@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
Biodiversity
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid41171126,
year = {2025},
author = {She, J and Qian, PY and Wu, L},
title = {DOO: integrated multi-omics resources for deep ocean organisms.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1096},
pmid = {41171126},
issn = {1362-4962},
support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; },
abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.},
}

@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

@article {pmid41168883,
year = {2025},
author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M},
title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {224},
pmid = {41168883},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; },
mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth & development/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.

RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (> 23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2 days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15 days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.

CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.},
}

*Groundwater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/growth & development/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Phylogeny
DNA, Bacterial/genetics
Adaptation, Physiological
Sequence Analysis, DNA

@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Tracheophyta/microbiology
Metagenome
Phylogeny
*Plant Leaves/microbiology
Pinus/microbiology

@article {pmid41168702,
year = {2025},
author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML},
title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {64},
pmid = {41168702},
issn = {1297-9686},
support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.

RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.

CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.},
}

Animals
Cattle/genetics/physiology
*Rumen/microbiology
*Metagenome
*Weight Gain/genetics
*Eating/genetics
Metagenomics/methods
Animal Feed
Phenotype
Genomics/methods
Diet/veterinary
Gastrointestinal Microbiome

@article {pmid41168291,
year = {2025},
author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM},
title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37987},
pmid = {41168291},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; },
abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Metagenome
*Microbiota/genetics
*Citrus sinensis/microbiology
*Rhizobiaceae
Plant Roots/microbiology
Soil Microbiology
*Bacteria/genetics/classification
Phylogeny
*Liberibacter
High-Throughput Nucleotide Sequencing

@article {pmid41066239,
year = {2025},
author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE},
title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116413},
doi = {10.1016/j.celrep.2025.116413},
pmid = {41066239},
issn = {2211-1247},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/virology/pathology ; *Bacteriophages/genetics/physiology ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Sputum/microbiology/virology ; Lung/microbiology/virology ; Severity of Illness Index ; },
abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/virology/pathology
*Bacteriophages/genetics/physiology
*Microbiota
Female
Male
Middle Aged
Aged
Sputum/microbiology/virology
Lung/microbiology/virology
Severity of Illness Index

@article {pmid40966087,
year = {2025},
author = {Pu, Y and Qi, X and Huang, L and Wu, W and Zhou, X and Li, W and Yang, Z and Kong, M and Shen, J and Qi, W and Sun, Z and Mei, Z and Wang, Q and Yang, W and Gao, X and Wang, X and Liu, Z and Yuan, C and Zheng, Y},
title = {Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116297},
doi = {10.1016/j.celrep.2025.116297},
pmid = {40966087},
issn = {2211-1247},
mesh = {Humans ; Aged ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; *Metabolome ; Male ; Middle Aged ; Aged, 80 and over ; *Metagenome ; *Sleep/physiology ; *Frailty/blood/microbiology/metabolism ; *Pyruvic Acid/metabolism ; },
abstract = {Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.},
}

Humans
Aged
*Gastrointestinal Microbiome/genetics/physiology
Female
*Metabolome
Male
Middle Aged
Aged, 80 and over
*Metagenome
*Sleep/physiology
*Frailty/blood/microbiology/metabolism
*Pyruvic Acid/metabolism

@article {pmid41165913,
year = {2025},
author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM},
title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1268},
pmid = {41165913},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; },
abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.},
}

*Wastewater/microbiology
Animals
*Abattoirs
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Poultry
Genes, Bacterial
Waste Disposal, Fluid
RNA, Ribosomal, 16S
Environmental Monitoring
Anti-Bacterial Agents
*Water Microbiology
Microbiota

@article {pmid41164885,
year = {2025},
author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T},
title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {10},
pages = {e70844},
doi = {10.1002/alz.70844},
pmid = {41164885},
issn = {1552-5279},
support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Genève/ ; //Fondation Segré, Genève/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Genève/ ; //Fondation Edmond J. Safra, Genève/ ; //Fondation Minkoff, Genève/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et René Keller, Genève/ ; //Fondation AETAS, Genève/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //Hôpitaux Universitaires de Genève/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; },
abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.

METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.

RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from < 2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.

DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.

HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology/chemistry
Male
Female
*Dysbiosis/metabolism
*Cognitive Dysfunction/metabolism/microbiology
Aged
*Inflammation/metabolism
*Brain/metabolism
Cytokines/blood
Multiomics

@article {pmid41163852,
year = {2025},
author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H},
title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660970},
pmid = {41163852},
issn = {2235-2988},
mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation & purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.

METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.

RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.

DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.},
}

Humans
*Autism Spectrum Disorder/virology
Feces/virology
*Gastrointestinal Microbiome
Child
Phylogeny
*Viruses/classification/genetics/isolation & purification
Male
*Virome
Female
Metagenomics
Child, Preschool
Case-Control Studies

@article {pmid41163226,
year = {2025},
author = {Huang, S and Chen, Y and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W},
title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {350},
pmid = {41163226},
issn = {1743-422X},
support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; },
mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.

RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n = 1), Paramyxoviridae (n = 1), Polyomaviridae (n = 1), Parvoviridae (n = 7), Circoviridae (n = 6), and Genomoviridae (n = 1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.

CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.},
}

Dogs
Animals
*Lymph Nodes/virology
Phylogeny
*Virome
*Zoonoses/virology
Genome, Viral
China
Humans
*Viruses/genetics/classification/isolation & purification
*Dog Diseases/virology
Metagenomics
*Viral Zoonoses/virology/transmission

@article {pmid41163171,
year = {2025},
author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z},
title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {59},
pmid = {41163171},
issn = {1476-0711},
support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&D Program of the China Ministry of Science and Technology/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.

METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.

RESULTS: No significant differences were observed in age (62.22 ± 5.74 vs. 58.23 ± 7.55, p = 0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p = 0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p < 0.05) and distinct beta diversity clustering (p < 0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p < 0.0001). Neutral modeling indicated stochastic assembly (R² >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.

CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.},
}

Humans
Female
*Vagina/microbiology
*Diabetes Mellitus, Type 2/microbiology
Middle Aged
*Postmenopause
*Microbiota
*Perimenopause
Aged
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Dysbiosis/microbiology

@article {pmid41163130,
year = {2025},
author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD},
title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {967},
pmid = {41163130},
issn = {1471-2164},
support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; },
abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.

RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.

CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.},
}

*Mycorrhizae/genetics/physiology
*Symbiosis/genetics
*Plant Roots/microbiology
Phylogeny
*Endophytes/genetics
*Genomics
*Metagenome
*Genome, Fungal
Glomeromycota/genetics

@article {pmid41162595,
year = {2025},
author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L},
title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37813},
pmid = {41162595},
issn = {2045-2322},
support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation & purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; },
abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.},
}

Humans
*COVID-19/microbiology/virology/diagnosis
Middle Aged
Male
Female
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Aged
SARS-CoV-2/isolation & purification
Adult
*Respiratory Tract Infections/microbiology
*Microbiota/genetics

@article {pmid41086517,
year = {2026},
author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q},
title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.},
journal = {Virology},
volume = {613},
number = {},
pages = {110712},
doi = {10.1016/j.virol.2025.110712},
pmid = {41086517},
issn = {1096-0341},
mesh = {*Extracellular Vesicles/virology/metabolism ; *Phosphatidylserines/metabolism ; Humans ; Feces/virology ; Metagenomics ; Gastrointestinal Microbiome ; Virome ; *Viruses/genetics/classification/isolation & purification/metabolism ; },
abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.},
}

*Extracellular Vesicles/virology/metabolism
*Phosphatidylserines/metabolism
Humans
Feces/virology
Metagenomics
Gastrointestinal Microbiome
Virome
*Viruses/genetics/classification/isolation & purification/metabolism

@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The sex related differences in health and Disease: A systematic review of sex-specific gut microbiota and Possible implications for microbial pathogenesis.},
journal = {Microbial pathogenesis},
volume = {209},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Female ; Male ; Sex Factors ; Mice ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Sex Characteristics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.

METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.

RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.

CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals
Female
Male
Sex Factors
Mice
Bacteria/classification/genetics/isolation & purification
Biodiversity
Sex Characteristics
High-Throughput Nucleotide Sequencing

@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
mesh = {*Rhizosphere ; *Cadmium/metabolism ; *Microbiota/drug effects ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Iron/metabolism ; Manganese/metabolism ; Oryza/microbiology ; Sulfur/metabolism ; Bacteria ; Environmental Restoration and Remediation/methods ; },
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems (1) iron/manganese oxidation (e.g., feoB): associated with iron-manganese plaque (IP) formation (2) sulfate reduction (e.g., dsrA); linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}

*Rhizosphere
*Cadmium/metabolism
*Microbiota/drug effects
*Soil Pollutants/metabolism
*Soil Microbiology
Iron/metabolism
Manganese/metabolism
Oryza/microbiology
Sulfur/metabolism
Bacteria
Environmental Restoration and Remediation/methods

@article {pmid41015172,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Qi, J and Zhu, M and Feng, H and Zhao, Y and Mei, W and Fu, F and Li, X and Song, C},
title = {Bacterial network complexity drives carbon, nitrogen and phosphorus metabolism potential under short-term soil water content changes in wetlands.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122952},
doi = {10.1016/j.envres.2025.122952},
pmid = {41015172},
issn = {1096-0953},
mesh = {*Wetlands ; *Phosphorus/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Carbon/metabolism ; Soil/chemistry ; China ; *Bacteria/metabolism ; Water/analysis ; Droughts ; Microbiota ; },
abstract = {Wetland soil microbial communities play pivotal roles in biogeochemical cycling; however, how their network complexity mediates carbon (C), nitrogen (N), and phosphorus (P) metabolism in response to soil water content (SWC) changes remains unclear. In this study, soil samples from the Zhalong, Momoge and Xianghai wetlands in Songnen Plain of China were incubated under natural (CK), drought (10 % SWC), and high SWC (50 % SWC) conditions, followed by metagenomic sequencing to evaluate the impact of SWC changes on bacterial community structure and function. The results showed that soil bacterial diversity and network complexity decreased under drought but recovered under high SWC, with Proteobacteria and Actinobacteria displaying divergent responses. C fixation pathways (rTCA and DC-HB cycles) were significantly enriched under 50 % SWC, which correlated strongly with enhanced bacterial interactions. The abundance of denitrification genes (norBC, nosZ) decreased under drought but increased under high SWC. P metabolism (purine metabolism and two-component systems) showed strong SWC dependence, with key genes (PstS, phnDC) increased in abundance under 50 % SWC. Notably, bacterial network complexity tightly coupled with metabolic pathways, indicating SWC driven community restructuring regulates wetland soil C, N and P cycling. These findings underscore the critical importance of hydrological management in maintaining bacterial-mediated nutrient cycling functions of wetland ecosystem under climate change.},
}

*Wetlands
*Phosphorus/metabolism
*Soil Microbiology
*Nitrogen/metabolism
*Carbon/metabolism
Soil/chemistry
China
*Bacteria/metabolism
Water/analysis
Droughts
Microbiota

@article {pmid41162178,
year = {2025},
author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H},
title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506012},
doi = {10.4014/jmb.2506.06012},
pmid = {41162178},
issn = {1738-8872},
mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.},
}

*Milk, Human/microbiology
Humans
Female
*Microbiota/genetics
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Bacteria/classification/genetics/isolation & purification
Adult
Metagenome
Sequence Analysis, DNA
Archaea/genetics/classification/isolation & purification
Phylogeny
DNA, Bacterial/genetics

@article {pmid41162143,
year = {2025},
author = {Hutchings, P and Rowe, CE and Byrne, M and Przeslawski, R},
title = {Taxonomy is a foundation of marine science, and it is in trouble.},
journal = {Advances in marine biology},
volume = {101},
number = {},
pages = {197-212},
doi = {10.1016/bs.amb.2025.08.003},
pmid = {41162143},
issn = {2162-5875},
mesh = {*Classification/methods ; Animals ; Conservation of Natural Resources ; *Aquatic Organisms/classification ; Biodiversity ; *Marine Biology/education ; Australia ; },
abstract = {This volume of Advances highlights not only the importance of marine benthic diversity in several regions of the world but also the impediments to describing this fauna. Taxonomy is the science of classifying organisms and is the bedrock of marine biodiversity research and conservation, yet it faces significant decline in Australia. Thus, it is critical that the scientific community understand why taxonomy is so important. This paper underscores the foundational role of taxonomy in marine ecology, using case studies that highlight its critical relevance to species management, conservation policy, and international trade regulation. Despite extensive research and funding, unresolved taxonomies continue to affect our management of ecologically and economically important taxa, including crown-of-thorns seastar (Acanthaster spp.), exploited sea cucumbers (Holothuroidea), and invasive Cassiopea jellyfish. These ambiguities hamper accurate species identification, hinder effective conservation strategies, and complicate regulatory listings under frameworks such as CITES and the IUCN Red List. Key challenges include dwindling taxonomic expertise, reduced funding, lack of university training, and limited career pathways, all of which contribute to Australia's inability to adequately explore and manage its vast marine jurisdiction. The paper advocates for immediate systemic reforms through a series of 11 recommendations related to revitalizing taxonomic education, fostering museum-university partnerships, supporting early career researchers, and investing in infrastructure to enable species discovery. Taxonomic rigor is also essential to validate modern tools like eDNA, metagenomics, and image-based analysis. Without it, efforts to safeguard biodiversity and to foster a sustainable blue economy risk failure.},
}

*Classification/methods
Animals
Conservation of Natural Resources
*Aquatic Organisms/classification
Biodiversity
*Marine Biology/education
Australia

@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 {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 {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 {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 {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 {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 {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 {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 {pmid41114530,
year = {2025},
author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N},
title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {43},
pages = {27450-27468},
doi = {10.1021/acs.jafc.5c07003},
pmid = {41114530},
issn = {1520-5118},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Phenylethyl Alcohol/analogs & derivatives/administration & dosage ; Humans ; Animals ; Male ; Mice ; Bacteria/classification/genetics/isolation & purification/drug effects/metabolism ; Middle Aged ; Female ; Adult ; *Fatty Liver/metabolism/drug therapy/microbiology ; Liver/metabolism/drug effects ; Feces/microbiology ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism/drug therapy ; },
abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.},
}

*Gastrointestinal Microbiome/drug effects
*Phenylethyl Alcohol/analogs & derivatives/administration & dosage
Humans
Animals
Male
Mice
Bacteria/classification/genetics/isolation & purification/drug effects/metabolism
Middle Aged
Female
Adult
*Fatty Liver/metabolism/drug therapy/microbiology
Liver/metabolism/drug effects
Feces/microbiology
Fecal Microbiota Transplantation
Mice, Inbred C57BL
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism/drug therapy

@article {pmid41036845,
year = {2025},
author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M},
title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0023425},
doi = {10.1128/msphere.00234-25},
pmid = {41036845},
issn = {2379-5042},
mesh = {*Rhizosphere ; *Wetlands ; *Poaceae/virology ; Plant Roots/virology/microbiology ; Soil Microbiology ; *Virome ; *Viruses/classification/genetics/isolation & purification ; Biodiversity ; Metagenome ; },
abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.},
}

*Rhizosphere
*Wetlands
*Poaceae/virology
Plant Roots/virology/microbiology
Soil Microbiology
*Virome
*Viruses/classification/genetics/isolation & purification
Biodiversity
Metagenome

@article {pmid41025782,
year = {2025},
author = {Boyd, AI and Kafer, LA and F Escapa, I and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP},
title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0049325},
doi = {10.1128/msphere.00493-25},
pmid = {41025782},
issn = {2379-5042},
support = {U19AI157981//National Institute of Allergy and Infectious Diseases/ ; U19AI144297//National Institute of Allergy and Infectious Diseases/ ; U19AI116497//National Institute of Allergy and Infectious Diseases/ ; F31AI172324//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *Cytokines/metabolism/immunology ; *Organoids/microbiology/immunology ; Streptococcus pneumoniae/growth & development/immunology ; Staphylococcus aureus/growth & development/immunology ; *Nasal Mucosa/microbiology/immunology ; *Microbiota ; Epithelial Cells/microbiology/immunology ; },
abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.

IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.},
}

Humans
*Cytokines/metabolism/immunology
*Organoids/microbiology/immunology
Streptococcus pneumoniae/growth & development/immunology
Staphylococcus aureus/growth & development/immunology
*Nasal Mucosa/microbiology/immunology
*Microbiota
Epithelial Cells/microbiology/immunology

@article {pmid40996044,
year = {2025},
author = {Kwon, J and Correa, MA and Kong, Y and Pelletiers, W and Wade, M and Olson, D and Pettigrew, MM},
title = {Microbiome signatures of Clostridioides difficile toxin production and toxin gene presence: a shotgun metagenomic approach.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0043525},
doi = {10.1128/msphere.00435-25},
pmid = {40996044},
issn = {2379-5042},
support = {NU50CK000488/CC/CDC HHS/United States ; },
mesh = {Humans ; *Clostridioides difficile/genetics ; *Bacterial Toxins/genetics ; Female ; Male ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; *Clostridium Infections/microbiology/diagnosis ; Aged ; Adult ; Anti-Bacterial Agents/therapeutic use ; Diarrhea/microbiology ; Aged, 80 and over ; },
abstract = {Clostridioides difficile is an opportunistic gastrointestinal pathogen capable of asymptomatic colonization and causes diseases ranging from diarrhea to pseudomembranous colitis. Accurate diagnosis of C. difficile infection (CDI) is challenging and critical for treatment and control. We hypothesized that gut microbiome profiles could help distinguish C. difficile colonized patients with diarrhea from those with true CDI. We analyzed 172 stool samples from individuals who tested glutamate dehydrogenase positive for C. difficile. Participants were categorized by toxin status (i.e., toxin positive or negative) and then further classified into three toxin groups based on the production of toxin, and if not produced, whether the C. difficile strain carried toxin-encoding genes. We examined associations between patient characteristics, prior antibiotics exposure, microbiome community structure and function, and toxin categories. Thirty-five percent of toxin-negative participants received antibiotics despite not meeting the criteria for true CDI. Enterococcus species were abundant in all groups. The relative abundance of E. faecalis was higher among individuals with prior antibiotics exposure. Alpha and beta diversity did not differ by toxin group. After controlling for prior antibiotics exposure and previous CDI episode, the abundance of Akkermansia muciniphila, Flavonifractor plautii, and Bifidobacterium adolescentis distinguished individuals with toxin-positive C. difficile. C. difficile abundance did not differentiate participants with true CDI from those who were colonized. We identified associations between the gut microbiome and C. difficile toxin gene presence and toxin production. These results highlight the potential for microbiome-informed diagnostics to improve CDI accuracy and guide treatment decisions.IMPORTANCEClostridioides difficile colonizes humans and causes diarrhea in community and hospital settings. C. difficile infection (CDI) is a toxin-mediated disease, and its diagnosis is challenging. The goal of this study was to determine whether differences in the gut microbiome could help distinguish between colonized individuals and those with CDI. We examined stool samples and data from 172 individuals categorized into three groups based on the detection of toxin and, if not detected, whether toxin-encoding genes were present in the C. difficile strain. We identified bacteria, such as Enterococcus faecalis, that were more abundant in people who had used antibiotics. While the diversity of the gut microbiome did not differ by toxin group, specific gut bacteria, antibiotic resistance genes, and metabolic pathways were associated with toxin group. Our findings suggest that considering the full gut microbiome and factors like past antibiotic use could help improve the diagnosis and treatment of CDI.},
}

Humans
*Clostridioides difficile/genetics
*Bacterial Toxins/genetics
Female
Male
Metagenomics
*Gastrointestinal Microbiome/genetics
Middle Aged
Feces/microbiology
*Clostridium Infections/microbiology/diagnosis
Aged
Adult
Anti-Bacterial Agents/therapeutic use
Diarrhea/microbiology
Aged, 80 and over

@article {pmid40967455,
year = {2025},
author = {Arffman, RK and Folch, BA and Leonés-Baños, I and Altmäe, S},
title = {Gut feelings-the gut microbiome as a regulator of mental health in polycystic ovary syndrome.},
journal = {Fertility and sterility},
volume = {124},
number = {5 Pt 2},
pages = {931-947},
doi = {10.1016/j.fertnstert.2025.09.014},
pmid = {40967455},
issn = {1556-5653},
mesh = {Humans ; *Polycystic Ovary Syndrome/psychology/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; *Mental Health ; *Emotions ; Animals ; },
abstract = {IMPORTANCE: Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with reproductive, metabolic, and mental health comorbidities. The exact mechanisms of PCOS-related psychological distress and the role of the microbiome in the process remain unclear.

OBJECTIVE: To systematically review the current literature on the gut microbiome's association with mental health in women with PCOS and to review the possible mechanisms.

EVIDENCE REVIEW: A comprehensive literature search across the PubMed database until July 2025. Studies were included if they met the following criteria: observational/intervention studies; assessing microbiome through 16S ribosomal ribonucleic acid amplicon/16S ribosomal ribonucleic acid gene sequencing/metagenomics; comparing microbiome between women with and without PCOS; published from 2007 until 2025, and articles available online. The exclusion criteria were: language other than English or Spanish; reviews; abstracts/posters; case reports; full text not available, and duplicates. Two independent reviewers screened all titles and abstracts to determine eligibility, and discrepancies were resolved through discussion. The methodological quality and the potential risk of bias were assessed following the Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies.

FINDINGS: A total of 159 studies were identified and screened for title, abstract, and full text. Eight studies met the criteria (2 rodent, 6 human studies). The quality assessment indicated that half of the studies (4/8) presented a high risk of bias. Regardless of the limited number of studies and the low quality scores, all the studies highlighted the association of the gut microbiome in PCOS with mental health problems.

CONCLUSIONS AND RELEVANCE: Our review provides the first summary of the studies performed to date on the gut-brain axis in PCOS. Our review highlights that the current state of the research is rather preliminary, and the existing studies possess various limitations and often lack rigorous study design. Nevertheless, all the studies indicated an association between changes in gut microbiome and mental health indicators in PCOS. We also noted a consistent increase in Gram-negative bacteria in women with PCOS and mental health issues. More research is needed on humans with a bigger sample size, different ethnicities, and wider age groups to clarify the microbial patterns involved, and in parallel, the field should move from descriptive studies to mechanistic approaches.},
}

Humans
*Polycystic Ovary Syndrome/psychology/microbiology
*Gastrointestinal Microbiome/physiology
Female
*Mental Health
*Emotions
Animals

@article {pmid40883892,
year = {2025},
author = {Kanaan, G and Deming, JW},
title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf198},
pmid = {40883892},
issn = {1751-7370},
support = {//Benjamin Hall Conservation Genetics/ ; 325405//Research Council of Norway BREATHE project/ ; },
mesh = {*DNA Methylation ; *Bacteria/genetics/classification ; *Ice Cover/microbiology/virology ; *Microbiota ; Metagenome ; Arctic Regions ; *Viruses/genetics ; DNA, Viral/genetics ; DNA, Bacterial/genetics ; Seawater/microbiology ; Epigenesis, Genetic ; },
abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea-ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6 mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and nonadapted bacteria (Pelagibacter); e.g. in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea-ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.},
}

*DNA Methylation
*Bacteria/genetics/classification
*Ice Cover/microbiology/virology
*Microbiota
Metagenome
Arctic Regions
*Viruses/genetics
DNA, Viral/genetics
DNA, Bacterial/genetics
Seawater/microbiology
Epigenesis, Genetic

@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 {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 {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 {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 {pmid41065113,
year = {2025},
author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC},
title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {108},
number = {1},
pages = {84-97},
doi = {10.1177/13872877251376911},
pmid = {41065113},
issn = {1875-8908},
mesh = {Humans ; *Hispanic or Latino/psychology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Cognition/physiology ; Aged ; Middle Aged ; Cohort Studies ; Feces/microbiology ; White ; },
abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.},
}

Humans
*Hispanic or Latino/psychology
*Gastrointestinal Microbiome/physiology
Male
Female
*Cognition/physiology
Aged
Middle Aged
Cohort Studies
Feces/microbiology
White

@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 {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 {pmid41139486,
year = {2025},
author = {Tran, T and Duong, DV and Le, TD and Bui, XT},
title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {10},
pages = {e70072},
doi = {10.1111/apm.70072},
pmid = {41139486},
issn = {1600-0463},
mesh = {*Biofilms/growth & development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; },
abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.},
}

*Biofilms/growth & development
*Wastewater/microbiology
Metagenomics
*Water Purification/methods
Aquaculture
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Drug Resistance, Microbial/genetics
Animals
Nitrogen/metabolism
Metagenome

@article {pmid41138002,
year = {2025},
author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {178},
pmid = {41138002},
issn = {1572-9699},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.},
}

Humans
*Microbiota
*Mouth/microbiology
Periodontal Diseases/microbiology/therapy
Dental Caries/microbiology/therapy
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid41137523,
year = {2025},
author = {Tegegne, HA and Savidge, TC},
title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2569739},
doi = {10.1080/19490976.2025.2569739},
pmid = {41137523},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; },
abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods

@article {pmid41137517,
year = {2025},
author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S},
title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2568706},
doi = {10.1080/19490976.2025.2568706},
pmid = {41137517},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation & purification ; Models, Animal ; Disease Models, Animal ; },
abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.},
}

Animals
*Gastrointestinal Microbiome/physiology
Swine
Ileum/microbiology/surgery
*Host Microbial Interactions
Humans
Feces/microbiology
Clostridioides difficile/physiology
Fecal Microbiota Transplantation
Bacteria/classification/genetics/isolation & purification
Models, Animal
Disease Models, Animal

@article {pmid41137068,
year = {2025},
author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM},
title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {426},
pmid = {41137068},
issn = {1756-3305},
mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.

METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Baños, Laguna, Philippines, that differ in topography and land use transformations.

RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.

CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.},
}

Animals
*Aedes/virology
Philippines
*Virome/genetics
*Mosquito Vectors/virology
Metagenomics
Phylogeny
*Insect Viruses/genetics/classification/isolation & purification

@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}

Humans
*Oxalates/metabolism
*Microbiota/genetics
Metagenome
Gene Transfer, Horizontal
*Bacteria/genetics/metabolism

@article {pmid40848995,
year = {2025},
author = {Wang, J and Xue, L and Zhang, M and Shen, P and Zhao, W and Tong, Q and Wu, S and Dai, W and Yang, X and Wang, H},
title = {Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.},
journal = {Brain, behavior, and immunity},
volume = {130},
number = {},
pages = {106086},
doi = {10.1016/j.bbi.2025.106086},
pmid = {40848995},
issn = {1090-2139},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Parkinson Disease/therapy/microbiology ; Aged ; Double-Blind Method ; Quality of Life ; *Colonoscopy/methods ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome/physiology ; Constipation ; },
abstract = {OBJECTIVE: Growing evidence supports the efficacy and safety of fecal microbiota transplantation (FMT) in treating Parkinson's disease (PD). Fecal microbiota are commonly transplanted via oral capsules, a nasojejunal tube, or colonoscopy, but freezing often decreases the diversity and viability of transplanted microbiota. This single-center, double-blind, randomized, placebo-controlled trial aims to explore the efficacy and safety of fresh FMT via colonoscopy in dealing with PD.

METHODS: Thirty patients with mild-to-moderate PD (Hoehn-Yahr stage I-III) were randomly assigned into the FMT group (fresh FMT via colonoscopy) and placebo group (saline injection via colonoscopy) in a 1:1 ratio. Motor and non-motor symptoms, constipation, quality of life, cognitive function, emotional state and sleep quality were assessed using relevant scales. Fecal samples were harvested before and at 4, 8 and 12 weeks after treatment for metagenomic and metabolomics analyses.

RESULTS: A total of 30 patients with mild-to-moderate PD were enrolled in the present study, involving 18 males and 12 females with a median age of 68 years, a median age of onset of 63.5 years, and a median disease duration of 3 years. At 12 weeks, scores of the UPDRS Ⅲ (group × time effect, B =  - 8.80 [-13.79, -3.81]), PAC-QOL (group × time effect, B =  - 29.67 [-45.35, -13.98]), UPDRS Ⅱ (group × time effect, B =  - 5.07 [-8.85, -1.28]), NMSS (group × time effect, B =  - 35.60 [-53.59, -17.61]), PDQ-39 (group × time effect, B =  - 17.80 [-28.21, -7.39]), HAMA (group × time effect, B =  - 1.66 [-2.92, -0.40]), and HAMD (group × time effect, B =  - 1.33 [-2.49, -0.16]) were significantly reduced in the FMT group, while CSBM per week (group × time effect, B = 3.03 [1.42, 4.63]) and the Bristol Stool Scale score (group × time effect, B = 1.95 [0.12, 3.79]) significantly increased (all P < 0.05). Significant alterations were seen in the gut microbiota and fecal metabolites in the FMT group. No adverse events were observed during the follow-up period.

CONCLUSION: Fresh FMT via colonoscopy is a safe and well-tolerated procedure for treating mild-to-moderate PD. It effectively alleviates motor and non-motor symptoms, thus facilitating defecation and improving the quality of life. These effects can be maintained for a minimum of 12 weeks and may be attributed to the optimization of gut microbiota and fecal metabolites.},
}

Humans
*Fecal Microbiota Transplantation/methods
Male
Female
Middle Aged
*Parkinson Disease/therapy/microbiology
Aged
Double-Blind Method
Quality of Life
*Colonoscopy/methods
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome/physiology
Constipation

@article {pmid40835054,
year = {2025},
author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q},
title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.},
journal = {Brain, behavior, and immunity},
volume = {130},
number = {},
pages = {106080},
doi = {10.1016/j.bbi.2025.106080},
pmid = {40835054},
issn = {1090-2139},
mesh = {Humans ; *Schizophrenia/virology/drug therapy/microbiology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/physiology ; *Virome/physiology ; Feces/virology ; Biomarkers ; Treatment Outcome ; Young Adult ; Antipsychotic Agents/therapeutic use ; },
abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.

METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.

RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR = 0.012), and two viral species were reduced in the low-response trajectory group.

CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.},
}

Humans
*Schizophrenia/virology/drug therapy/microbiology
Male
Female
Adult
*Gastrointestinal Microbiome/physiology
*Virome/physiology
Feces/virology
Biomarkers
Treatment Outcome
Young Adult
Antipsychotic Agents/therapeutic use

@article {pmid41136439,
year = {2025},
author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z},
title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9353},
pmid = {41136439},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; },
abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.},
}

*Metagenome/genetics
*Metagenomics/methods
*Microbiota/genetics
Humans
Cluster Analysis
Gastrointestinal Microbiome/genetics
*Software
Algorithms

@article {pmid41131658,
year = {2025},
author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y},
title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {214},
pmid = {41131658},
issn = {2049-2618},
mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; },
abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.

RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15 days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.

CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.},
}

*Oryza/virology/microbiology
*Rhizosphere
*Reoviridae/physiology/pathogenicity
Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
Metagenomics/methods
*Plant Diseases/virology/microbiology
Metabolomics/methods

@article {pmid41131656,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {215},
pmid = {41131656},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metagenome ; },
abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.

RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.

CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.},
}

Animals
Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
Animal Feed/analysis
*Tryptophan/metabolism
*Indoleacetic Acids/metabolism
*Gastrointestinal Microbiome
*Inflammation
*Goat Diseases/microbiology/metabolism
Diet
Female
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification
Fermentation
Metagenome

@article {pmid41131583,
year = {2025},
author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y},
title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1162},
pmid = {41131583},
issn = {1479-5876},
support = {No. CCCF-QF-2022B04-4//the China Crohn's & Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.

METHODS: A cohort of treatment-naïve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.

RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p = 0.02) compared to HC, which was restored after EEN treatment at remission status (p < 0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r = 0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-α, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).

CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.},
}

Humans
*Gastrointestinal Microbiome
Animals
Male
*Bile Acids and Salts/metabolism
*Inflammatory Bowel Diseases/microbiology
*Ruminococcus/physiology
*Intestinal Mucosa/pathology/microbiology
Child
Colitis/pathology/microbiology
Mice
Female
Mice, Inbred C57BL
Crohn Disease/microbiology
Adolescent

@article {pmid41131465,
year = {2025},
author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N},
title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {683},
pmid = {41131465},
issn = {1471-2180},
mesh = {Tunisia ; *Salt-Tolerant Plants/microbiology ; *Endophytes/classification/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; DNA, Bacterial/genetics ; Soil/chemistry ; *Microbiota ; Salinity ; Biodiversity ; Sequence Analysis, DNA ; Amaranthaceae/microbiology ; },
abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.},
}

Tunisia
*Salt-Tolerant Plants/microbiology
*Endophytes/classification/isolation & purification/genetics
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology
DNA, Bacterial/genetics
Soil/chemistry
*Microbiota
Salinity
Biodiversity
Sequence Analysis, DNA
Amaranthaceae/microbiology

@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
mesh = {*Drinking Water/microbiology/parasitology ; *Amoeba/genetics/physiology ; *Drug Resistance, Microbial/genetics ; Symbiosis ; *Water Microbiology ; Bacteria/genetics ; Microbiota ; },
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}

*Drinking Water/microbiology/parasitology
*Amoeba/genetics/physiology
*Drug Resistance, Microbial/genetics
Symbiosis
*Water Microbiology
Bacteria/genetics
Microbiota

@article {pmid40889349,
year = {2025},
author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K},
title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70039},
doi = {10.1111/1755-0998.70039},
pmid = {40889349},
issn = {1755-0998},
support = {2019-00275//Svenska Forskningsrådet Formas/ ; },
mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; },
abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.},
}

*Metagenomics/methods
*Dental Calculus/microbiology
*Mammals/microbiology/classification
Animals
*Microbiota
*Gene Library
Metagenome
Computational Biology

@article {pmid40885278,
year = {2025},
author = {Bastón-Paz, N and Moreno-Blanco, A and Palacios, E and Olavarrieta, L and Galeano, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oteo-Iglesias, J and López-Causapé, C and Fuentes, I and Oliver, A and Cantón, R and Del Campo, R and de Dios-Caballero, J},
title = {Exploring the complexities of intestinal and pulmonary microbiota in cystic fibrosis: A multi-omics approach.},
journal = {Respiratory medicine},
volume = {248},
number = {},
pages = {108331},
doi = {10.1016/j.rmed.2025.108331},
pmid = {40885278},
issn = {1532-3064},
mesh = {Humans ; *Cystic Fibrosis/microbiology/physiopathology ; Male ; Female ; Feces/microbiology ; Sputum/microbiology ; Adult ; *Gastrointestinal Microbiome/genetics ; *Lung/microbiology ; Metagenomics/methods ; Adolescent ; Fatty Acids, Volatile/metabolism/analysis ; Child ; Young Adult ; *Microbiota ; Multiomics ; },
abstract = {BACKGROUND: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).

METHODS: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.

RESULTS: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum. Viruses accounted for 0.4 % of the relative abundance in the gut and 0.6 % in lungs. Mycobacteroides abscessus was genetically identified in 10 individuals, although only 2 had positive cultures. Patients with higher levels of Pseudomonas filamentous phages had negative cultures for P. aeruginosa. The protozoan Toxoplasma gondii was detected in all sputum samples, accounting for 0.25 % of the metagenomic reads, with further PCR-confirmation in 50 % of subjects, including children. No correlation was found between SCFA and lung function or microbial composition. The resistome of the fecal compartment was higher than that of the lungs, and a greater abundance of SCFAs in the intestine was associated with poorer lung function.

CONCLUSIONS: Patients with normal-mild lung function had higher alpha diversity in the respiratory microbiota; however, beta diversity in the stool was statistically different compared with the group with poorer lung function. Although there were no differences in SCFA concentrations, butyrate-producing bacteria were more abundant in the sputum of the group with better lung function. In fecal samples, resistome to tetracyclines, glycopeptides, and aminoglycosides predominated, whereas in sputum an enrichment of ARGs related to tetracyclines, beta-lactams, and macrolides was observed.},
}

Humans
*Cystic Fibrosis/microbiology/physiopathology
Male
Female
Feces/microbiology
Sputum/microbiology
Adult
*Gastrointestinal Microbiome/genetics
*Lung/microbiology
Metagenomics/methods
Adolescent
Fatty Acids, Volatile/metabolism/analysis
Child
Young Adult
*Microbiota
Multiomics

@article {pmid40755083,
year = {2025},
author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H},
title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70023},
doi = {10.1111/1755-0998.70023},
pmid = {40755083},
issn = {1755-0998},
support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; },
mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; },
abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).},
}

*DNA, Environmental/genetics
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods
*Genetic Variation
*Metagenomics/methods
*Software
Sequence Analysis, DNA/methods

@article {pmid40580061,
year = {2025},
author = {Rathour, R and Ma, Y and Xiong, J and Wang, XW and Petersen, J and Zhang, X},
title = {Hemolymph microbiota and host immunity of crustaceans and mollusks.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf133},
pmid = {40580061},
issn = {1751-7370},
support = {//Synthetic Biology Research Centre of Shenzhen University/ ; //Austrian Science Fund/ ; //ERC Starting Grant EvoLucin/ ; 42476113//National Natural Science Foundation of China/ ; JCYJ20241202124403006//Shenzhen Science and Technology Program/ ; 2025A1515010475//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; },
mesh = {Animals ; *Hemolymph/microbiology/immunology ; *Microbiota/immunology ; Immunity, Innate ; *Mollusca/microbiology/immunology ; *Crustacea/microbiology/immunology ; },
abstract = {Crustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defense mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host's immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unraveling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustacean and mollusk species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.},
}

Animals
*Hemolymph/microbiology/immunology
*Microbiota/immunology
Immunity, Innate
*Mollusca/microbiology/immunology
*Crustacea/microbiology/immunology

@article {pmid41131078,
year = {2025},
author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B},
title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37098},
pmid = {41131078},
issn = {2045-2322},
support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; },
mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention & control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; },
abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.},
}

*Bacillus/physiology
*Glycine max/microbiology/metabolism/immunology
*Plant Roots/microbiology/metabolism
*Botrytis/pathogenicity
*Microbiota
*Plant Diseases/microbiology/prevention & control
Rhizosphere
*Disease Resistance
Soil Microbiology

@article {pmid41130610,
year = {2025},
author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K},
title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.},
journal = {BMJ open respiratory research},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003456},
pmid = {41130610},
issn = {2052-4439},
mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; },
abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.

METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.

RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.

CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.

PROSPERO REGISTRATION NUMBER: CRD42023436934.},
}

Humans
*Trachea/microbiology
*Microbiota
*Bronchoalveolar Lavage Fluid/microbiology
*Bronchoalveolar Lavage/methods
*Specimen Handling/methods

@article {pmid41130083,
year = {2025},
author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP},
title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118872},
doi = {10.1016/j.marpolbul.2025.118872},
pmid = {41130083},
issn = {1879-3363},
abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.},
}

@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {68},
number = {20},
pages = {21786-21806},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
mesh = {Humans ; *Thiazoles/pharmacology/chemistry/chemical synthesis ; *Colorectal Neoplasms/drug therapy/pathology/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; *Antineoplastic Agents/pharmacology/chemistry/chemical synthesis ; *Pyruvate Kinase/antagonists & inhibitors/metabolism ; *Membrane Proteins/antagonists & inhibitors/metabolism ; Cell Line, Tumor ; *Thyroid Hormones/metabolism ; Thyroid Hormone-Binding Proteins ; *Carrier Proteins/antagonists & inhibitors/metabolism ; Cell Proliferation/drug effects ; Structure-Activity Relationship ; Animals ; *Enzyme Inhibitors/pharmacology/chemistry ; },
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}

Humans
*Thiazoles/pharmacology/chemistry/chemical synthesis
*Colorectal Neoplasms/drug therapy/pathology/metabolism/microbiology
Gastrointestinal Microbiome/drug effects
*Antineoplastic Agents/pharmacology/chemistry/chemical synthesis
*Pyruvate Kinase/antagonists & inhibitors/metabolism
*Membrane Proteins/antagonists & inhibitors/metabolism
Cell Line, Tumor
*Thyroid Hormones/metabolism
Thyroid Hormone-Binding Proteins
*Carrier Proteins/antagonists & inhibitors/metabolism
Cell Proliferation/drug effects
Structure-Activity Relationship
Animals
*Enzyme Inhibitors/pharmacology/chemistry

@article {pmid41002268,
year = {2025},
author = {Aminu, S and Ascandari, A and Benhida, R and Daoud, R},
title = {GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
doi = {10.1093/bioinformatics/btaf548},
pmid = {41002268},
issn = {1367-4811},
support = {//Mohammed VI Polytechnic University/ ; //African Supercomputing Center at UM6P/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Software ; *Metagenome ; Machine Learning ; Humans ; Cities ; },
abstract = {SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.

GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.},
}

*Microbiota/genetics
*Metagenomics/methods
*Software
*Metagenome
Machine Learning
Humans
Cities

@article {pmid40613917,
year = {2025},
author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M},
title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.},
journal = {Journal of gastroenterology},
volume = {60},
number = {11},
pages = {1384-1399},
pmid = {40613917},
issn = {1435-5922},
support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/genetics ; Biomarkers/blood/metabolism ; Middle Aged ; Metagenomics/methods ; Metabolomics/methods ; Poland ; Feces/microbiology/chemistry ; Case-Control Studies ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Disease Progression ; Young Adult ; Remission Induction ; },
abstract = {BACKGROUND & AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.

METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.

RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.

CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.},
}

Humans
*Colitis, Ulcerative/microbiology/metabolism
Male
Female
Adult
*Gastrointestinal Microbiome/genetics
Biomarkers/blood/metabolism
Middle Aged
Metagenomics/methods
Metabolomics/methods
Poland
Feces/microbiology/chemistry
Case-Control Studies
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Metabolome
Disease Progression
Young Adult
Remission Induction

@article {pmid41122951,
year = {2025},
author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH},
title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70062},
doi = {10.1111/1755-0998.70062},
pmid = {41122951},
issn = {1755-0998},
support = {//U.S. National Science Foundation/ ; },
abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.},
}

@article {pmid41122237,
year = {2025},
author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT},
title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20232},
pmid = {41122237},
issn = {2167-8359},
mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Firmicutes/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; },
abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.},
}

*Gastrointestinal Microbiome/genetics
*Machine Learning
*Spores, Bacterial/genetics
Animals
Humans
*Firmicutes/genetics/physiology
Cattle
Feces/microbiology
Metagenome
Swine
Phylogeny
Ensemble Learning

@article {pmid41121668,
year = {2025},
author = {Enagbonma, BJ and Modise, DM and Babalola, OO},
title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70085},
doi = {10.1002/mbo3.70085},
pmid = {41121668},
issn = {2045-8827},
support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; },
mesh = {*Sorghum/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fabaceae/growth & development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth & development ; *Edible Grain/growth & development/microbiology ; Agriculture/methods ; },
abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.},
}

*Sorghum/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Fabaceae/growth & development/microbiology
Nitrogen/metabolism
*Nitrogen Cycle
Soil/chemistry
Zea mays/microbiology/growth & development
*Edible Grain/growth & development/microbiology
Agriculture/methods

@article {pmid41121093,
year = {2025},
author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S},
title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {447},
pmid = {41121093},
issn = {1478-811X},
support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND & AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.

METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.

RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.

CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism
*NF-E2-Related Factor 2/metabolism
Mice
*Reperfusion Injury/metabolism/pathology/drug therapy
*Down-Regulation/drug effects
*STAT3 Transcription Factor/metabolism
*Indoles/pharmacology
*Intestinal Mucosa/metabolism/drug effects/pathology
Male
Mice, Inbred C57BL
Gastrointestinal Microbiome/drug effects
*Basic Helix-Loop-Helix Transcription Factors/metabolism
Tryptophan
*Intestines/pathology/blood supply/drug effects
*Protective Agents/pharmacology
Signal Transduction/drug effects

@article {pmid41005300,
year = {2025},
author = {Zhao, CN and Li, SS and Yau, T and Chen, WQ and Ji, R and Guan, XY and Kong, FS},
title = {Phocaeicola vulgatus induces immunotherapy resistance in hepatocellular carcinoma via reducing indoleacetic acid production.},
journal = {Cell reports. Medicine},
volume = {6},
number = {10},
pages = {102370},
doi = {10.1016/j.xcrm.2025.102370},
pmid = {41005300},
issn = {2666-3791},
mesh = {*Carcinoma, Hepatocellular/microbiology/therapy/immunology/metabolism/pathology ; Humans ; *Indoleacetic Acids/metabolism ; *Liver Neoplasms/microbiology/therapy/immunology/metabolism/pathology ; Animals ; *Immunotherapy/methods ; Mice ; CD8-Positive T-Lymphocytes/immunology ; *Drug Resistance, Neoplasm ; Male ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; *Enterobacteriaceae ; Female ; },
abstract = {Immunotherapy has made remarkable achievements in various cancers, but response rates in hepatocellular carcinoma (HCC) remain highly variable. Understanding mechanisms behind this heterogeneity and identifying responsive patients are urgent clinical challenges. In this study, the metagenomic analysis of 65 HCC patients reveals distinct gut microbiota profiles distinguishing responders (Rs) from non-responders (NRs). These findings are further validated through fecal microbiota transplantation (FMT) in mouse models. Notably, Phocaeicola vulgatus (P. vulgatus) is enriched in NRs and diminishes anti-PD-1 efficacy in both syngeneic and orthotopic tumor models. Mechanistically, P. vulgatus suppresses the production of indoleacetic acid (IAA), thereby weakening interferon (IFN)-γ[+] and granzyme B (GzmB)[+]CD8[+] T cells and impairing the antitumor immune response. Furthermore, supplementation with IAA restores CD8[+] T cell cytotoxicity and counteracts the immune-suppressive effects of P. vulgatus. Our findings establish a causal relationship between P. vulgatus and anti-PD-1 resistance in HCC, highlighting IAA as a potential therapeutic target to enhance immunotherapy outcomes.},
}

*Carcinoma, Hepatocellular/microbiology/therapy/immunology/metabolism/pathology
Humans
*Indoleacetic Acids/metabolism
*Liver Neoplasms/microbiology/therapy/immunology/metabolism/pathology
Animals
*Immunotherapy/methods
Mice
CD8-Positive T-Lymphocytes/immunology
*Drug Resistance, Neoplasm
Male
Cell Line, Tumor
Gastrointestinal Microbiome
Mice, Inbred C57BL
Programmed Cell Death 1 Receptor/antagonists & inhibitors
*Enterobacteriaceae
Female

@article {pmid40985733,
year = {2025},
author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM},
title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0057425},
doi = {10.1128/aem.00574-25},
pmid = {40985733},
issn = {1098-5336},
mesh = {*Dioxanes/metabolism ; Biodegradation, Environmental ; *Bioreactors/microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/metabolism ; *Microbiota ; Phylogeny ; },
abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.

IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.},
}

*Dioxanes/metabolism
Biodegradation, Environmental
*Bioreactors/microbiology
*Bacteria/metabolism/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics/analysis
Waste Disposal Facilities
*Water Pollutants, Chemical/metabolism
*Microbiota
Phylogeny

@article {pmid40981429,
year = {2025},
author = {Ferretti, P},
title = {The gut remembers: the long-lasting effect of medication use on the gut microbiome.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0107625},
doi = {10.1128/msystems.01076-25},
pmid = {40981429},
issn = {2379-5077},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology/adverse effects ; Electronic Health Records ; Proton Pump Inhibitors/pharmacology ; Feces/microbiology ; },
abstract = {Growing evidence suggests that antibiotics and many human-targeted medications can alter the gut microbiome composition, but the persistence of these effects remains unclear. In their article, Aasmets and colleagues (O. Aasmets, N. Taba, K. L. Krigu, R. Andreson, et al., mSystems e00541-25, 2025, https://doi.org/10.1128/msystems.00541-25) leveraged electronic health records (EHR) and stool metagenomic data from 2,509 individuals to assess the impact of past medication use (up to 5 years prior to sampling) on the gut microbiome composition. They found that nearly half of the 186 tested drugs had long-term effects, with antibiotics, beta-blockers, benzodiazepine derivatives, proton-pump inhibitors, and antidepressants associated with microbiome changes that persisted for years after intake. For some medications, the effects were additive, with greater impact observed after repeated use. Overall, the authors highlight how medication use in the years preceding sample collection represents an often overlooked confounding factor in microbiome studies and emphasize the utility of combining EHR with microbiome data to assess the impact of past medication use.},
}

*Gastrointestinal Microbiome/drug effects
Humans
Anti-Bacterial Agents/pharmacology/adverse effects
Electronic Health Records
Proton Pump Inhibitors/pharmacology
Feces/microbiology

@article {pmid40980873,
year = {2025},
author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR},
title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0060125},
doi = {10.1128/msystems.00601-25},
pmid = {40980873},
issn = {2379-5077},
support = {0054575-SuPAcow//Novo Nordisk Fonden/ ; 101000213//HORIZON EUROPE European Research Council/ ; FT230100560//Australian Research Council/ ; },
mesh = {Animals ; Cattle/microbiology ; *Methane/metabolism ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Animal Feed ; Bacteria/metabolism/genetics/classification ; },
abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.

IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.},
}

Animals
Cattle/microbiology
*Methane/metabolism
*Rumen/microbiology/metabolism
*Gastrointestinal Microbiome
*Microbiota
Metagenome
Animal Feed
Bacteria/metabolism/genetics/classification

@article {pmid40960303,
year = {2025},
author = {Qie, J and Cao, M and Xu, M and Zhang, Y and Luo, L and Sun, C and Ke, D and Yuan, S and Jia, W and Qiu, T and Li, T and Du, X and Xiao, C and Hong, Z and Zhang, B},
title = {Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0109125},
doi = {10.1128/msystems.01091-25},
pmid = {40960303},
issn = {2379-5077},
mesh = {Humans ; *Hyperuricemia/microbiology/therapy ; *Gout/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Female ; Cohort Studies ; Uric Acid/metabolism ; Adult ; Aged ; Bacteria/genetics/classification ; Metagenomics ; },
abstract = {The gut microbiota plays a crucial role in the development of hyperuricemia (HUA) and gout. However, the variability in study designs and analytical methods has led to inconsistent conclusions across different studies. Here, we conducted a comprehensive analysis of the gut microbiota associated with HUA and gout by examining 368 16S rRNA sequencing data from four Chinese cohorts, including 159 healthy controls (HC), 136 HUA patients, and 73 gout patients. Our findings indicate that there were significant differences in the gut microbiota composition between the three groups. Specifically, the HUA and gout groups demonstrated an increased abundance of pro-inflammatory bacteria, such as Fusobacterium and Bilophila, while beneficial bacteria known for their anti-inflammatory properties and metabolic benefits, including Christensenellaceae R-7 group, Anaerostipes, and Collinsella, are relatively reduced. Additionally, we developed a predictive model using microbial markers that achieved a high accuracy (area under the curve [AUC] > 0.8) in distinguishing between the HC, HUA, and gout groups. Notably, further metagenomic analysis identified a species-level genome bin (SGB), designated as Phil1 sp00194085, belonging to the order Christensenellales. For the first time, we discovered that this SGB carries a uric acid metabolic gene cluster and possesses enzymes associated with purine metabolism, suggesting its potential role in uric acid metabolism. Overall, our study deepens the understanding of the gut microbiota's role in HUA and gout and lays a foundation for developing innovative therapeutic strategies to effectively control uric acid levels through gut microbiota modulation.In this study, we conducted a comprehensive analysis of gut microbiota across multiple cohorts, identifying distinct microbial signatures in healthy controls, hyperuricemia (HUA), and gout patients. We observed an increase in pro-inflammatory bacteria and a decrease in beneficial bacteria for host metabolism in both the HUA and gout groups. Additionally, we developed a predictive model with high accuracy (area under the curve [AUC] > 0.8) based on microbial markers and discovered a novel species with potential for uric acid metabolism, providing new therapeutic targets for HUA and gout.},
}

Humans
*Hyperuricemia/microbiology/therapy
*Gout/microbiology/therapy
*Gastrointestinal Microbiome/genetics
Male
RNA, Ribosomal, 16S/genetics
Middle Aged
Female
Cohort Studies
Uric Acid/metabolism
Adult
Aged
Bacteria/genetics/classification
Metagenomics

@article {pmid40960301,
year = {2025},
author = {Yan, Y and Zhao, X and Liang, X and Xue, Y and Niu, Q and Li, D and Zhou, X and Li, Y and Dong, S and Gai, Y},
title = {Global wastewater microbiome reveals core bacterial community and viral diversity with regional antibiotic resistance patterns.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0142824},
doi = {10.1128/msystems.01428-24},
pmid = {40960301},
issn = {2379-5077},
support = {BLX202162//Central University Basic Research Fund of China/ ; },
mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Microbial/genetics ; Humans ; Metagenome ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; Drug Resistance, Bacterial ; Biodiversity ; },
abstract = {Municipal wastewater treatment plants (WWTPs) serve as global repositories for diverse and dynamic microbial communities, reflecting the complex interplay of human activities, environmental conditions, and public health challenges. Despite their importance, a comprehensive understanding of the global distribution, composition, and functional roles of these microbial ecosystems has remained elusive. Here, we present a comprehensive analysis of bacterial and viral diversities in global wastewater systems by examining 575 sampling sites across 74 cities in 60 countries. Through metagenomic analysis, we reconstructed 12,758 non-redundant bacterial metagenome-assembled genomes (MAGs) spanning 70 phyla, with 4,499 MAGs representing novel species. Despite considerable regional variation, we identified a consistent core microbiome present across 70% of global samples predominantly comprising Proteobacteria. We further assembled 1.7 million viral genomes, revealing unprecedented viral diversity with over 1.5 million species-level viral operational taxonomic units (vOTUs). Network analysis demonstrated that transport proteins play crucial roles in maintaining WWTP functional resilience against disturbances. Machine learning approaches effectively predicted continental origins of wastewater samples based on microbial signatures, confirming that microbial communities reflect local environmental and socioeconomic conditions while maintaining functional conservation. We observed significant variation in the antibiotic resistance gene (ARG) distribution, with elevated prevalence in certain African and Asian regions compared to Europe and North America. Our results establish wastewater microbiomes as important indicators of human activity and provide critical insights for advancing environmental monitoring, antimicrobial resistance surveillance, and wastewater-based epidemiology.IMPORTANCEIntensifying urbanization and human activities have dramatically increased global wastewater generation, creating complex microbial ecosystems that significantly impact environmental and public health. This study presents the first large-scale, comprehensive characterization of bacterial and viral communities in wastewater treatment systems worldwide. By analyzing samples from diverse geographical, climatic, and socioeconomic contexts, we reveal how wastewater microbiomes serve as microbial fingerprints of human society, reflecting regional characteristics while maintaining functional conservation. Our findings demonstrate that these communities function as ecological extensions of human gut microbiota in the external environment, with important implications for the spread of antibiotic resistance and pathogens. The identification of viruses as key metabolic regulators in these systems provides new perspectives on microbial community dynamics. This global-scale analysis advances our understanding of wastewater microbiology and offers valuable insights for improving wastewater management, enhancing environmental monitoring systems, and strengthening public health surveillance through wastewater-based epidemiology.},
}

*Wastewater/microbiology/virology
*Microbiota/genetics
*Bacteria/genetics/classification/drug effects/isolation & purification
*Drug Resistance, Microbial/genetics
Humans
Metagenome
*Viruses/genetics/classification/isolation & purification
Metagenomics
Drug Resistance, Bacterial
Biodiversity

@article {pmid40956075,
year = {2025},
author = {Yu, D and Mai, Y and Zhang, L and Xiao, Y and Zhang, M and Shao, B and Chen, B and Wang, T and Zhang, K and Zhang, L and Gao, N and Zhang, J and Yan, J},
title = {Viral community succession during cadaver decomposition and its potential for estimating postmortem intervals.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0145325},
doi = {10.1128/aem.01453-25},
pmid = {40956075},
issn = {1098-5336},
support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; },
mesh = {Cadaver ; Animals ; Rats ; *Postmortem Changes ; *Viruses/classification/genetics/isolation & purification ; *Microbiota ; Metagenomics ; },
abstract = {UNLABELLED: Microbial communities play a vital role in cadaver decomposition and serve as reliable tools for postmortem interval (PMI) estimation. However, current research focuses primarily on bacterial/fungal communities, though viruses-as Earth's most abundant biological entities-play key roles in biogeochemical cycles by regulating bacterial communities via lysis-lysogeny switching. Viral succession patterns during decomposition remain insufficiently characterized, and their PMI biomarker potential is unexamined. We present metagenomic analysis of viral succession during 35-day decomposition of buried rat cadavers, revealing stage-specific dynamics: early dominance of Peduoviridae (0-3 days), mid-stage proliferation of Herelleviridae (7-21 days), and late-stage resurgence of Peduoviridae (28-35 days). Viral α-diversity exhibits a fluctuating downward trend. β-Diversity analysis (PCoA, ANOSIM, PERMANOVA; P < 0.001) confirmed PMI as a major structural driver (27% variance explained). Nine viral families exhibited significant PMI correlations (P < 0.05): Zierdtviridae, Casjensviridae, Schitoviridae, and Ackermannviridae showed strong negative correlations (r = -0.82 to -0.78), while Straboviridae correlated positively (r = 0.59). Using integrated viral abundance data, our Extremely Randomized Trees model achieved exceptional PMI prediction accuracy (test set: R[2] = 0.96, MAE = 2.54 days). Spearman correlations between dominant bacterial phyla (Bacteroidota, Bacillota, etc.) and viral families, combined with Procrustes analysis (M[2] =0.3385, P = 0.001) and Mantel tests (r = 0.8059, P = 0.001), confirmed strong virus-bacteria community consistency. This indicates viruses may regulate decomposition by targeting bacteria for lysis, releasing nutrients (e.g., organic nitrogen/phosphorus) to drive bacterial succession. Our study establishes a novel virus-based PMI prediction tool and discusses ecological drivers of decomposition.

IMPORTANCE: We present a viral succession-based framework for estimating PMI in buried remains. Our study identifies stage-specific viral biomarkers and identified nine viral families significantly correlated with PMI. By combining metagenomics and machine learning, we developed an Extremely Randomized Trees (ERT) model that achieved a low prediction error (test set: R² = 0.96, MAE = 2.54 days). Furthermore, our findings demonstrate that viral and bacterial communities exhibit significant consistency and correlation during cadaver decomposition. This study not only provides a novel tool for the accurate estimation of forensic PMI but also advances our insight into viral regulation of bacteria and their interactions during cadaver decomposition.},
}

Cadaver
Animals
Rats
*Postmortem Changes
*Viruses/classification/genetics/isolation & purification
*Microbiota
Metagenomics

@article {pmid40952003,
year = {2025},
author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L},
title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0002325},
doi = {10.1128/msystems.00023-25},
pmid = {40952003},
issn = {2379-5077},
support = {2022-PUMCH-A-264//National High Level Hospital Clinical Reasearch Fungding/ ; 2022-PUMCH-A-042//National High Level Hospital Clinical Reasearch Fungding/ ; L232074//Natural Science Foundation of Beijing Municipality/ ; 2021-12M-C&TA-008//CAMS Innovation Funds for Medical Sciences/ ; 2022-PUMCH-C-031//National High Level Hospital Clinical Resarch Funding/ ; 2022-PUMCH-C-060//National High Level Hospital Clinical Research Funding/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; Adult ; *Polyps/microbiology/classification ; *Cervix Uteri/microbiology ; Metagenomics/methods ; Endometrium/microbiology/pathology ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.},
}

Humans
Female
*Vagina/microbiology
*Microbiota/genetics
Adult
*Polyps/microbiology/classification
*Cervix Uteri/microbiology
Metagenomics/methods
Endometrium/microbiology/pathology
Middle Aged
Bacteria/classification/genetics/isolation & purification

@article {pmid40952001,
year = {2025},
author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO},
title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0099125},
doi = {10.1128/msystems.00991-25},
pmid = {40952001},
issn = {2379-5077},
support = {988415//Crohn's and Colitis Foundation/ ; APP2011047//National Health and Medical Research Council/ ; Investigator grant//National Health and Medical Research Council/ ; Scientia fellowship//University of New South Wales/ ; },
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Freeze Drying ; Female ; Male ; Administration, Oral ; Double-Blind Method ; Feces/microbiology ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; },
abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.

IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.},
}

Humans
*Colitis, Ulcerative/therapy/microbiology
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
Freeze Drying
Female
Male
Administration, Oral
Double-Blind Method
Feces/microbiology
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged

@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0103925},
doi = {10.1128/msystems.01039-25},
pmid = {40928232},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; *Gene Library ; *Drug Resistance, Microbial/genetics ; Metagenome ; Biomass ; Bacteria/genetics ; Humans ; Microbiota/genetics ; },
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}

*Metagenomics/methods
*Gene Library
*Drug Resistance, Microbial/genetics
Metagenome
Biomass
Bacteria/genetics
Humans
Microbiota/genetics

@article {pmid40928220,
year = {2025},
author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F},
title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0004425},
doi = {10.1128/msystems.00044-25},
pmid = {40928220},
issn = {2379-5077},
support = {No. 81670979,No. 31300424//National Natural Science Foundation of China/ ; 24-4-4-zrjj-158-jch//Natural Science Foundation of Qingdao Municipality/ ; ZR2024MH235//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; 202408010669//Shandong Medical and Health Technology Development Project/ ; },
mesh = {*Dental Caries/microbiology/diagnosis ; Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Child ; Female ; Male ; Child, Preschool ; },
abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.},
}

*Dental Caries/microbiology/diagnosis
Humans
*Dental Plaque/microbiology
*Microbiota/genetics
*Metagenomics/methods
Child
Female
Male
Child, Preschool

@article {pmid40919923,
year = {2025},
author = {Francis, JD and Yanaç, K and Uyaguari-Diaz, MI},
title = {Seasonal patterns of viromes in urban aquatic environments of Manitoba.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0040824},
doi = {10.1128/aem.00408-24},
pmid = {40919923},
issn = {1098-5336},
support = {RGPIN-2022-04508//Natural Sciences and Engineering Research Council of Canada/ ; ALLRP 553987//Natural Sciences and Engineering Research Council of Canada/ ; 322388//University of Manitoba/ ; },
mesh = {Seasons ; Manitoba ; *Virome ; *Wastewater/virology ; *Rivers/virology ; *Water Microbiology ; Metagenomics ; *RNA Viruses/isolation & purification/genetics/classification ; Cities ; *DNA Viruses/isolation & purification/genetics/classification ; },
abstract = {UNLABELLED: Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as Autographiviridae, Kyanoviridae, and Peduoviridae, which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or "naked viruses" such as Partiviridae, Picobirnaviridae, Tombusviridae, and Picornaviridae, which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.

IMPORTANCE: Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.},
}

Seasons
Manitoba
*Virome
*Wastewater/virology
*Rivers/virology
*Water Microbiology
Metagenomics
*RNA Viruses/isolation & purification/genetics/classification
Cities
*DNA Viruses/isolation & purification/genetics/classification