel methods to disentangle the roles of these bacterial species.},
}

@article {pmid41144256,
year = {2025},
author = {Dziegiel, AH and Duong, VT and Bloomfield, SJ and Thomson, NR and Maskell, DJ and Wain, J and Janecko, N and Baker, S and Mather, AE},
title = {Metagenomic identification of disease-causing Salmonella enterica serovars and antimicrobial resistance genes from paediatric faecal samples.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001547},
pmid = {41144256},
issn = {2057-5858},
mesh = {Humans ; *Feces/microbiology ; *Salmonella enterica/genetics/isolation & purification/drug effects/classification ; *Metagenomics/methods ; *Salmonella Infections/microbiology ; Child, Preschool ; *Drug Resistance, Bacterial/genetics ; Infant ; Child ; Serogroup ; Metagenome ; Vietnam ; Anti-Bacterial Agents/pharmacology ; Male ; Female ; },
abstract = {Background. Nontyphoidal Salmonella (NTS) is a common cause of enterocolitis and a major cause of death in children in low- and middle-income countries (LMICs). High antimicrobial resistance (AMR) prevalence in LMICs reduces treatment options for individuals at risk of severe infections.Methods. We investigated the use of metagenomics to identify NTS and associated AMR genes in 28 faecal metagenomes from children with culture-confirmed salmonellosis in Vietnam, using accompanying NTS genomes from isolated serovars (one per metagenome). Read-based and assembly-based methods were utilised for NTS and AMR detection. Case metagenomes were compared to healthy control metagenomes (n=21) with respect to the microbiome composition, NTS relative abundances, number of unique AMR genes and antimicrobial classes to which the genes confer resistance, including classes used in Salmonella treatment.Results. Salmonellosis cases displayed significantly higher relative abundances of Enterobacteriaceae than controls. Bracken and Centrifuge analysis facilitated the identification of Salmonella enterica sequences in case metagenomes at varying relative abundances (0.00259-27.7 % of total reads), which were significantly higher than controls. MetaPhlAn4 did not detect S. enterica in any control metagenomes, though 12 case metagenomes were also negative. The isolated serovars were identified in 78.6% of the associated case metagenomes with Centrifuge, suggesting this method is the most sensitive; however, the isolated genome serovar was the most abundant in only six case metagenomes, and serovar sequences were also identified in control metagenomes. Alignment to a Salmonella reference database, followed by local assembly and realignment, predicted the isolated serovar as the most likely serovar present in 35.7% of metagenomes, whereas Salmonella in silico typing resource classification of the local assembly was concordant with the isolate genome in 28.6% of cases. Metagenome-assembled genomes produced using two tools following de novo assembly identified the isolated serovar in 17.8-21.4% of cases. The percentage of NTS AMR genes identified in each case metagenome ranged between 0.00 and 100%. There was no significant difference in the number of unique AMR genes or antimicrobial classes between cases and controls, indicating comparable resistomes between cohorts.Conclusions. This study highlights the potential of metagenomics for NTS identification in faecal samples, although overlap in S. enterica relative abundance between cohorts calls for further work to identify a diagnostic cutoff. Reliable characterisation of the organism to the serovar and AMR genotype level is affected by the complexity of the microbiome, sequencing and analysis approaches. Increased sequencing depth, for example through improved host DNA depletion, may facilitate enhanced characterisation. Detection of multiple serovars within individual samples with the Centrifuge suggests inaccurate classification or the presence of multiple serovars, making characterisation difficult.},
}

Humans
*Feces/microbiology
*Salmonella enterica/genetics/isolation & purification/drug effects/classification
*Metagenomics/methods
*Salmonella Infections/microbiology
Child, Preschool
*Drug Resistance, Bacterial/genetics
Infant
Child
Serogroup
Metagenome
Vietnam
Anti-Bacterial Agents/pharmacology
Male
Female

@article {pmid41143690,
year = {2025},
author = {Kim, KJ and Garcia, M and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY},
title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfaf145},
pmid = {41143690},
issn = {1096-0929},
abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. Microplastics, defined as plastic particles less than 5 mm in diameter, are formed through degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested microplastics. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57BL/6 mice were orally gavaged mixed plastic (5 µm) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly(lactic-co-glycolic acid), twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. A total of 1162 bacterial species and 1437 metabolites were evaluated for downstream analysis. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways such as amino acid metabolism, sugar metabolism, and inflammation. Additionally, SCFA-targeted metabolomics showed significant changes in neuroprotective SCFAs levels in both sexes. Our study demonstrates that microplastics dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.},
}

@article {pmid41143557,
year = {2025},
author = {Shi, Z and Liu, Q and Zhou, M and Xu, W and Luo, G},
title = {Persistent Risks in the Effluents of Wastewater Treatment Plants: Mobile Genetic Elements and Viral-Mediated Dissemination of Pathogenic Antibiotic-Resistant Bacteria.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08352},
pmid = {41143557},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are recognized as reservoirs of pathogenic antibiotic-resistant bacteria (PARB), yet their genomic risk dynamics remain unclear. This study recovered PARB genomes from 102 influent and effluent metagenomes from six countries; their activity and risk potential were then experimentally validated with metatranscriptomics on samples from a Shanghai WWTP. A total of 44 PARB genomes were reconstructed, which carried both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and they persisted in the effluent. Mobile genetic elements might mediate ARG transfer in 13 PARB genomes. Moreover, bacteriophages infecting PARB harbored and were transcribing ARGs/VFGs, and antiviral defense systems of PARB correlated with horizontal gene transfer (HGT). Evolutionary analyses indicated that influent PARB maintained high microdiversity via homologous recombination, while effluent populations underwent purifying selection, suggesting that wastewater treatment reduced the genetic diversity of PARB through purifying selection. However, the persistent accumulation of PARB as well as HGT might maintain the dissemination of ARGs. This study emphasized the necessity of selecting the PARB genomes for wastewater monitoring, thereby optimizing treatment strategies and mitigating the potential health risks posed by pathogenic bacteria.},
}

@article {pmid41143534,
year = {2025},
author = {Conrad, R and Gerhardt, K and Konstantinidis, KT and Williams-Newkirk, AJ and Huang, AD},
title = {ROCker models for reliable detection and typing of short-read sequences carrying mcr, erm, mph, and lnu antibiotic resistance genes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0241325},
doi = {10.1128/spectrum.02413-25},
pmid = {41143534},
issn = {2165-0497},
abstract = {Quantitative monitoring of emerging antimicrobial resistance genes (ARGs) using short-read sequences remains challenging due to the high frequency of amino acid functional domains and motifs shared with related but functionally distinct (non-target) proteins. To facilitate ARG monitoring efforts using unassembled short reads, we present novel ROCker models for mcr, mph, erm, and lnu ARG families, as well as models for variants of special public health concern within these families, including mcr-1, mphA, ermB, lnuF, lnuB, and lnuG genes. For this, we curated target gene sequence sets for model training and built these models using the recently updated ROCker V2 pipeline (Gerhardt et al., in review). To validate our models, we simulated reads from the whole genome of ARG-carrying isolates spanning a range of common read lengths and used them to challenge the filtering efficacy of ROCker versus common static filtering approaches, such as similarity searches using BLASTx with various e-value thresholds or hidden Markov models. ROCker models consistently showed F1 scores up to 10× higher (31% higher on average) and lower false-positive (by 30%, on average) and false-negative (by 16%, on average) rates based on 250 bp reads compared to alternative methods. The ROCker models and all related reference materials and data are freely available through http://enve-omics.ce.gatech.edu/rocker/models, further expanding the available model collection previously developed for other genes. Their application to short-read metagenomes, metatranscriptomes, and PCR amplicon data should facilitate more accurate classification and quantification of unassembled short-read sequences for these ARG families and specific genes.IMPORTANCEAntimicrobial resistance gene families encoding erm and mph genes confer resistance to the macrolide class of antimicrobials, which are used to treat a wide range of infections. Similarly, the mcr gene family confers resistance to polymyxin E (colistin), a drug of last resort for many serious drug-resistant bacterial infections, and the lnu gene family confers resistance to lincomycin, which is reserved for patients allergic to penicillin or where bacteria have developed resistance to other antimicrobials. Assessing the prevalence of these genes in clinical or environmental samples and monitoring their spread to new pathogens are thus important for quantifying the associated public health risk. However, detecting these and other resistance genes in short-read sequence data is technically challenging. Our ROCker bioinformatic pipeline achieves reliable detection and typing of broad-range target gene sequences in complex data sets, thus contributing toward solving an important problem in ongoing surveillance efforts of antimicrobial resistance.},
}

@article {pmid41143528,
year = {2025},
author = {Mukherjee, SD and Adler, A and Dang, T and Taylor, EN and Curhan, G and Miller, AW},
title = {Evaluating the use of biobanked urine specimens for human urobiome studies.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0216424},
doi = {10.1128/spectrum.02164-24},
pmid = {41143528},
issn = {2165-0497},
abstract = {Case-control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. While these sample sizes are sufficient to detect large effect sizes, they have not been able to differentiate disease phenotypes within a larger disease complex (e.g., different types of kidney stones), which have unique etiological origins. Biobanked urine specimens can help fill this void. However, since these specimens were not collected specifically for urobiome studies, they must be validated before drawing any strong conclusions. The objective of this study was to evaluate microbiome data derived from metagenomic analysis of biobanked urine specimens against the following criteria: (i) level of contaminants; (ii) retention of high-quality DNA; (iii) overgrowth of a few dominant bacteria; and (iv) preservation of sex-specific taxa. A total of 174 samples were assessed from biobanked or freshly collected specimens (N = 118 patients total), in addition to multiple positive and negative controls. While there were significant differences in diversity (alpha/beta; P < 0.001) based on whether or not samples were biobanked, these differences can largely be explained by study-specific variation. With these criteria, we find that biobanked urine specimens provide similar data to fresh specimens collected using standardized protocols and can be used for clinical urobiome studies.IMPORTANCEThe urinary tract microbiome, or urobiome, is an emerging field of study that has shown promise as an important contributor to urologic health and disease. However, since this field is relatively new, clinical studies to evaluate the urobiome in the context of urologic disease have been relatively small. The use of biobanked urine specimens would allow for much larger studies to be conducted in a relatively short period of time. However, the use of biobanked urine specimens must first be validated. In this study, we sought to evaluate the use of biobanked urine specimens through multiple metrics, compared to previous studies conducted specifically to assess the impact of the urobiome. Results of our study suggest that biobanked urine specimens produce similar data to urine samples collected under rigorously controlled conditions and can be used in casecontrol studies of urologic conditions.},
}

@article {pmid41143408,
year = {2025},
author = {Liao, Y and Cheng, J and Xiong, S and Liu, Y and Qian, J and Shi, M and Guo, Y and Kang, Y-J},
title = {Dynamics of the respiratory infectome in children with community-acquired pneumonia: insights from large and short time-scale analyses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145025},
doi = {10.1128/spectrum.01450-25},
pmid = {41143408},
issn = {2165-0497},
abstract = {UNLABELLED: Community-acquired pneumonia (CAP) has emerged as a significant health challenge for young children, especially after the relaxation of COVID-19 restrictions, which coincided with a sharp increase in CAP cases. While pathogen profiling is commonly performed, comprehensive studies examining the total infectome and its dynamic changes during disease progression and in relation to the pandemic remain scarce. To address this gap, we conducted a prospective cohort study involving 58 children hospitalized with CAP in Wuxi, China, during and after COVID-19 control measures. Sputum samples were analyzed using metagenomic and metatranscriptomic sequencing to characterize the total infectome. Results showed that RNA sequencing offers a more comprehensive view of the infectome, while DNA sequencing excels in detecting DNA viruses with greater sensitivity. Notable increases in Mycoplasma pneumoniae, human respiratory syncytial virus (RSV), and Haemophilus influenzae were observed after COVID-19 restrictions were lifted. During disease progression, some patients exhibited a decline in pathogen abundance, while others developed secondary infections, frequently involving co-infections, which might contribute to prolonged pneumonia or complicated disease course. Viral-bacterial co-infections were common, with M. pneumoniae and RSV being the most prevalent combination. In summary, this study highlights the shifting respiratory infectome in children with CAP, both after the relaxation of COVID-19 control measures and throughout hospitalization. It emphasizes the need for comprehensive infectome monitoring to track dynamic changes across broader timeframes and during disease progression, offering insights for improved clinical management and future research.

IMPORTANCE: Community-acquired pneumonia (CAP) remains a leading threat to children's health globally, with shifting pathogen dynamics post-COVID-19 posing new challenges. This study reveals how pandemic control measures and their relaxation influenced the respiratory "infectome"-the full spectrum of pathogens-in children with CAP. By integrating multi-sequencing technologies, we uncovered critical trends: a resurgence of virulent pathogens like Mycoplasma pneumoniae and respiratory syncytial virus after restrictions eased, frequent viral-bacterial co-infections linked to prolonged pneumonia, and distinct infection patterns during hospitalization that predict recovery or complications. These findings highlight the need for dynamic, multi-pathogen surveillance to guide clinical decisions, particularly in managing co-infections and preventing secondary infections. Our work provides actionable insights for pediatricians and public health experts to anticipate post-pandemic pathogen behavior, tailor treatments, and mitigate risks during future outbreaks, ultimately improving care for vulnerable young patients.},
}

@article {pmid41142817,
year = {2025},
author = {Lee, JY and Mahurkar-Joshi, S and Young, A and Labus, JS and He, B and Aja, E and Jacobs, JP and Volkmann, ER},
title = {Ultra-processed food intake is associated with increased gastrointestinal tract symptoms and alterations in gut microbiota in patients with systemic sclerosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1610360},
pmid = {41142817},
issn = {1664-3224},
mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Adult ; Aged ; *Gastrointestinal Diseases/etiology/microbiology ; *Dysbiosis ; Feces/microbiology ; Food Handling ; Food, Processed ; },
abstract = {BACKGROUND: Alterations in the gastrointestinal (GI) microbiome (i.e., dysbiosis) are a feature of systemic sclerosis (SSc). Diet is a known modifier of the GI microbiome, and ultra-processed food (UPF) consumption has been associated with adverse changes in GI microbial composition. This study aimed to determine whether UPF consumption affects the GI microbiota and GI symptoms in patients with SSc.

METHODS: Adult SSc patients provided stool samples and completed both the Diet History Questionnaire II (DHQ-2) and the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0). Shotgun metagenomics were performed using the Illumina NovaSeq 6000 with a target depth of 10 million 150x2 sequences per sample. UPF items (N=54) on the DHQ-2 were identified using the NOVA scale of food classification, and UPF intake was calculated as gram-per-week consumption according to patient reported frequency. General linear models were created to identify differentially abundant species based on UPF consumption and to evaluate the relationship between UPF consumption and GI symptoms as measured by the GIT 2.0. These models adjusted for body mass index (BMI), current proton pump inhibitor (PPI) use, current probiotic use, current or prior immunomodulatory therapy, and presence of small intestinal bacterial overgrowth (SIBO).

RESULTS: Of the 65 total SSc patients included, 84.6% were female. The mean age was 53.83 ± 13.19 years, and the mean BMI was 25.25 ± 4.75. The median UPF consumption was 2395.82 g/week. Increased UPF consumption was significantly associated with increased GI symptoms in our multivariate model (β=0.34; p<0.01). Among 257 species analyzed, 5 bacterial species were significantly associated with UPF consumption in the multivariate models, including Limosilactobacillus fermentum (β=0.32; p<0.01) and Faecalicatena fissicatena (β= -0.36; p-value<0.01), while the abundance of 6 bacterial species was significantly associated with GI symptom severity after adjusting for the aforementioned covariates.

CONCLUSIONS: SSc patients reporting a higher UPF consumption demonstrated alterations in GI microbial composition as well as increased GI symptoms, even after adjusting for factors known to affect the microbiota of patients with SSc. Future studies are needed to determine whether interventions aimed at lowering UPF consumption may improve GI outcomes for patients with SSc.},
}

Humans
*Scleroderma, Systemic/microbiology/complications
Female
*Gastrointestinal Microbiome
Male
Middle Aged
Adult
Aged
*Gastrointestinal Diseases/etiology/microbiology
*Dysbiosis
Feces/microbiology
Food Handling
Food, Processed

@article {pmid41142066,
year = {2025},
author = {Kyrychenko, A},
title = {Molecular architecture of giant viruses infecting microbial eukaryotes (protists).},
journal = {Biotechnologia},
volume = {106},
number = {3},
pages = {361-376},
pmid = {41142066},
issn = {2353-9461},
abstract = {In this review, I describe recent findings on the molecular architecture and genomic characterization of giant viruses that infect microbial eukaryotes (protists) across diverse ecosystems and ecological niches. Giant viruses are distinguished by their large and complex genomes, which encode a wide range of functions, including protein translation, carbohydrate and lipid metabolism, nitrogen cycling, light assimilation, and key metabolic pathways such as glycolysis and the tricarboxylic acid cycle. Additionally, these genomes feature unique genes, often acquired through horizontal gene transfer, that are not found in other viruses and contribute to the viruses' ability to manipulate host metabolism and evade host defenses. A core set of genes conserved across different families of giant viruses is highlighted, serving as essential components for key life-cycle processes and providing valuable phylogenetic markers. The review also discusses the role of ORFans and virophages in contributing to the genetic diversity and evolutionary adaptation of these viruses. These findings are crucial for understanding the diversity, evolutionary mechanisms, and complex virus-host interactions of giant viruses, as well as for developing more advanced classification systems. Furthermore, the potential biotechnological applications of unique viral genes and pathways are explored, underscoring the importance of ongoing research in this field.},
}

@article {pmid41140871,
year = {2025},
author = {Talamantes-Becerra, B and Chang, WS and Michie, M and Hodda, M and Hopper, M and Caron, V},
title = {RNA-seq dataset of land snails collected in Australia.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112122},
pmid = {41140871},
issn = {2352-3409},
abstract = {Snails are known to be host of pathogens and parasites and they can play an important role in the transmission of some parasites and pathogens, including nematodes and trematodes of medical and veterinary importance. They have a diverse diet, and can be classified as detritivores, plant feeders, or carnivores. The datasets presented here include raw RNA-seq data of 10 terrestrial land snails collected in three locations in Australia, including Northern Territory, Queensland and South Australia. The snails were identified morphologically, and RNA was extracted from whole organisms using a modified version of the Maxwell ® RSC simplyRNA Tissue Kit. The sequencing was performed in all samples and generated an average of at least 56 million paired-end reads per sample. RNA-seq raw reads and assembled transcripts including both host-derived and non-host sequences were deposited into a DRYAD repository. Assembled transcripts including only host data are also provided in this project. The dataset has reuse potential for environmental studies related to conservation biology, invasive species surveillance, disease research, educational purposes, development of bioinformatic tools for environmental transcriptomics or host-pathogen interactions. Moreover, the dataset can be used for benchmarking metatranscriptomic classification tools in non-model invertebrates.},
}

@article {pmid41140851,
year = {2025},
author = {Tran, SH and Restrepo-Ortiz, CX and Vu, DQ and Troussellier, M and Bettarel, Y and Bouvier, T and Bui, VN and Minh, NH and Hoang, TD and Nguyen, QH and Auguet, JC},
title = {NEMESISdb: A full length 16S rRNA gene dataset for the detection of human, fish, and crustacean potentially pathogenic bacteria.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112135},
pmid = {41140851},
issn = {2352-3409},
abstract = {NEMESISdb is a 16S rRNA full length sequence curated dataset designed to enable the identification and tracking of potentially pathogenic bacteria (PPB) for human, fish, and crustacean hosts. It addresses the limited focus on marine and coastal environments as key reservoirs for PPB, where bacteria from diverse sources-terrestrial, marine, and animal-can coexist. Leveraging recent advances in high-throughput sequencing, NEMESISdb provides a robust resource for the detection of PPB in 16S rRNA gene metabarcoding or metagenomic data. The database comprises three datasets corresponding to human, fish, and crustacean hosts, containing 1703, 222, and 64 PPB species, respectively, with a total of over 150,000 16S rRNA full length sequences curated for accuracy. This resource was constructed by extracting sequences from the SILVA 138.2 SSU Ref NR99 database, refining them through a rigorous curation pipeline to ensure taxonomic consistency and eliminate misclassifications. The resulting datasets are optimized for use with popular tools such as BLAST and classifier software, enabling rapid and accurate detection of PPB in metabarcoding and metagenomic data. NEMESISdb supports diverse applications, including pathogen surveillance in aquatic ecosystems, studies on environmental factors influencing PPB dynamics, and the development of targeted strategies for mitigating pathogen impacts in aquaculture. Additionally, it facilitates research within the One Health framework by linking the circulation of PPB across environmental, animal, and human compartments.},
}

@article {pmid41140834,
year = {2025},
author = {Van Uffelen, A and Posadas, A and Fraiture, MA and Roosens, NHC and De Keersmaecker, SCJ and Marchal, K and Vanneste, K},
title = {Detection of Bacillus production strains and contaminants in food enzyme products.},
journal = {Food chemistry. Molecular sciences},
volume = {11},
number = {},
pages = {100309},
pmid = {41140834},
issn = {2666-5662},
abstract = {Shotgun metagenomics enables taxonomic analysis of microbial communities by aligning sequencing reads to reference genomes, for which interpretation of alignment results often lacks standardization and relies on arbitrary abundance thresholds. This can bias species detection, especially for low-abundance or taxonomically complex genera like Bacillus, where closely related species may differ in safety and function, and their co-occurrence increases misclassification risk. This study presents a bioinformatics framework for defining detection thresholds of biological contaminations in samples using nanopore shotgun metagenomics data, demonstrated through a case study on Bacillus subtilis sensu lato (s.l.) and Bacillus cereus s.l. contaminations in food enzyme (FE) products. The framework was developed by employing in silico mixes of isolate sequencing data of different B. subtilis and B. cereus species, and uses the tool KMA for taxonomic classification with post-processing steps based on template identity to differentiate true positives from false positives, coupled with curation of the underlying reference genomic database. The performance of the developed framework was afterwards validated with five in vitro mixes mimicking potential FE contaminations. Finally, the applicability of the validated framework was evaluated with six real and well-characterized commercial contaminated FE samples, confirming its ability to accurately detect B. subtilis and B. cereus contaminants, even at low abundances up to a relative abundance of 1 %. In conclusion, we present a bioinformatics framework allowing reliable species-level detection of challenging low-level contaminants in samples using nanopore shotgun metagenomics sequencing, which was successfully applied to identify B. subtilis and B. cereus contaminations in FE products.},
}

@article {pmid41140673,
year = {2025},
author = {Ao, D and Li, X and Zhang, G and Ma, H and Yang, L and Tian, H and Ao, S and Feng, J and Geng, W},
title = {Diagnostic value of metagenomic next-generation sequencing in atypical brucellosis: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1652671},
pmid = {41140673},
issn = {2296-858X},
abstract = {BACKGROUND: Brucellosis with atypical presentations, such as submandibular abscess without fever, is frequently misdiagnosed.

METHODS: Metagenomic next-generation sequencing (mNGS) was applied to pus samples from a 47-year-old female with a treatment-refractory submandibular abscess and a history of livestock exposure; results were confirmed serologically.

RESULTS: Within 48 h, mNGS identified Brucella suis-representing, to our knowledge, the first reported afebrile submandibular infection caused by this pathogen. Targeted therapy with doxycycline and rifamycin led to symptom resolution within 6 days.

CONCLUSION: This case highlights that mNGS, combined with a thorough epidemiological history, can resolve diagnostic dilemmas in atypical brucellosis, guide precise treatment, and mitigate antibiotic misuse.},
}